Starting phenix.real_space_refine on Sat Aug 23 23:34:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f4n_28855/08_2025/8f4n_28855.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f4n_28855/08_2025/8f4n_28855.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f4n_28855/08_2025/8f4n_28855.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f4n_28855/08_2025/8f4n_28855.map" model { file = "/net/cci-nas-00/data/ceres_data/8f4n_28855/08_2025/8f4n_28855.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f4n_28855/08_2025/8f4n_28855.cif" } resolution = 2.95 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= 0.078 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 88 5.16 5 C 9954 2.51 5 N 2617 2.21 5 O 2915 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15574 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 7864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 7864 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 42, 'TRANS': 991} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 7710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1009, 7710 Classifications: {'peptide': 1009} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 41, 'TRANS': 967} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 18 Time building chain proxies: 4.19, per 1000 atoms: 0.27 Number of scatterers: 15574 At special positions: 0 Unit cell: (79.18, 119.84, 144.45, 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 88 16.00 O 2915 8.00 N 2617 7.00 C 9954 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.45 Conformation dependent library (CDL) restraints added in 944.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3768 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 16 sheets defined 61.4% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'B' and resid 1 through 7 Processing helix chain 'B' and resid 8 through 29 removed outlier: 3.588A pdb=" N ALA B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 61 through 70 Processing helix chain 'B' and resid 99 through 118 removed outlier: 3.761A pdb=" N SER B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ARG B 116 " --> pdb=" O GLN B 112 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LYS B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 150 through 162 Processing helix chain 'B' and resid 162 through 168 removed outlier: 3.613A pdb=" N ARG B 168 " --> pdb=" O ASP B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 196 Processing helix chain 'B' and resid 199 through 211 Processing helix chain 'B' and resid 242 through 248 removed outlier: 3.647A pdb=" N PHE B 246 " --> pdb=" O THR B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 265 Processing helix chain 'B' and resid 298 through 316 removed outlier: 3.935A pdb=" N TYR B 316 " --> pdb=" O GLU B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 359 Processing helix chain 'B' and resid 361 through 386 Proline residue: B 368 - end of helix removed outlier: 3.810A pdb=" N ALA B 371 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL B 372 " --> pdb=" O PRO B 368 " (cutoff:3.500A) Proline residue: B 373 - end of helix Processing helix chain 'B' and resid 391 through 424 removed outlier: 4.575A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ASP B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ALA B 409 " --> pdb=" O LEU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 452 removed outlier: 5.716A pdb=" N GLY B 440 " --> pdb=" O GLY B 436 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ALA B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL B 452 " --> pdb=" O VAL B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 459 removed outlier: 4.228A pdb=" N ALA B 457 " --> pdb=" O PHE B 453 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N PHE B 458 " --> pdb=" O VAL B 454 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE B 459 " --> pdb=" O PRO B 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 453 through 459' Processing helix chain 'B' and resid 460 through 486 Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.952A pdb=" N ALA B 491 " --> pdb=" O ILE B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 504 Processing helix chain 'B' and resid 510 through 536 Processing helix chain 'B' and resid 536 through 558 removed outlier: 4.124A pdb=" N TRP B 540 " --> pdb=" O ARG B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 600 Processing helix chain 'B' and resid 642 through 657 Processing helix chain 'B' and resid 690 through 708 Processing helix chain 'B' and resid 730 through 737 Processing helix chain 'B' and resid 740 through 753 Processing helix chain 'B' and resid 782 through 786 removed outlier: 4.222A pdb=" N ASN B 785 " --> pdb=" O ASP B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 802 No H-bonds generated for 'chain 'B' and resid 799 through 802' Processing helix chain 'B' and resid 834 through 849 Processing helix chain 'B' and resid 859 through 891 Proline residue: B 872 - end of helix Processing helix chain 'B' and resid 893 through 901 removed outlier: 3.529A pdb=" N PHE B 897 " --> pdb=" O TRP B 893 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 918 removed outlier: 3.613A pdb=" N GLY B 906 " --> pdb=" O VAL B 902 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY B 909 " --> pdb=" O LEU B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 922 through 954 removed outlier: 3.872A pdb=" N ILE B 943 " --> pdb=" O ASN B 939 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE B 946 " --> pdb=" O LEU B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 983 removed outlier: 5.108A pdb=" N ARG B 970 " --> pdb=" O ARG B 966 " (cutoff:3.500A) Proline residue: B 971 - end of helix removed outlier: 3.766A pdb=" N PHE B 979 " --> pdb=" O THR B 975 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 988 Processing helix chain 'B' and resid 993 through 1030 removed outlier: 4.293A pdb=" N GLY B1003 " --> pdb=" O ALA B 999 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL B1004 " --> pdb=" O VAL B1000 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N TYR B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Proline residue: B1020 - end of helix Processing helix chain 'A' and resid 2 through 8 Processing helix chain 'A' and resid 8 through 29 removed outlier: 3.906A pdb=" N ALA A 12 " --> pdb=" O ARG A 8 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 28 " --> pdb=" O THR A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 61 through 70 Processing helix chain 'A' and resid 99 through 118 removed outlier: 4.272A pdb=" N SER A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA A 114 " --> pdb=" O GLN A 110 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ARG A 116 " --> pdb=" O GLN A 112 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYS A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 150 through 162 Processing helix chain 'A' and resid 162 through 168 removed outlier: 3.542A pdb=" N ARG A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 Processing helix chain 'A' and resid 199 through 211 removed outlier: 4.588A pdb=" N ASN A 211 " --> pdb=" O ILE A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 248 removed outlier: 3.677A pdb=" N PHE A 246 " --> pdb=" O THR A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 265 No H-bonds generated for 'chain 'A' and resid 262 through 265' Processing helix chain 'A' and resid 298 through 315 Processing helix chain 'A' and resid 329 through 359 Processing helix chain 'A' and resid 361 through 387 Proline residue: A 368 - end of helix removed outlier: 3.779A