Starting phenix.real_space_refine on Fri Sep 19 04:07:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e9f_47796/09_2025/9e9f_47796.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e9f_47796/09_2025/9e9f_47796.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e9f_47796/09_2025/9e9f_47796.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e9f_47796/09_2025/9e9f_47796.map" model { file = "/net/cci-nas-00/data/ceres_data/9e9f_47796/09_2025/9e9f_47796.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e9f_47796/09_2025/9e9f_47796.cif" } resolution = 3.63 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= 0.029 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 105 5.16 5 C 14812 2.51 5 N 3951 2.21 5 O 4180 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23048 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 7556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7556 Classifications: {'peptide': 993} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 46, 'TRANS': 946} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 7669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 7669 Classifications: {'peptide': 1011} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 46, 'TRANS': 964} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "A" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1031, 7823 Classifications: {'peptide': 1031} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 48, 'TRANS': 982} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 5.10, per 1000 atoms: 0.22 Number of scatterers: 23048 At special positions: 0 Unit cell: (121.98, 123.05, 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 105 16.00 O 4180 8.00 N 3951 7.00 C 14812 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: 1.74 Conformation dependent library (CDL) restraints added in 936.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5554 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 21 sheets defined 60.6% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'B' and resid 1 through 8 Processing helix chain 'B' and resid 8 through 30 Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'B' and resid 61 through 70 Processing helix chain 'B' and resid 98 through 115 removed outlier: 4.458A pdb=" N SER B 115 " --> pdb=" O LYS B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 125 Processing helix chain 'B' and resid 149 through 160 Processing helix chain 'B' and resid 160 through 168 Processing helix chain 'B' and resid 188 through 195 Processing helix chain 'B' and resid 199 through 211 Processing helix chain 'B' and resid 241 through 247 Processing helix chain 'B' and resid 262 through 266 Processing helix chain 'B' and resid 271 through 275 removed outlier: 3.698A pdb=" N TYR B 274 " --> pdb=" O GLN B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 315 Processing helix chain 'B' and resid 328 through 359 removed outlier: 3.566A pdb=" N VAL B 332 " --> pdb=" O THR B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 386 Proline residue: B 367 - end of helix Proline residue: B 372 - end of helix Processing helix chain 'B' and resid 390 through 422 removed outlier: 4.701A pdb=" N GLY B 402 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE B 403 " --> pdb=" O LEU B 399 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASP B 407 " --> pdb=" O ILE B 403 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ALA B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 453 removed outlier: 5.656A pdb=" N GLY B 439 " --> pdb=" O ARG B 435 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ALA B 440 " --> pdb=" O GLN B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 458 removed outlier: 4.140A pdb=" N PHE B 457 " --> pdb=" O VAL B 453 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE B 458 " --> pdb=" O PRO B 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 453 through 458' Processing helix chain 'B' and resid 459 through 495 removed outlier: 4.786A pdb=" N THR B 488 " --> pdb=" O ALA B 484 " (cutoff:3.500A) Proline residue: B 489 - end of helix Processing helix chain 'B' and resid 500 through 505 Processing helix chain 'B' and resid 508 through 534 removed outlier: 3.706A pdb=" N ARG B 534 " --> pdb=" O GLY B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 556 Processing helix chain 'B' and resid 580 through 596 removed outlier: 3.645A pdb=" N THR B 584 " --> pdb=" O PRO B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 650 Processing helix chain 'B' and resid 686 through 704 Processing helix chain 'B' and resid 726 through 734 Processing helix chain 'B' and resid 736 through 748 Processing helix chain 'B' and resid 830 through 843 Processing helix chain 'B' and resid 855 through 887 Proline residue: B 868 - end of helix Processing helix chain 'B' and resid 889 through 914 removed outlier: 3.758A pdb=" N VAL B 899 " --> pdb=" O VAL B 895 " (cutoff:3.500A) Proline residue: B 900 - end of helix Processing helix chain 'B' and resid 918 through 950 removed outlier: 3.649A pdb=" N ILE B 939 " --> pdb=" O ASN B 935 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL B 942 " --> pdb=" O LEU B 938 " (cutoff:3.500A) Processing helix chain 'B' and resid 952 through 984 removed outlier: 4.435A pdb=" N ARG B 966 " --> pdb=" O ARG B 962 " (cutoff:3.500A) Proline residue: B 967 - end of helix Proline residue: B 981 - end of helix Processing helix chain 'B' and resid 990 through 1010 removed outlier: 3.822A pdb=" N GLY B 999 " --> pdb=" O ALA B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1010 through 1026 Proline residue: B1016 - end of helix Processing helix chain 'C' and resid 2 through 8 Processing helix chain 'C' and resid 8 through 30 Processing helix chain 'C' and resid 53 through 70 removed outlier: 3.729A pdb=" N THR C 62 " --> pdb=" O GLU C 58 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ALA C 63 " --> pdb=" O GLU C 59 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 113 removed outlier: 3.663A pdb=" N VAL C 113 " --> pdb=" O ARG C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 125 Processing helix chain 'C' and resid 149 through 168 removed outlier: 4.104A pdb=" N LEU C 162 " --> pdb=" O SER C 158 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N GLN C 163 " --> pdb=" O SER C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 195 Processing helix chain 'C' and resid 198 through 210 removed outlier: 3.714A pdb=" N LEU C 202 " --> pdb=" O SER C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 247 Processing helix chain 'C' and resid 297 through 316 Processing helix chain 'C' and resid 328 through 358 removed outlier: 3.521A pdb=" N VAL C 332 " --> pdb=" O THR C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 386 Proline residue: C 367 - end of helix Proline residue: C 372 - end of helix Processing helix chain 'C' and resid 390 through 422 removed outlier: 4.420A pdb=" N GLY C 402 " --> pdb=" O VAL C 398 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE C 403 " --> pdb=" O LEU C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 453 removed outlier: 5.453A pdb=" N GLY C 439 " --> pdb=" O ARG C 435 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ALA C 440 " --> pdb=" O GLN C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 458 Processing helix chain 'C' and resid 460 through 475 removed outlier: 3.712A pdb=" N ALA C 470 " --> pdb=" O TYR C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 481 Processing helix chain 'C' and resid 486 through 495 Processing helix chain 'C' and resid 508 through 534 removed outlier: 3.518A pdb=" N ARG C 534 " --> pdb=" O GLY C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 555 removed outlier: 3.788A pdb=" N TRP C 538 " --> pdb=" O ARG C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 599 Processing helix chain 'C' and resid 634 through 637 Processing helix chain 'C' and resid 638 through 646 Processing helix chain 'C' and resid 686 through 704 Processing helix chain 'C' and resid 