pdb=" N ALA A 371 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL A 372 " --> pdb=" O PRO A 368 " (cutoff:3.500A) Proline residue: A 373 - end of helix Processing helix chain 'A' and resid 391 through 423 removed outlier: 3.724A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ASP A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ASP A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ALA A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 438 removed outlier: 3.569A pdb=" N GLY A 436 " --> pdb=" O ARG A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 452 removed outlier: 3.559A pdb=" N VAL A 443 " --> pdb=" O GLN A 439 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL A 452 " --> pdb=" O VAL A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 457 removed outlier: 4.324A pdb=" N MET A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 452 through 457' Processing helix chain 'A' and resid 460 through 496 removed outlier: 4.548A pdb=" N THR A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Proline residue: A 490 - end of helix Processing helix chain 'A' and resid 510 through 536 Processing helix chain 'A' and resid 536 through 558 removed outlier: 4.228A pdb=" N TRP A 540 " --> pdb=" O ARG A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 601 Processing helix chain 'A' and resid 642 through 655 Processing helix chain 'A' and resid 690 through 708 Processing helix chain 'A' and resid 730 through 737 Processing helix chain 'A' and resid 740 through 752 Processing helix chain 'A' and resid 775 through 778 Processing helix chain 'A' and resid 780 through 786 removed outlier: 3.539A pdb=" N ILE A 784 " --> pdb=" O PRO A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 849 Processing helix chain 'A' and resid 858 through 891 removed outlier: 3.614A pdb=" N GLN A 863 " --> pdb=" O ALA A 859 " (cutoff:3.500A) Proline residue: A 872 - end of helix Processing helix chain 'A' and resid 893 through 901 Processing helix chain 'A' and resid 902 through 918 removed outlier: 4.069A pdb=" N GLY A 909 " --> pdb=" O LEU A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 954 removed outlier: 4.549A pdb=" N PHE A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 988 removed outlier: 5.005A pdb=" N ARG A 970 " --> pdb=" O ARG A 966 " (cutoff:3.500A) Proline residue: A 971 - end of helix removed outlier: 3.633A pdb=" N PHE A 979 " --> pdb=" O THR A 975 " (cutoff:3.500A) Proline residue: A 985 - end of helix Processing helix chain 'A' and resid 993 through 1030 removed outlier: 4.338A pdb=" N GLY A1003 " --> pdb=" O ALA A 999 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL A1004 " --> pdb=" O VAL A1000 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N TYR A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Proline residue: A1020 - end of helix Processing sheet with id=AA1, first strand: chain 'B' and resid 127 through 131 removed outlier: 4.119A pdb=" N GLN B 87 " --> pdb=" O SER B 83 " (cutoff:3.500A) removed outlier: 12.330A pdb=" N ARG B 813 " --> pdb=" O GLU B 824 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N GLU B 824 " --> pdb=" O ARG B 813 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLU B 815 " --> pdb=" O ALA B 822 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU B 828 " --> pdb=" O ARG B 713 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ARG B 713 " --> pdb=" O GLU B 828 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 127 through 131 removed outlier: 4.119A pdb=" N GLN B 87 " --> pdb=" O SER B 83 " (cutoff:3.500A) removed outlier: 12.330A pdb=" N ARG B 813 " --> pdb=" O GLU B 824 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N GLU B 824 " --> pdb=" O ARG B 813 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLU B 815 " --> pdb=" O ALA B 822 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N SER B 821 " --> pdb=" O ASP B 685 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 172 through 177 removed outlier: 3.861A pdb=" N ASP B 174 " --> pdb=" O LYS B 292 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N SER B 144 " --> pdb=" O PRO B 285 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU B 138 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU B 293 " --> pdb=" O ASN B 136 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASN B 136 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N ILE B 137 " --> pdb=" O GLU B 328 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N GLU B 328 " --> pdb=" O ILE B 137 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N THR B 139 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 172 through 177 removed outlier: 3.861A pdb=" N ASP B 174 " --> pdb=" O LYS B 292 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER B 279 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL B 612 " --> pdb=" O LEU B 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 266 through 269 removed outlier: 3.951A pdb=" N ASN B 758 " --> pdb=" O VAL B 769 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL B 771 " --> pdb=" O TYR B 756 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N TYR B 756 " --> pdb=" O VAL B 771 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N ALA B 773 " --> pdb=" O SER B 754 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N SER B 754 " --> pdb=" O ALA B 773 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 215 through 219 removed outlier: 3.869A pdb=" N GLY B 217 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N THR B 233 " --> pdb=" O LEU A 725 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ILE A 727 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ASN B 235 " --> pdb=" O ILE A 727 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ILE A 729 " --> pdb=" O ASN B 235 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 722 through 725 Processing sheet with id=AA8, first strand: chain 'B' and resid 728 through 729 Processing sheet with id=AA9, first strand: chain 'B' and resid 788 through 790 Processing sheet with id=AB1, first strand: chain 'A' and resid 128 through 131 removed outlier: 3.999A pdb=" N GLN A 87 " --> pdb=" O SER A 83 " (cutoff:3.500A) removed outlier: 12.415A pdb=" N ARG A 813 " --> pdb=" O GLU A 824 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N GLU A 824 " --> pdb=" O ARG A 813 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU A 815 " --> pdb=" O ALA A 822 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLU A 828 " --> pdb=" O ARG A 713 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ARG A 713 " --> pdb=" O GLU A 828 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 128 through 131 removed outlier: 3.999A pdb=" N GLN A 87 " --> pdb=" O SER A 83 " (cutoff:3.500A) removed outlier: 12.415A pdb=" N ARG A 813 " --> pdb=" O GLU A 824 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N GLU A 824 " --> pdb=" O ARG A 813 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU A 815 " --> pdb=" O ALA A 822 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N SER A 821 " --> pdb=" O ASP A 685 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.639A pdb=" N ASP A 174 " --> pdb=" O LYS A 292 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N SER A 144 " --> pdb=" O PRO A 285 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 138 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LEU A 293 " --> pdb=" O ASN A 136 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ASN A 136 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ILE A 137 " --> pdb=" O GLU A 328 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLU A 328 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N THR A 139 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.639A pdb=" N ASP A 174 " --> pdb=" O LYS A 292 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER A 279 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N VAL A 623 " --> pdb=" O GLY A 613 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 266 through 272 removed outlier: 8.431A pdb=" N TYR A 182 " --> pdb=" O VAL A 766 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N LYS A 768 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASN A 758 " --> pdb=" O VAL A 769 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL A 771 " --> pdb=" O TYR A 756 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N TYR A 756 " --> pdb=" O VAL A 771 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 250 through 253 Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 1116 hydrogen bonds defined for protein. 3270 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: 3.81 Time building geometry restraints manager: 1.97 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: 5111 1.34 - 1.46: 2380 1.46 - 1.57: 8217 1.57 - 1.69: 0 1.69 - 1.81: 168 Bond restraints: 15876 Sorted by residual: bond pdb=" N GLY B 460 " pdb=" CA GLY B 460 " ideal model delta sigma weight residual 1.442 1.456 -0.014 7.70e-03 1.69e+04 3.31e+00 bond pdb=" CA ALA B 645 " pdb=" C ALA B 645 " ideal model delta sigma weight residual 1.524 1.505 0.019 1.24e-02 6.50e+03 2.34e+00 bond pdb=" CA TYR A 467 " pdb=" C TYR A 467 " ideal model delta sigma weight residual 1.524 1.506 0.018 1.27e-02 6.20e+03 1.96e+00 bond pdb=" CA LEU A 874 " pdb=" C LEU A 874 " ideal model delta sigma weight residual 1.524 1.505 0.018 1.32e-02 5.74e+03 1.94e+00 bond pdb=" CA TYR A 157 " pdb=" C TYR A 157 " ideal model delta sigma weight residual 1.524 1.506 0.017 1.27e-02 6.20e+03 1.89e+00 ... (remaining 15871 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 21147 1.57 - 3.14: 356 3.14 - 4.72: 54 4.72 - 6.29: 18 6.29 - 7.86: 5 Bond angle restraints: 21580 Sorted by residual: angle pdb=" C PHE B1030 " pdb=" N PRO B1031 " pdb=" CA PRO B1031 " ideal model delta sigma weight residual 120.03 116.51 3.52 9.90e-01 1.02e+00 1.26e+01 angle pdb=" CA LYS A1033 " pdb=" C LYS A1033 " pdb=" N PRO A1034 " ideal model delta sigma weight residual 120.77 117.49 3.28 9.70e-01 1.06e+00 1.14e+01 angle pdb=" CA LYS B1033 " pdb=" C LYS B1033 " pdb=" N PRO B1034 " ideal model delta sigma weight residual 120.77 117.57 3.20 9.70e-01 1.06e+00 1.09e+01 angle pdb=" C PHE A1030 " pdb=" N PRO A1031 " pdb=" CA PRO A1031 " ideal model delta sigma weight residual 119.85 116.61 3.24 1.01e+00 9.80e-01 1.03e+01 angle pdb=" N GLY A 147 " pdb=" CA GLY A 147 " pdb=" C GLY A 147 " ideal model delta sigma weight residual 115.43 110.94 4.49 1.41e+00 5.03e-01 1.01e+01 ... (remaining 21575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 9097 17.97 - 35.94: 302 35.94 - 53.92: 55 53.92 - 71.89: 10 71.89 - 89.86: 6 Dihedral angle restraints: 9470 sinusoidal: 3602 harmonic: 5868 Sorted by residual: dihedral pdb=" CA ILE B 249 " pdb=" C ILE B 249 " pdb=" N THR B 250 " pdb=" CA THR B 250 " ideal model delta harmonic sigma weight residual 180.00 -163.49 -16.51 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA ASP A 156 " pdb=" CB ASP A 156 " pdb=" CG ASP A 156 " pdb=" OD1 ASP A 156 " ideal model delta sinusoidal sigma weight residual -30.00 -83.75 53.75 1 2.00e+01 2.50e-03 9.81e+00 dihedral pdb=" N LEU A 748 " pdb=" CA LEU A 748 " pdb=" CB LEU A 748 " pdb=" CG LEU A 748 " ideal model delta sinusoidal sigma weight residual -180.00 -121.55 -58.45 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 9467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1665 0.028 - 0.056: 552 0.056 - 0.084: 176 0.084 - 0.113: 110 0.113 - 0.141: 11 Chirality restraints: 2514 Sorted by residual: chirality pdb=" CA THR B 489 " pdb=" N THR B 489 " pdb=" C THR B 489 " pdb=" CB THR B 489 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" CA THR A 489 " pdb=" N THR A 489 " pdb=" C THR A 489 " pdb=" CB THR A 489 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA ILE A 466 " pdb=" N ILE A 466 " pdb=" C ILE A 466 " pdb=" CB ILE A 466 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.05e-01 ... (remaining 2511 not shown) Planarity restraints: 2784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 250 " 0.007 2.00e-02 2.50e+03 1.40e-02 1.96e+00 pdb=" C THR B 250 " -0.024 2.00e-02 2.50e+03 pdb=" O THR B 250 " 0.009 2.00e-02 2.50e+03 pdb=" N LEU B 251 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 970 " 0.022 5.00e-02 4.00e+02 3.33e-02 1.78e+00 pdb=" N PRO B 971 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 971 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 971 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 872 " 0.006 2.00e-02 2.50e+03 1.24e-02 1.55e+00 pdb=" C PRO B 872 " -0.022 2.00e-02 2.50e+03 pdb=" O PRO B 872 " 0.008 2.00e-02 2.50e+03 pdb=" N ALA B 873 " 0.007 2.00e-02 2.50e+03 ... (remaining 2781 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4209 2.80 - 3.33: 16030 3.33 - 3.85: 26593 3.85 - 4.38: 31118 4.38 - 4.90: 54008 Nonbonded interactions: 131958 Sorted by model distance: nonbonded pdb=" OD1 ASN A 415 " pdb=" NH1 ARG A 418 " model vdw 2.278 3.120 nonbonded pdb=" OE1 GLU B 66 " pdb=" NH1 ARG B 816 " model vdw 2.283 3.120 nonbonded pdb=" OD1 ASN B 415 " pdb=" NH1 ARG B 418 " model vdw 2.284 3.120 nonbonded pdb=" OG1 THR A 46 " pdb=" OG1 THR A 128 " model vdw 2.294 3.040 nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 759 " model vdw 2.294 3.040 ... (remaining 131953 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 1 through 657 or (resid 658 and (name N or name CA or name \ C or name O or name CB )) or resid 659 through 731 or (resid 732 and (name N or \ name CA or name C or name O or name CB )) or resid 733 through 791 or (resid 79 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 793 through \ 1028 or (resid 1029 and (name N or name CA or name C or name O or name CB )) or \ resid 1030 through 1034)) selection = (chain 'B' and (resid 1 through 211 or resid 237 through 303 or (resid 304 and ( \ name N or name CA or name C or name O or name CB )) or resid 305 through 1034)) } 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: 4.020 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: 0.030 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.820 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.010 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:7.