726 through 733 Processing helix chain 'C' and resid 736 through 748 Processing helix chain 'C' and resid 796 through 798 No H-bonds generated for 'chain 'C' and resid 796 through 798' Processing helix chain 'C' and resid 830 through 843 Processing helix chain 'C' and resid 854 through 863 Processing helix chain 'C' and resid 865 through 887 removed outlier: 3.509A pdb=" N ALA C 869 " --> pdb=" O ALA C 865 " (cutoff:3.500A) Processing helix chain 'C' and resid 891 through 914 removed outlier: 4.005A pdb=" N VAL C 895 " --> pdb=" O ILE C 891 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL C 899 " --> pdb=" O VAL C 895 " (cutoff:3.500A) Proline residue: C 900 - end of helix removed outlier: 3.687A pdb=" N VAL C 903 " --> pdb=" O VAL C 899 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY C 905 " --> pdb=" O LEU C 901 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA C 906 " --> pdb=" O GLY C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 918 through 950 Processing helix chain 'C' and resid 952 through 964 Processing helix chain 'C' and resid 965 through 984 Proline residue: C 981 - end of helix Processing helix chain 'C' and resid 989 through 1027 removed outlier: 3.552A pdb=" N GLN C 993 " --> pdb=" O GLY C 989 " (cutoff:3.500A) Proline residue: C1016 - end of helix Processing helix chain 'A' and resid 2 through 8 Processing helix chain 'A' and resid 8 through 30 Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 61 through 70 Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.553A pdb=" N SER A 115 " --> pdb=" O LYS A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 125 Processing helix chain 'A' and resid 149 through 160 Processing helix chain 'A' and resid 160 through 168 Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 198 through 211 Processing helix chain 'A' and resid 241 through 248 Processing helix chain 'A' and resid 260 through 264 Processing helix chain 'A' and resid 299 through 315 Processing helix chain 'A' and resid 328 through 359 removed outlier: 4.029A pdb=" N VAL A 332 " --> pdb=" O THR A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 386 Proline residue: A 367 - end of helix Proline residue: A 372 - end of helix Processing helix chain 'A' and resid 390 through 422 removed outlier: 4.492A pdb=" N GLY A 402 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASP A 406 " --> pdb=" O GLY A 402 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ASP A 407 " --> pdb=" O ILE A 403 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 453 removed outlier: 5.389A pdb=" N GLY A 439 " --> pdb=" O ARG A 435 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ALA A 440 " --> pdb=" O GLN A 436 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE A 452 " --> pdb=" O LEU A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 458 removed outlier: 3.607A pdb=" N PHE A 458 " --> pdb=" O MET A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 495 removed outlier: 4.909A pdb=" N THR A 488 " --> pdb=" O ALA A 484 " (cutoff:3.500A) Proline residue: A 489 - end of helix Processing helix chain 'A' and resid 508 through 534 removed outlier: 3.714A pdb=" N ARG A 534 " --> pdb=" O GLY A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 556 removed outlier: 3.638A pdb=" N TRP A 538 " --> pdb=" O ARG A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 598 Processing helix chain 'A' and resid 634 through 637 Processing helix chain 'A' and resid 638 through 650 Processing helix chain 'A' and resid 686 through 704 Processing helix chain 'A' and resid 727 through 734 Processing helix chain 'A' and resid 737 through 749 removed outlier: 4.240A pdb=" N ASN A 741 " --> pdb=" O MET A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 775 Processing helix chain 'A' and resid 778 through 783 Processing helix chain 'A' and resid 830 through 843 Processing helix chain 'A' and resid 855 through 887 removed outlier: 3.593A pdb=" N ALA A 865 " --> pdb=" O ARG A 861 