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 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 : 0.004 0.037 15876 Z= 0.198 Angle : 0.547 7.861 21580 Z= 0.323 Chirality : 0.036 0.141 2514 Planarity : 0.003 0.033 2784 Dihedral : 9.959 89.860 5702 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.12 % Allowed : 4.60 % Favored : 93.28 % 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 aren not related in a simple way. whole: 2.00 (0.19), residues: 2037 helix: 2.31 (0.15), residues: 1143 sheet: -0.36 (0.30), residues: 317 loop : 0.43 (0.27), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 280 TYR 0.010 0.001 TYR B 157 PHE 0.009 0.001 PHE B 958 TRP 0.012 0.001 TRP B 540 HIS 0.002 0.001 HIS B 600 Details of bonding type rmsd covalent geometry : bond 0.00357 (15876) covalent geometry : angle 0.54718 (21580) hydrogen bonds : bond 0.15982 ( 1062) hydrogen bonds : angle 6.60320 ( 3270) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 463 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 555 PHE cc_start: 0.6866 (OUTLIER) cc_final: 0.6312 (t80) REVERT: B 920 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7740 (mt-10) REVERT: A 151 LYS cc_start: 0.7573 (ttpm) cc_final: 0.7032 (tttp) REVERT: A 435 MET cc_start: 0.8107 (mmm) cc_final: 0.7848 (mmm) REVERT: A 897 PHE cc_start: 0.7353 (m-80) cc_final: 0.6915 (t80) outliers start: 35 outliers final: 6 residues processed: 487 average time/residue: 0.6479 time to fit residues: 346.7256 Evaluate side-chains 253 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 245 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 920 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 0.5980 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 GLN B 59 ASN B 63 GLN ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 GLN B 108 GLN B 112 GLN ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 GLN B 228 GLN B 237 GLN B 437 GLN B 439 GLN B 604 ASN B 684 GLN B 700 GLN B 724 GLN B 735 GLN B 870 GLN B 926 GLN B 967 GLN A 112 GLN A 360 GLN A 437 GLN A 439 GLN A 516 ASN A 517 GLN A 584 GLN A 691 HIS A 700 GLN A 848 GLN A 870 GLN A 952 GLN A 955 HIS A 967 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.131932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.107287 restraints weight = 18162.234| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.54 r_work: 0.3041 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15876 Z= 0.136 Angle : 0.534 7.861 21580 Z= 0.278 Chirality : 0.039 0.159 2514 Planarity : 0.004 0.033 2784 Dihedral : 4.402 57.659 2203 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 4.06 % Allowed : 13.98 % Favored : 81.96 % 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 aren not related in a simple way. whole: 2.19 (0.19), residues: 2037 helix: 2.48 (0.15), residues: 1150 sheet: -0.25 (0.30), residues: 311 loop : 0.41 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 568 TYR 0.016 0.001 TYR A 182 PHE 0.019 0.001 PHE A 4 TRP 0.010 0.001 TRP B 540 HIS 0.006 0.001 HIS A 955 Details of bonding type rmsd covalent geometry : bond 0.00298 (15876) covalent geometry : angle 0.53371 (21580) hydrogen bonds : bond 0.04863 ( 1062) hydrogen bonds : angle 4.98518 ( 3270) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 276 time to evaluate : 0.444 Fit side-chains REVERT: B 68 ASN cc_start: 0.7663 (t0) cc_final: 0.7405 (t0) REVERT: B 115 MET cc_start: 0.7075 (OUTLIER) cc_final: 0.6777 (mtp) REVERT: B 152 GLN cc_start: 0.7348 (OUTLIER) cc_final: 0.6595 (mt0) REVERT: B 170 ASN cc_start: 0.8225 (m110) cc_final: 0.7953 (t0) REVERT: B 267 THR cc_start: 0.8382 (p) cc_final: 0.8120 (p) REVERT: B 478 MET cc_start: 0.8711 (mmp) cc_final: 0.8267 (mmp) REVERT: B 522 ASN cc_start: 0.8389 (m-40) cc_final: 0.8109 (m110) REVERT: B 524 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7188 (tm-30) REVERT: B 536 ARG cc_start: 0.6470 (mtm180) cc_final: 0.6126 (mtm180) REVERT: B 555 PHE cc_start: 0.7402 (OUTLIER) cc_final: 0.6862 (t80) REVERT: B 588 LYS cc_start: 0.7927 (mptt) cc_final: 0.7693 (mmpt) REVERT: B 652 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7549 (mtpt) REVERT: B 724 GLN cc_start: 0.6273 (OUTLIER) cc_final: 0.6047 (mm-40) REVERT: B 762 ASP cc_start: 0.8265 (t0) cc_final: 0.7969 (t0) REVERT: B 824 GLU cc_start: 0.8234 (tt0) cc_final: 0.7950 (tt0) REVERT: B 839 MET cc_start: 0.8943 (mtp) cc_final: 0.8607 (mtm) REVERT: B 860 MET cc_start: 0.7479 (ttp) cc_final: 0.7091 (tpp) REVERT: B 920 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8510 (pt0) REVERT: A 115 MET cc_start: 0.8470 (tpp) cc_final: 0.7683 (mmt) REVERT: A 184 MET cc_start: 0.9001 (tpp) cc_final: 0.8571 (tpp) REVERT: A 244 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7406 (tm-30) REVERT: A 261 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.7525 (mtt90) REVERT: A 363 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.8086 (mtp85) REVERT: A 435 MET cc_start: 0.8643 (mmm) cc_final: 0.8275 (mmm) REVERT: A 570 MET cc_start: 0.9167 (OUTLIER) cc_final: 0.8900 (ptt) REVERT: A 635 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.7432 (mt-10) REVERT: A 860 MET cc_start: 0.8379 (ttp) cc_final: 0.7695 (ttp) outliers start: 67 outliers final: 24 residues processed: 321 average time/residue: 0.6101 time to fit residues: 215.1588 Evaluate side-chains 272 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 237 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 652 LYS Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 676 SER Chi-restraints excluded: chain B residue 724 GLN Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 844 SER Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 676 SER Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 920 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 42 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 138 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 195 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 157 optimal weight: 0.6980 chunk 171 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 GLN B 68 ASN B 520 ASN B 731 GLN B 735 GLN ** B 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 ASN A 517 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.130372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.105432 restraints weight = 18393.557| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.55 r_work: 0.3047 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15876 Z= 0.144 Angle : 0.524 7.503 21580 Z= 0.270 Chirality : 0.039 0.179 2514 Planarity : 0.004 0.037 2784 Dihedral : 4.411 56.807 2201 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 4.36 % Allowed : 15.38 % Favored : 80.27 % 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 aren not related in a simple way. whole: 2.02 (0.19), residues: 2037 helix: 2.34 (0.15), residues: 1155 sheet: -0.39 (0.30), residues: 307 loop : 0.36 (0.27), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 966 TYR 0.016 0.001 TYR B 596 PHE 0.022 0.001 PHE A 4 TRP 0.013 0.001 TRP B 807 HIS 0.003 0.001 HIS A 955 Details of bonding type rmsd covalent geometry : bond 0.00329 (15876) covalent geometry : angle 0.52368 (21580) hydrogen bonds : bond 0.04579 ( 1062) hydrogen bonds : angle 4.78249 ( 3270) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 245 time to evaluate : 0.595 Fit side-chains REVERT: B 68 ASN cc_start: 0.7680 (OUTLIER) cc_final: 0.7464 (t0) REVERT: B 115 MET cc_start: 0.7082 (OUTLIER) cc_final: 0.6755 (mtp) REVERT: B 152 GLN cc_start: 0.7249 (OUTLIER) cc_final: 0.6480 (mt0) REVERT: B 170 ASN cc_start: 0.8224 (m110) cc_final: 0.8005 (t0) REVERT: B 267 THR cc_start: 0.8417 (p) cc_final: 0.8200 (p) REVERT: B 395 MET cc_start: 0.8943 (mmp) cc_final: 0.8720 (mmm) REVERT: B 414 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7818 (tm-30) REVERT: B 478 MET cc_start: 0.8717 (mmp) cc_final: 0.8509 (mmp) REVERT: B 496 LEU cc_start: 0.8682 (mt) cc_final: 0.8444 (mp) REVERT: B 522 ASN cc_start: 0.8445 (m-40) cc_final: 0.8152 (m110) REVERT: B 524 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7253 (tm-30) REVERT: B 555 PHE cc_start: 0.7516 (OUTLIER) cc_final: 0.7012 (t80) REVERT: B 652 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7640 (mtpt) REVERT: B 748 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7447 (tp) REVERT: B 824 GLU cc_start: 0.8226 (tt0) cc_final: 0.8019 (tt0) REVERT: B 839 MET cc_start: 0.8979 (mtp) cc_final: 0.8683 (mtm) REVERT: B 860 MET cc_start: 0.7598 (ttp) cc_final: 0.7144 (tpp) REVERT: B 920 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8529 (pt0) REVERT: A 69 MET cc_start: 0.8545 (mmt) cc_final: 0.8156 (mmt) REVERT: A 76 MET cc_start: 0.7660 (OUTLIER) cc_final: 0.7343 (ttt) REVERT: A 115 MET cc_start: 0.8482 (tpp) cc_final: 0.8248 (mmt) REVERT: A 435 MET cc_start: 0.8711 (mmm) cc_final: 0.8387 (mmm) REVERT: A 478 MET cc_start: 0.8438 (mmm) cc_final: 0.7979 (mmp) REVERT: A 518 MET cc_start: 0.7506 (ttp) cc_final: 0.7278 (ptt) REVERT: A 635 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.7398 (mt-10) REVERT: A 824 GLU cc_start: 0.8926 (tt0) cc_final: 0.8612 (tp30) REVERT: A 860 MET cc_start: 0.8373 (ttp) cc_final: 0.7690 (ttp) REVERT: A 953 LYS cc_start: 0.7364 (mmtp) cc_final: 0.7111 (mmtt) outliers start: 72 outliers final: 37 residues processed: 286 average time/residue: 0.6188 time to fit residues: 194.7315 Evaluate side-chains 267 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 219 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 652 LYS Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 692 ASP Chi-restraints excluded: chain B residue 731 GLN Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 844 SER Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 676 SER Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 920 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 2 optimal weight: 0.9990 chunk 39 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 181 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 143 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 GLN B 731 GLN B 735 GLN ** B 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 967 GLN A 55 GLN A 67 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 716 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.129753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.104687 restraints weight = 18367.215| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.53 r_work: 0.3061 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15876 Z= 0.142 Angle : 0.516 7.746 21580 Z= 0.265 Chirality : 0.039 0.172 2514 Planarity : 0.004 0.040 2784 Dihedral : 4.418 55.951 2201 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 4.30 % Allowed : 15.80 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.95 (0.19), residues: 2037 helix: 2.27 (0.15), residues: 1156 sheet: -0.29 (0.31), residues: 299 loop : 0.27 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 966 TYR 0.015 0.001 TYR B 596 PHE 0.017 0.001 PHE A 4 TRP 0.013 0.001 TRP B 540 HIS 0.002 0.001 HIS B 319 Details of bonding type rmsd covalent geometry : bond 0.00326 (15876) covalent geometry : angle 0.51588 (21580) hydrogen bonds : bond 0.04419 ( 1062) hydrogen bonds : angle 4.67556 ( 3270) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 234 time to evaluate : 0.674 Fit side-chains REVERT: B 115 MET cc_start: 0.7047 (OUTLIER) cc_final: 0.6781 (mtp) REVERT: B 152 GLN cc_start: 0.7299 (OUTLIER) cc_final: 0.6489 (mt0) REVERT: B 254 ASN cc_start: 0.7287 (m-40) cc_final: 0.6912 (m110) REVERT: B 395 MET cc_start: 0.8912 (mmp) cc_final: 0.8702 (mmm) REVERT: B 414 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7842 (tm-30) REVERT: B 522 ASN cc_start: 0.8448 (m-40) cc_final: 0.8174 (m110) REVERT: B 555 PHE cc_start: 0.7575 (OUTLIER) cc_final: 0.7112 (t80) REVERT: B 652 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7621 (mtpt) REVERT: B 748 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7559 (tp) REVERT: B 824 GLU cc_start: 0.8241 (tt0) cc_final: 0.7983 (tt0) REVERT: B 860 MET cc_start: 0.7637 (ttp) cc_final: 0.7214 (tpp) REVERT: B 920 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8553 (pt0) REVERT: A 69 MET cc_start: 0.8544 (mmt) cc_final: 0.8039 (mmt) REVERT: A 76 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.7415 (ttt) REVERT: A 435 MET cc_start: 0.8756 (mmm) cc_final: 0.8259 (mmm) REVERT: A 635 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.7409 (mt-10) REVERT: A 763 ARG cc_start: 0.8201 (mtm110) cc_final: 0.7896 (mtm110) REVERT: A 796 MET cc_start: 0.8486 (mmm) cc_final: 0.8057 (mtm) REVERT: A 860 MET cc_start: 0.8398 (ttp) cc_final: 0.7721 (ttp) REVERT: A 953 LYS cc_start: 0.7291 (mmtp) cc_final: 0.7048 (mmtt) outliers start: 71 outliers final: 37 residues processed: 274 average time/residue: 0.6408 time to fit residues: 192.9162 Evaluate side-chains 264 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 218 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 652 LYS Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 692 ASP Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 784 ILE Chi-restraints excluded: chain B residue 844 SER Chi-restraints excluded: chain B residue 867 SER Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 676 SER Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 920 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 182 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 185 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 100 optimal weight: 0.0980 chunk 127 optimal weight: 0.2980 chunk 10 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 121 optimal weight: 0.8980 chunk 202 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 GLN B 68 ASN B 726 GLN B 731 GLN B 735 GLN ** B 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 GLN A 745 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.131431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.106684 restraints weight = 18451.084| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.47 r_work: 0.3101 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15876 Z= 0.127 Angle : 0.504 8.315 21580 Z= 0.256 Chirality : 0.039 0.163 2514 Planarity : 0.004 0.045 2784 Dihedral : 4.379 54.571 2201 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 4.66 % Allowed : 16.04 % Favored : 79.30 % 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 aren not related in a simple way. whole: 1.94 (0.19), residues: 2037 helix: 2.33 (0.15), residues: 1154 sheet: -0.41 (0.31), residues: 282 loop : 0.17 (0.26), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 966 TYR 0.016 0.001 TYR B 596 PHE 0.015 0.001 PHE A 4 TRP 0.014 0.001 TRP B 540 HIS 0.002 0.001 HIS B 955 Details of bonding type rmsd covalent geometry : bond 0.00287 (15876) covalent geometry : angle 0.50436 (21580) hydrogen bonds : bond 0.04189 ( 1062) hydrogen bonds : angle 4.55954 ( 3270) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 234 time to evaluate : 0.565 Fit side-chains REVERT: B 81 GLN cc_start: 0.7922 (mp10) cc_final: 0.7624 (pm20) REVERT: B 152 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.6670 (mt0) REVERT: B 304 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7328 (tp30) REVERT: B 414 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7818 (tm-30) REVERT: B 478 MET cc_start: 0.8646 (mmp) cc_final: 0.8244 (mmp) REVERT: B 486 MET cc_start: 0.8458 (mtm) cc_final: 0.8203 (mmm) REVERT: B 522 ASN cc_start: 0.8589 (m-40) cc_final: 0.8330 (m110) REVERT: B 524 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7649 (tp30) REVERT: B 555 PHE cc_start: 0.7602 (OUTLIER) cc_final: 0.7154 (t80) REVERT: B 652 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7689 (mtpt) REVERT: B 748 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7640 (tp) REVERT: B 860 MET cc_start: 0.7673 (ttp) cc_final: 0.7340 (tpp) REVERT: B 920 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8521 (pt0) REVERT: A 62 THR cc_start: 0.8691 (m) cc_final: 0.8414 (m) REVERT: A 69 MET cc_start: 0.8544 (mmt) cc_final: 0.8042 (mmt) REVERT: A 76 MET cc_start: 0.7859 (OUTLIER) cc_final: 0.7565 (ttt) REVERT: A 115 MET cc_start: 0.8587 (tpp) cc_final: 0.8380 (mmt) REVERT: A 241 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7873 (mm110) REVERT: A 435 MET cc_start: 0.8762 (mmm) cc_final: 0.8475 (mmm) REVERT: A 538 LEU cc_start: 0.8026 (tp) cc_final: 0.7802 (tp) REVERT: A 625 ARG cc_start: 0.8311 (ttp80) cc_final: 0.8044 (ttp-170) REVERT: A 635 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.7413 (mt-10) REVERT: A 715 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.7872 (ptp-170) REVERT: A 763 ARG cc_start: 0.8225 (mtm110) cc_final: 0.7753 (mtm110) REVERT: A 796 MET cc_start: 0.8504 (mmm) cc_final: 0.8037 (mtm) REVERT: A 860 MET cc_start: 0.8437 (ttp) cc_final: 0.7813 (ttp) REVERT: A 953 LYS cc_start: 0.7338 (mmtp) cc_final: 0.7137 (mmtt) outliers start: 77 outliers final: 37 residues processed: 281 average time/residue: 0.5925 time to fit residues: 183.4378 Evaluate side-chains 267 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 219 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 652 LYS Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 692 ASP Chi-restraints excluded: chain B residue 731 GLN Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 844 SER Chi-restraints excluded: chain B residue 867 SER Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 536 ARG Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 676 SER Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 715 ARG Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 920 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 122 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 149 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 72 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 GLN B 125 GLN B 655 ASN B 684 GLN B 726 GLN B 735 GLN ** B 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 967 GLN A 59 ASN A 67 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.129975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.105065 restraints weight = 18328.673| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.48 r_work: 0.3082 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15876 Z= 0.148 Angle : 0.521 7.961 21580 Z= 0.265 Chirality : 0.039 0.157 2514 Planarity : 0.004 0.046 2784 Dihedral : 4.414 54.037 2201 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 4.06 % Allowed : 16.95 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.88 (0.19), residues: 2037 helix: 2.27 (0.15), residues: 1153 sheet: -0.36 (0.31), residues: 282 loop : 0.15 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 813 TYR 0.018 0.001 TYR B 596 PHE 0.010 0.001 PHE B 853 TRP 0.015 0.001 TRP B 540 HIS 0.004 0.001 HIS B 955 Details of bonding type rmsd covalent geometry : bond 0.00347 (15876) covalent geometry : angle 0.52098 (21580) hydrogen bonds : bond 0.04328 ( 1062) hydrogen bonds : angle 4.57348 ( 3270) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 233 time to evaluate : 0.550 Fit side-chains REVERT: B 59 ASN cc_start: 0.7411 (m110) cc_final: 0.7079 (m110) REVERT: B 152 GLN cc_start: 0.7469 (OUTLIER) cc_final: 0.6620 (mt0) REVERT: B 254 ASN cc_start: 0.7269 (m-40) cc_final: 0.6953 (m110) REVERT: B 304 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7340 (tp30) REVERT: B 414 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7835 (tm-30) REVERT: B 478 MET cc_start: 0.8666 (mmp) cc_final: 0.8441 (mmp) REVERT: B 486 MET cc_start: 0.8452 (mtm) cc_final: 0.8190 (mmm) REVERT: B 522 ASN cc_start: 0.8528 (m-40) cc_final: 0.8223 (m110) REVERT: B 524 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7591 (tp30) REVERT: B 536 ARG cc_start: 0.6890 (mtm180) cc_final: 0.6402 (ptt180) REVERT: B 555 PHE cc_start: 0.7598 (OUTLIER) cc_final: 0.7174 (t80) REVERT: B 652 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7704 (mtpt) REVERT: B 748 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7602 (tp) REVERT: B 860 MET cc_start: 0.7705 (ttp) cc_final: 0.7331 (tpp) REVERT: B 920 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8567 (pt0) REVERT: A 62 THR cc_start: 0.8840 (m) cc_final: 0.8559 (m) REVERT: A 69 MET cc_start: 0.8538 (mmt) cc_final: 0.8053 (mmt) REVERT: A 76 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7558 (ttt) REVERT: A 241 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7895 (mm110) REVERT: A 435 MET cc_start: 0.8826 (mmm) cc_final: 0.8531 (mmm) REVERT: A 538 LEU cc_start: 0.8013 (tp) cc_final: 0.7805 (tp) REVERT: A 625 ARG cc_start: 0.8372 (ttp80) cc_final: 0.8095 (ttp-170) REVERT: A 635 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.7388 (mt-10) REVERT: A 656 GLN cc_start: 0.8211 (mm-40) cc_final: 0.7890 (mt0) REVERT: A 715 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.7874 (ptp-170) REVERT: A 763 ARG cc_start: 0.8201 (mtm110) cc_final: 0.7946 (mtm110) REVERT: A 796 MET cc_start: 0.8561 (mmm) cc_final: 0.8101 (mtm) REVERT: A 824 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8589 (tp30) REVERT: A 860 MET cc_start: 0.8431 (ttp) cc_final: 0.7798 (ttp) REVERT: A 891 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7455 (mm-30) REVERT: A 953 LYS cc_start: 0.7343 (mmtp) cc_final: 0.7142 (mmtt) outliers start: 67 outliers final: 34 residues processed: 272 average time/residue: 0.5920 time to fit residues: 177.6355 Evaluate side-chains 268 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 221 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 652 LYS Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 692 ASP Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 765 ARG Chi-restraints excluded: chain B residue 844 SER Chi-restraints excluded: chain B residue 867 SER Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 536 ARG Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 676 SER Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 715 ARG Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 920 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 42 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 163 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 GLN ** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 GLN B 735 GLN B 772 GLN B 967 GLN A 67 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 106 GLN A 360 GLN A 516 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.128863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.103881 restraints weight = 18323.253| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.48 r_work: 0.3032 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15876 Z= 0.160 Angle : 0.533 8.117 21580 Z= 0.272 Chirality : 0.040 0.159 2514 Planarity : 0.004 0.042 2784 Dihedral : 4.488 52.987 2201 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 4.00 % Allowed : 17.37 % Favored : 78.63 % 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 aren not related in a simple way. whole: 1.77 (0.19), residues: 2037 helix: 2.19 (0.15), residues: 1151 sheet: -0.45 (0.32), residues: 283 loop : 0.11 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 966 TYR 0.021 0.001 TYR B 596 PHE 0.010 0.001 PHE B 853 TRP 0.016 0.001 TRP B 540 HIS 0.006 0.001 HIS B 955 Details of bonding type rmsd covalent geometry : bond 0.00379 (15876) covalent geometry : angle 0.53288 (21580) hydrogen bonds : bond 0.04435 ( 1062) hydrogen bonds : angle 4.59371 ( 3270) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 232 time to evaluate : 0.445 Fit side-chains revert: symmetry clash REVERT: B 59 ASN cc_start: 0.7382 (m110) cc_final: 0.7035 (m110) REVERT: B 254 ASN cc_start: 0.7153 (m-40) cc_final: 0.6868 (m110) REVERT: B 304 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7334 (tp30) REVERT: B 414 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7792 (tm-30) REVERT: B 486 MET cc_start: 0.8455 (mtm) cc_final: 0.8173 (mmm) REVERT: B 522 ASN