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLN A 866 " --> pdb=" O LEU A 862 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A 867 " --> pdb=" O SER A 863 " (cutoff:3.500A) Proline residue: A 868 - end of helix removed outlier: 3.591A pdb=" N PHE A 871 " --> pdb=" O ALA A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 913 removed outlier: 4.210A pdb=" N ALA A 894 " --> pdb=" O SER A 890 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL A 895 " --> pdb=" O ILE A 891 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL A 899 " --> pdb=" O VAL A 895 " (cutoff:3.500A) Proline residue: A 900 - end of helix Processing helix chain 'A' and resid 918 through 950 removed outlier: 4.001A pdb=" N VAL A 942 " --> pdb=" O LEU A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 984 removed outlier: 5.010A pdb=" N ARG A 966 " --> pdb=" O ARG A 962 " (cutoff:3.500A) Proline residue: A 967 - end of helix Proline residue: A 981 - end of helix Processing helix chain 'A' and resid 989 through 1010 removed outlier: 3.658A pdb=" N GLN A 993 " --> pdb=" O GLY A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1027 Proline residue: A1016 - end of helix Processing sheet with id=AA1, first strand: chain 'B' and resid 127 through 129 removed outlier: 3.528A pdb=" N GLN B 86 " --> pdb=" O SER B 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 171 through 176 removed outlier: 4.166A pdb=" N THR B 286 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU B 141 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 171 through 176 removed outlier: 4.166A pdb=" N THR B 286 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU B 141 " --> pdb=" O THR B 286 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TYR B 326 " --> pdb=" O ILE B 138 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 283 through 284 removed outlier: 3.642A pdb=" N TYR B 605 " --> pdb=" O PHE B 623 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N MET B 621 " --> pdb=" O VAL B 607 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA B 620 " --> pdb=" O VAL B 573 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 707 through 712 removed outlier: 4.462A pdb=" N VAL B 710 " --> pdb=" O GLU B 822 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLU B 822 " --> pdb=" O VAL B 710 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N PHE B 712 " --> pdb=" O ASN B 820 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ASN B 820 " --> pdb=" O PHE B 712 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY B 823 " --> pdb=" O PHE B 675 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ASP B 676 " --> pdb=" O SER B 854 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 718 through 720 Processing sheet with id=AA7, first strand: chain 'B' and resid 723 through 725 Processing sheet with id=AA8, first strand: chain 'C' and resid 127 through 130 Processing sheet with id=AA9, first strand: chain 'C' and resid 171 through 173 removed outlier: 3.596A pdb=" N LYS C 173 " --> pdb=" O LYS C 291 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 137 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE C 138 " --> pdb=" O PRO C 325 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 601 through 608 removed outlier: 3.917A pdb=" N MET C 570 " --> pdb=" O MET C 661 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 675 through 678 removed outlier: 4.534A pdb=" N ASN C 709 " --> pdb=" O GLN C 824 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 800 through 804 Processing sheet with id=AB4, first strand: chain 'C' and resid 784 through 786 Processing sheet with id=AB5, first strand: chain 'A' and resid 127 through 129 removed outlier: 3.594A pdb=" N GLN A 86 " --> pdb=" O SER A 83 " (cutoff:3.500A) removed outlier: 12.055A pdb=" N GLN A 809 " --> pdb=" O ASN A 820 " (cutoff:3.500A) removed outlier: 9.213A pdb=" N ASN A 820 " --> pdb=" O GLN A 809 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N THR A 811 " --> pdb=" O SER A 818 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ASN A 820 " --> pdb=" O PHE A 712 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N PHE A 712 " --> pdb=" O ASN A 820 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLU A 822 " --> pdb=" O VAL A 710 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VAL A 710 " --> pdb=" O GLU A 822 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 127 through 129 removed outlier: 3.594A pdb=" N GLN A 86 " --> pdb=" O SER A 83 " (cutoff:3.500A) removed outlier: 12.055A pdb=" N GLN A 809 " --> pdb=" O ASN A 820 " (cutoff:3.500A) removed outlier: 9.213A pdb=" N ASN A 820 " --> pdb=" O GLN A 809 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N THR A 811 " --> pdb=" O SER A 818 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ASP A 676 " --> pdb=" O SER A 854 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER A 854 " --> pdb=" O ASP A 676 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 171 through 173 removed outlier: 6.605A pdb=" N LYS A 291 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N THR A 284 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER A 143 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ILE A 138 " --> pdb=" O PRO A 325 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 171 through 173 removed outlier: 6.605A pdb=" N LYS A 291 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N SER A 278 " --> pdb=" O ALA A 285 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 265 through 268 removed outlier: 6.548A pdb=" N MET A 183 " --> pdb=" O VAL A 766 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N GLN A 761 " --> pdb=" O MET A 757 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N MET A 757 " --> pdb=" O GLN A 761 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ARG A 763 " --> pdb=" O ASP A 755 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASP A 755 " --> pdb=" O ARG A 763 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL A 765 " --> pdb=" O ILE A 753 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP A 751 " --> pdb=" O VAL A 767 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 718 through 721 Processing sheet with id=AC2, first strand: chain 'A' and resid 724 through 725 Processing sheet with id=AC3, first strand: chain 'A' and resid 784 through 786 1543 hydrogen bonds defined for protein. 4500 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: 4.73 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7587 1.34 - 1.46: 2997 1.46 - 1.57: 12701 1.57 - 1.69: 0 1.69 - 1.81: 207 Bond restraints: 23492 Sorted by residual: bond pdb=" C VAL C 453 " pdb=" N PRO C 454 " ideal model delta sigma weight residual 1.333 1.357 -0.023 1.44e-02 4.82e+03 2.63e+00 bond pdb=" C THR C 241 " pdb=" N PRO C 242 " ideal model delta sigma weight residual 1.335 1.356 -0.021 1.38e-02 5.25e+03 2.21e+00 bond pdb=" C VAL C 980 " pdb=" N PRO C 981 " ideal model delta sigma weight residual 1.335 1.355 -0.020 1.38e-02 5.25e+03 2.11e+00 bond pdb=" N VAL B 767 " pdb=" CA VAL B 767 " ideal model delta sigma weight residual 1.474 1.453 0.022 1.57e-02 4.06e+03 1.91e+00 bond pdb=" N VAL B 573 " pdb=" CA VAL B 573 " ideal model delta sigma weight residual 1.474 1.455 0.020 1.57e-02 4.06e+03 1.59e+00 ... (remaining 23487 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 31405 1.88 - 3.75: 450 3.75 - 5.63: 61 5.63 - 7.50: 9 7.50 - 9.38: 3 Bond angle restraints: 31928 Sorted by residual: angle pdb=" C VAL A 898 " pdb=" N VAL A 899 " pdb=" CA VAL A 899 " ideal model delta sigma weight residual 120.43 124.94 -4.51 9.60e-01 1.09e+00 2.21e+01 angle pdb=" N ILE C 38 " pdb=" CA ILE C 38 " pdb=" C ILE C 38 " ideal model delta sigma weight residual 113.53 109.27 4.26 9.80e-01 1.04e+00 1.89e+01 angle pdb=" C VAL A 899 " pdb=" CA VAL A 899 " pdb=" CB VAL A 899 " ideal model delta sigma weight residual 113.70 109.82 3.88 9.50e-01 1.11e+00 1.66e+01 angle pdb=" N SER C 438 " pdb=" CA SER C 438 " pdb=" C SER C 438 " ideal model delta sigma weight residual 