cc_start: 0.8519 (m-40) cc_final: 0.8215 (m110) REVERT: B 524 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7592 (tp30) REVERT: B 536 ARG cc_start: 0.6876 (mtm180) cc_final: 0.6423 (ptt180) REVERT: B 555 PHE cc_start: 0.7611 (OUTLIER) cc_final: 0.7171 (t80) REVERT: B 652 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7706 (mtpt) REVERT: A 62 THR cc_start: 0.8931 (m) cc_final: 0.8667 (m) REVERT: A 69 MET cc_start: 0.8500 (mmt) cc_final: 0.7920 (mmt) REVERT: A 435 MET cc_start: 0.8852 (mmm) cc_final: 0.8535 (mmm) REVERT: A 525 ARG cc_start: 0.7207 (OUTLIER) cc_final: 0.6826 (ttp-170) REVERT: A 538 LEU cc_start: 0.7986 (tp) cc_final: 0.7785 (tp) REVERT: A 625 ARG cc_start: 0.8401 (ttp80) cc_final: 0.8136 (ttp-170) REVERT: A 635 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.7450 (mt-10) REVERT: A 656 GLN cc_start: 0.8180 (mm-40) cc_final: 0.7868 (mp10) REVERT: A 715 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.7833 (ptp-170) REVERT: A 763 ARG cc_start: 0.8244 (mtm110) cc_final: 0.7975 (mtm110) REVERT: A 796 MET cc_start: 0.8586 (mmm) cc_final: 0.8045 (mtm) REVERT: A 860 MET cc_start: 0.8449 (ttp) cc_final: 0.7793 (ttp) REVERT: A 891 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7564 (mm-30) outliers start: 66 outliers final: 36 residues processed: 264 average time/residue: 0.6225 time to fit residues: 180.8581 Evaluate side-chains 264 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 220 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 652 LYS Chi-restraints excluded: chain B residue 692 ASP Chi-restraints excluded: chain B residue 731 GLN Chi-restraints excluded: chain B residue 761 MET Chi-restraints excluded: chain B residue 844 SER Chi-restraints excluded: chain B residue 867 SER Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 525 ARG Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 536 ARG Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 676 SER Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 715 ARG Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 851 ASN Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 920 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 60 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 139 optimal weight: 0.0980 chunk 25 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 143 optimal weight: 0.3980 chunk 125 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 183 optimal weight: 0.0570 chunk 170 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 GLN ** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 724 GLN B 726 GLN B 731 GLN B 735 GLN B 772 GLN A 67 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.131347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.107431 restraints weight = 18401.664| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.35 r_work: 0.3041 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15876 Z= 0.122 Angle : 0.510 7.684 21580 Z= 0.260 Chirality : 0.038 0.151 2514 Planarity : 0.004 0.043 2784 Dihedral : 4.419 51.768 2201 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.03 % Allowed : 18.40 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.86 (0.19), residues: 2037 helix: 2.27 (0.15), residues: 1150 sheet: -0.42 (0.32), residues: 283 loop : 0.13 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 816 TYR 0.019 0.001 TYR B 596 PHE 0.010 0.001 PHE B 853 TRP 0.016 0.001 TRP B 540 HIS 0.005 0.001 HIS B 955 Details of bonding type rmsd covalent geometry : bond 0.00269 (15876) covalent geometry : angle 0.50954 (21580) hydrogen bonds : bond 0.04087 ( 1062) hydrogen bonds : angle 4.52833 ( 3270) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 225 time to evaluate : 0.629 Fit side-chains REVERT: B 59 ASN cc_start: 0.7337 (m110) cc_final: 0.7111 (m110) REVERT: B 304 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7269 (tp30) REVERT: B 414 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7735 (tm-30) REVERT: B 478 MET cc_start: 0.8697 (mmp) cc_final: 0.8376 (mmp) REVERT: B 486 MET cc_start: 0.8265 (mtm) cc_final: 0.8023 (mmm) REVERT: B 522 ASN cc_start: 0.8432 (m-40) cc_final: 0.8115 (m110) REVERT: B 524 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7487 (tp30) REVERT: B 536 ARG cc_start: 0.6723 (mtm180) cc_final: 0.6212 (ptt180) REVERT: B 555 PHE cc_start: 0.7576 (OUTLIER) cc_final: 0.7176 (t80) REVERT: B 652 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7591 (mtpt) REVERT: B 860 MET cc_start: 0.7508 (ttp) cc_final: 0.7169 (tpp) REVERT: A 62 THR cc_start: 0.8760 (m) cc_final: 0.8487 (m) REVERT: A 69 MET cc_start: 0.8442 (mmt) cc_final: 0.7774 (mmt) REVERT: A 241 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7795 (mm110) REVERT: A 625 ARG cc_start: 0.8360 (ttp80) cc_final: 0.8115 (ttp-170) REVERT: A 635 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.7422 (mt-10) REVERT: A 656 GLN cc_start: 0.8130 (mm-40) cc_final: 0.7792 (mp10) REVERT: A 715 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.7720 (ptp-170) REVERT: A 763 ARG cc_start: 0.8227 (mtm110) cc_final: 0.7810 (mtm110) REVERT: A 796 MET cc_start: 0.8624 (mmm) cc_final: 0.8016 (mtm) REVERT: A 860 MET cc_start: 0.8387 (ttp) cc_final: 0.7689 (ttp) REVERT: A 891 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7528 (mm-30) outliers start: 50 outliers final: 28 residues processed: 255 average time/residue: 0.6381 time to fit residues: 179.4398 Evaluate side-chains 253 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 217 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 652 LYS Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 692 ASP Chi-restraints excluded: chain B residue 731 GLN Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain B residue 844 SER Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 536 ARG Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 715 ARG Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 851 ASN Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 920 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 166 optimal weight: 0.0370 chunk 44 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 193 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 GLN B 731 GLN B 772 GLN A 67 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.131303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.106407 restraints weight = 18288.085| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.48 r_work: 0.3120 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15876 Z= 0.128 Angle : 0.513 7.886 21580 Z= 0.261 Chirality : 0.039 0.158 2514 Planarity : 0.004 0.042 2784 Dihedral : 4.421 51.212 2201 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.72 % Allowed : 19.07 % Favored : 78.21 % 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 aren not related in a simple way. whole: 1.89 (0.19), residues: 2037 helix: 2.28 (0.15), residues: 1150 sheet: -0.23 (0.33), residues: 260 loop : 0.05 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 816 TYR 0.021 0.001 TYR B 596 PHE 0.011 0.001 PHE B 853 TRP 0.015 0.001 TRP B 540 HIS 0.005 0.001 HIS B 955 Details of bonding type rmsd covalent geometry : bond 0.00290 (15876) covalent geometry : angle 0.51252 (21580) hydrogen bonds : bond 0.04080 ( 1062) hydrogen bonds : angle 4.51747 ( 3270) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 226 time to evaluate : 0.616 Fit side-chains REVERT: B 55 GLN cc_start: 0.7855 (tp40) cc_final: 0.7512 (tp-100) REVERT: B 59 ASN cc_start: 0.7308 (m110) cc_final: 0.6859 (m110) REVERT: B 123 GLN cc_start: 0.7629 (OUTLIER) cc_final: 0.7389 (mp10) REVERT: B 125 GLN cc_start: 0.6941 (mm-40) cc_final: 0.6436 (tp40) REVERT: B 304 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7332 (tp30) REVERT: B 414 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7813 (tm-30) REVERT: B 435 MET cc_start: 0.8531 (mmm) cc_final: 0.8168 (mmp) REVERT: B 478 MET cc_start: 0.8682 (mmp) cc_final: 0.8355 (mmp) REVERT: B 486 MET cc_start: 0.8361 (mtm) cc_final: 0.8152 (mmm) REVERT: B 522 ASN cc_start: 0.8520 (m-40) cc_final: 0.8198 (m110) REVERT: B 524 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7610 (tp30) REVERT: B 536 ARG cc_start: 0.6871 (mtm180) cc_final: 0.6382 (ptt180) REVERT: B 652 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7688 (mtpt) REVERT: B 860 MET cc_start: 0.7629 (ttp) cc_final: 0.7344 (tpp) REVERT: A 62 THR cc_start: 0.8898 (m) cc_final: 0.8628 (m) REVERT: A 69 MET cc_start: 0.8443 (mmt) cc_final: 0.7799 (mmt) REVERT: A 149 MET cc_start: 0.8770 (mtp) cc_final: 0.8531 (mtm) REVERT: A 625 ARG cc_start: 0.8337 (ttp80) cc_final: 0.8077 (ttp-170) REVERT: A 635 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.7455 (mt-10) REVERT: A 656 GLN cc_start: 0.8207 (mm-40) cc_final: 0.7873 (mp10) REVERT: A 715 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.7814 (ptp-170) REVERT: A 763 ARG cc_start: 0.8258 (mtm110) cc_final: 0.7994 (mtm110) REVERT: A 796 MET cc_start: 0.8580 (mmm) cc_final: 0.7981 (mtm) REVERT: A 860 MET cc_start: 0.8417 (ttp) cc_final: 0.7789 (ttp) REVERT: A 891 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7557 (mm-30) outliers start: 45 outliers final: 27 residues processed: 249 average time/residue: 0.6802 time to fit residues: 186.5006 Evaluate side-chains 255 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 221 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 652 LYS Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 844 SER Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 536 ARG Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 715 ARG Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 920 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 144 optimal weight: 0.9990 chunk 3 optimal weight: 0.0980 chunk 52 optimal weight: 4.9990 chunk 126 optimal weight: 10.0000 chunk 195 optimal weight: 3.9990 chunk 75 optimal weight: 0.4980 chunk 109 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 188 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 GLN B 772 GLN A 67 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 600 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.131289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.106302 restraints weight = 18379.446| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.49 r_work: 0.3026 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 15876 Z= 0.128 Angle : 0.516 7.879 21580 Z= 0.263 Chirality : 0.039 0.167 2514 Planarity : 0.004 0.041 2784 Dihedral : 4.257 50.363 2199 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.54 % Allowed : 19.37 % Favored : 78.09 % 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 aren not related in a simple way. whole: 1.88 (0.19), residues: 2037 helix: 2.27 (0.15), residues: 1150 sheet: -0.24 (0.33), residues: 260 loop : 0.04 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 816 TYR 0.021 0.001 TYR B 596 PHE 0.022 0.001 PHE B 958 TRP 0.015 0.001 TRP B 540 HIS 0.005 0.001 HIS B 955 Details of bonding type rmsd covalent geometry : bond 0.00292 (15876) covalent geometry : angle 0.51573 (21580) hydrogen bonds : bond 0.04048 ( 1062) hydrogen bonds : angle 4.50045 ( 3270) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 222 time to evaluate : 0.623 Fit side-chains REVERT: B 59 ASN cc_start: 0.7303 (m110) cc_final: 0.6902 (m110) REVERT: B 123 GLN cc_start: 0.7306 (OUTLIER) cc_final: 0.7057 (mp10) REVERT: B 254 ASN cc_start: 0.7155 (m-40) cc_final: 0.6780 (m110) REVERT: B 304 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7310 (tp30) REVERT: B 414 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7661 (tm-30) REVERT: B 435 MET cc_start: 0.8383 (mmm) cc_final: 0.7999 (mmp) REVERT: B 478 MET cc_start: 0.8606 (mmp) cc_final: 0.8274 (mmp) REVERT: B 486 MET cc_start: 0.8248 (mtm) cc_final: 0.7946 (mmm) REVERT: B 518 MET cc_start: 0.8066 (tmm) cc_final: 0.7691 (tmm) REVERT: B 522 ASN cc_start: 0.8320 (m-40) cc_final: 0.7891 (m110) REVERT: B 524 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7398 (tp30) REVERT: B 536 ARG cc_start: 0.6398 (mtm180) cc_final: 0.5964 (ptt180) REVERT: B 652 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7518 (mtpt) REVERT: B 731 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7611 (tt0) REVERT: B 860 MET cc_start: 0.7529 (ttp) cc_final: 0.7005 (tpp) REVERT: A 62 THR cc_start: 0.8682 (m) cc_final: 0.8414 (m) REVERT: A 69 MET cc_start: 0.8340 (mmt) cc_final: 0.7651 (mmt) REVERT: A 625 ARG cc_start: 0.8408 (ttp80) cc_final: 0.8185 (ttp-170) REVERT: A 635 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.7395 (mt-10) REVERT: A 656 GLN cc_start: 0.8075 (mm-40) cc_final: 0.7665 (mp10) REVERT: A 715 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.7669 (ptp-170) REVERT: A 763 ARG cc_start: 0.8176 (mtm110) cc_final: 0.7732 (mtm110) REVERT: A 796 MET cc_start: 0.8687 (mmm) cc_final: 0.8065 (mtm) REVERT: A 860 MET cc_start: 0.8330 (ttp) cc_final: 0.7573 (ttp) REVERT: A 891 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7518 (mm-30) outliers start: 42 outliers final: 27 residues processed: 246 average time/residue: 0.6696 time to fit residues: 181.3832 Evaluate side-chains 250 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 215 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 652 LYS Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 731 GLN Chi-restraints excluded: chain B residue 844 SER Chi-restraints excluded: chain B residue 867 SER Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 536 ARG Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 715 ARG Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 920 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 179 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 183 optimal weight: 0.2980 chunk 165 optimal weight: 0.6980 chunk 185 optimal weight: 0.9980 chunk 153 optimal weight: 0.7980 chunk 169 optimal weight: 6.9990 chunk 94 optimal weight: 0.2980 chunk 116 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 ASN ** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 GLN B 735 GLN B 772 GLN A 67 GLN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.131360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.106347 restraints weight = 18320.356| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.49 r_work: 0.3031 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15876 Z= 0.127 Angle : 0.519 7.846 21580 Z= 0.264 Chirality : 0.039 0.157 2514 Planarity : 0.004 0.041 2784 Dihedral : 4.260 50.283 2199 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.72 % Allowed : 19.37 % Favored : 77.91 % 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 aren not related in a simple way. whole: 1.86 (0.19), residues: 2037 helix: 2.26 (0.15), residues: 1150 sheet: -0.33 (0.32), residues: 270 loop : 0.09 (0.26), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 816 TYR 0.021 0.001 TYR B 596 PHE 0.021 0.001 PHE B 958 TRP 0.015 0.001 TRP B 540 HIS 0.007 0.001 HIS B 955 Details of bonding type rmsd covalent geometry : bond 0.00286 (15876) covalent geometry : angle 0.51880 (21580) hydrogen bonds : bond 0.04016 ( 1062) hydrogen bonds : angle 4.48225 ( 3270) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5414.95 seconds wall clock time: 93 minutes 1.62 seconds (5581.62 seconds total)