111.11 115.03 -3.92 1.20e+00 6.94e-01 1.07e+01 angle pdb=" C PRO C 576 " pdb=" N GLU C 577 " pdb=" CA GLU C 577 " ideal model delta sigma weight residual 120.82 125.60 -4.78 1.50e+00 4.44e-01 1.01e+01 ... (remaining 31923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.47: 13021 15.47 - 30.93: 741 30.93 - 46.40: 161 46.40 - 61.86: 106 61.86 - 77.33: 9 Dihedral angle restraints: 14038 sinusoidal: 5375 harmonic: 8663 Sorted by residual: dihedral pdb=" CA VAL C 475 " pdb=" C VAL C 475 " pdb=" N SER C 476 " pdb=" CA SER C 476 " ideal model delta harmonic sigma weight residual 180.00 156.01 23.99 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA SER C 476 " pdb=" C SER C 476 " pdb=" N ILE C 477 " pdb=" CA ILE C 477 " ideal model delta harmonic sigma weight residual 180.00 158.82 21.18 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA LYS B 55 " pdb=" C LYS B 55 " pdb=" N VAL B 56 " pdb=" CA VAL B 56 " ideal model delta harmonic sigma weight residual 180.00 160.01 19.99 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 14035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2361 0.028 - 0.056: 838 0.056 - 0.084: 351 0.084 - 0.112: 167 0.112 - 0.140: 34 Chirality restraints: 3751 Sorted by residual: chirality pdb=" CA ILE C 259 " pdb=" N ILE C 259 " pdb=" C ILE C 259 " pdb=" CB ILE C 259 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA VAL A 765 " pdb=" N VAL A 765 " pdb=" C VAL A 765 " pdb=" CB VAL A 765 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.76e-01 chirality pdb=" CB VAL C 398 " pdb=" CA VAL C 398 " pdb=" CG1 VAL C 398 " pdb=" CG2 VAL C 398 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.75e-01 ... (remaining 3748 not shown) Planarity restraints: 4106 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 467 " 0.011 2.00e-02 2.50e+03 2.13e-02 4.55e+00 pdb=" C ARG C 467 " -0.037 2.00e-02 2.50e+03 pdb=" O ARG C 467 " 0.014 2.00e-02 2.50e+03 pdb=" N GLN C 468 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 960 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.80e+00 pdb=" C ALA B 960 " -0.034 2.00e-02 2.50e+03 pdb=" O ALA B 960 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA B 961 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 997 " -0.009 2.00e-02 2.50e+03 1.87e-02 3.49e+00 pdb=" C GLY C 997 " 0.032 2.00e-02 2.50e+03 pdb=" O GLY C 997 " -0.012 2.00e-02 2.50e+03 pdb=" N THR C 998 " -0.011 2.00e-02 2.50e+03 ... (remaining 4103 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1706 2.74 - 3.28: 25966 3.28 - 3.82: 42706 3.82 - 4.36: 50029 4.36 - 4.90: 81606 Nonbonded interactions: 202013 Sorted by model distance: nonbonded pdb=" OG SER A 278 " pdb=" O ALA A 285 " model vdw 2.196 3.040 nonbonded pdb=" OG1 THR C 378 " pdb=" OG SER C 476 " model vdw 2.200 3.040 nonbonded pdb=" O LEU A 365 " pdb=" OG1 THR A 368 " model vdw 2.214 3.040 nonbonded pdb=" OG1 THR A 811 " pdb=" O SER A 818 " model vdw 2.217 3.040 nonbonded pdb=" O SER C 480 " pdb=" N ALA C 484 " model vdw 2.230 3.120 ... (remaining 202008 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 211 or (resid 240 and (name N or name CA or name \ C or name O or name CB )) or resid 241 through 251 or resid 261 or (resid 262 a \ nd (name N or name CA or name C or name O or name CB )) or resid 263 through 420 \ or (resid 421 through 422 and (name N or name CA or name C or name O or name CB \ )) or resid 423 through 609 or (resid 610 and (name N or name CA or name C or n \ ame O or name CB )) or resid 611 or (resid 612 and (name N or name CA or name C \ or name O or name CB )) or resid 613 through 763 or (resid 764 and (name N or na \ me CA or name C or name O or name CB )) or resid 765 through 772 or (resid 773 a \ nd (name N or name CA or name C or name O or name CB )) or resid 774 through 103 \ 0)) selection = (chain 'B' and (resid 1 through 211 or (resid 240 and (name N or name CA or name \ C or name O or name CB )) or resid 241 through 261 or (resid 262 and (name N or \ name CA or name C or name O or name CB )) or resid 263 through 420 or (resid 42 \ 1 through 422 and (name N or name CA or name C or name O or name CB )) or resid \ 423 through 504 or (resid 505 and (name N or name CA or name C or name O or name \ CB )) or resid 506 through 609 or (resid 610 and (name N or name CA or name C o \ r name O or name CB )) or resid 611 through 772 or (resid 773 and (name N or nam \ e CA or name C or name O or name CB )) or resid 774 through 1030)) selection = (chain 'C' and (resid 1 through 211 or resid 240 through 251 or resid 261 throug \ h 504 or (resid 505 and (name N or name CA or name C or name O or name CB )) or \ resid 506 through 611 or (resid 612 and (name N or name CA or name C or name O o \ r name CB )) or resid 613 through 763 or (resid 764 and (name N or name CA or na \ me C or name O or name CB )) or resid 765 through 1030)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 21.020 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23492 Z= 0.159 Angle : 0.580 9.379 31928 Z= 0.328 Chirality : 0.039 0.140 3751 Planarity : 0.004 0.043 4106 Dihedral : 11.624 77.326 8484 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.54 % Favored : 96.43 % Rotamer: Outliers : 2.83 % Allowed : 6.20 % Favored : 90.98 % 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: 0.89 (0.15), residues: 3021 helix: 1.86 (0.12), residues: 1732 sheet: -1.56 (0.26), residues: 363 loop : -0.89 (0.21), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 417 TYR 0.017 0.001 TYR C 181 PHE 0.022 0.001 PHE C 469 TRP 0.016 0.001 TRP B 186 HIS 0.002 0.001 HIS B 598 Details of bonding type rmsd covalent geometry : bond 0.00309 (23492) covalent geometry : angle 0.58014 (31928) hydrogen bonds : bond 0.12456 ( 1510) hydrogen bonds : angle 6.80739 ( 4500) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 796 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 TYR cc_start: 0.8032 (p90) cc_final: 0.7798 (p90) REVERT: B 240 VAL cc_start: 0.4057 (OUTLIER) cc_final: 0.3733 (m) REVERT: B 357 PHE cc_start: 0.8923 (m-80) cc_final: 0.7981 (m-10) REVERT: B 403 ILE cc_start: 0.9383 (mt) cc_final: 0.9026 (mt) REVERT: B 405 VAL cc_start: 0.9412 (m) cc_final: 0.9028 (p) REVERT: B 409 ILE cc_start: 0.9545 (mt) cc_final: 0.9327 (mt) REVERT: B 552 LEU cc_start: 0.9237 (mt) cc_final: 0.8909 (mp) REVERT: B 626 LEU cc_start: 0.9158 (mt) cc_final: 0.8914 (mp) REVERT: B 874 SER cc_start: 0.9307 (m) cc_final: 0.8927 (p) REVERT: B 965 LEU cc_start: 0.9286 (tp) cc_final: 0.9047 (tp) REVERT: C 69 MET cc_start: 0.8941 (mmm) cc_final: 0.8599 (mmm) REVERT: C 177 TRP cc_start: 0.7197 (m-10) cc_final: 0.6838 (m-10) REVERT: C 241 THR cc_start: 0.3392 (OUTLIER) cc_final: 0.3018 (p) REVERT: C 288 LEU cc_start: 0.8697 (tt) cc_final: 0.8467 (tp) REVERT: C 305 ILE cc_start: 0.9302 (mt) cc_final: 0.9095 (tt) REVERT: C 320 VAL cc_start: 0.6625 (OUTLIER) cc_final: 0.5639 (t) REVERT: C 455 MET cc_start: 0.8028 (mtm) cc_final: 0.7806 (mtm) REVERT: C 697 LEU cc_start: 0.8554 (tp) cc_final: 0.8322 (tp) REVERT: C 835 MET cc_start: 0.7700 (mtp) cc_final: 0.7426 (mtp) REVERT: C 873 LEU cc_start: 0.9405 (mt) cc_final: 0.9120 (mm) REVERT: C 920 TYR cc_start: 0.8978 (m-80) cc_final: 0.8713 (m-80) REVERT: C 937 ILE cc_start: 0.9499 (mt) cc_final: 0.9233 (mt) REVERT: A 106 VAL cc_start: 0.9513 (t) cc_final: 0.9230 (t) REVERT: A 112 ILE cc_start: 0.9087 (mt) cc_final: 0.8886 (mt) REVERT: A 381 VAL cc_start: 0.9586 (t) cc_final: 0.9340 (p) REVERT: A 388 SER cc_start: 0.9405 (m) cc_final: 0.9022 (t) REVERT: A 464 ASN cc_start: 0.7832 (t0) cc_final: 0.7594 (t0) REVERT: A 538 TRP cc_start: 0.7900 (m100) cc_final: 0.7664 (m100) REVERT: A 766 VAL cc_start: 0.9205 (OUTLIER) cc_final: 0.8935 (t) REVERT: A 871 PHE cc_start: 0.7567 (m-10) cc_final: 0.7328 (m-80) REVERT: A 922 LYS cc_start: 0.8754 (mttt) cc_final: 0.8531 (mttp) REVERT: A 931 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8791 (mp) outliers start: 68 outliers final: 14 residues processed: 838 average time/residue: 0.1581 time to fit residues: 204.8229 Evaluate side-chains 519 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 500 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 760 SER Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 564 GLU Chi-restraints excluded: chain C residue 779 ASP Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 851 HIS Chi-restraints excluded: chain A residue 931 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 3.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 GLN B 504 HIS ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 836 GLN C 34 GLN C 70 ASN C 98 ASN C 210 ASN C 598 HIS C 648 GLN C 836 GLN ** C 851 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 948 GLN ** C 955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 34 GLN ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN A 390 ASN A 414 ASN A 436 GLN A 696 GLN A 720 GLN A 741 ASN A 758 HIS A 866 GLN A 948 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.087539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.068071 restraints weight = 80204.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.070155 restraints weight = 41461.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.071508 restraints weight = 26407.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.072355 restraints weight = 19471.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.072804 restraints weight = 15966.476| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 23492 Z= 0.202 Angle : 0.696 8.993 31928 Z= 0.360 Chirality : 0.043 0.187 3751 Planarity : 0.005 0.061 4106 Dihedral : 4.999 53.303 3331 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.01 % Favored : 95.93 % Rotamer: Outliers : 4.03 % Allowed : 15.80 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.16), residues: 3021 helix: 1.84 (0.12), residues: 1734 sheet: -1.18 (0.26), residues: 368 loop : -0.83 (0.22), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 649 TYR 0.027 0.002 TYR B 605 PHE 0.023 0.002 PHE C 469 TRP 0.012 0.001 TRP C 803 HIS 0.015 0.002 HIS C 209 Details of bonding type rmsd covalent geometry : bond 0.00442 (23492) covalent geometry : angle 0.69554 (31928) hydrogen bonds : bond 0.05487 ( 1510) hydrogen bonds : angle 5.81595 ( 4500) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 527 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 VAL cc_start: 0.9375 (OUTLIER) cc_final: 0.9097 (p) REVERT: B 77 TYR cc_start: 0.8379 (p90) cc_final: 0.8001 (p90) REVERT: B 183 MET cc_start: 0.6076 (tpt) cc_final: 0.5787 (tpp) REVERT: B 283 MET cc_start: 0.7754 (mtp) cc_final: 0.7392 (mpp) REVERT: B 409 ILE cc_start: 0.9725 (mt) cc_final: 0.9408 (mt) REVERT: B 524 TYR cc_start: 0.8918 (t80) cc_final: 0.8704 (t80) REVERT: B 792 MET cc_start: 0.3197 (mmm) cc_final: 0.2728 (mmm) REVERT: B 874 SER cc_start: 0.9529 (m) cc_final: 0.9192 (p) REVERT: B 904 LEU cc_start: 0.9479 (OUTLIER) cc_final: 0.9079 (tp) REVERT: B 965 LEU cc_start: 0.9464 (tp) cc_final: 0.9125 (tp) REVERT: C 69 MET cc_start: 0.8920 (mmm) cc_final: 0.8616 (mmm) REVERT: C 90 THR cc_start: 0.9319 (m) cc_final: 0.9072 (p) REVERT: C 94 ARG cc_start: 0.8775 (ttp-170) cc_final: 0.8370 (ttp-110) REVERT: C 177 TRP cc_start: 0.8232 (m-10) cc_final: 0.7672 (m-10) REVERT: C 183 MET cc_start: 0.7906 (tmm) cc_final: 0.7698 (tmm) REVERT: C 245 PHE cc_start: 0.4708 (m-10) cc_final: 0.4501 (m-10) REVERT: C 288 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8292 (tt) REVERT: C 331 PHE cc_start: 0.8467 (t80) cc_final: 0.7821 (t80) REVERT: C 514 ASN cc_start: 0.8326 (m-40) cc_final: 0.7994 (m-40) REVERT: C 538 TRP cc_start: 0.8875 (m100) cc_final: 0.8667 (m100) REVERT: C 552 LEU cc_start: 0.9542 (mt) cc_final: 0.9243 (mt) REVERT: C 723 LEU cc_start: 0.8978 (tt) cc_final: 0.8743 (pt) REVERT: C 729 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7644 (ttpt) REVERT: C 835 MET cc_start: 0.8981 (mtp) cc_final: 0.8262 (mtp) REVERT: C 853 TRP cc_start: 0.8153 (m100) cc_final: 0.7747 (m100) REVERT: C 919 ILE cc_start: 0.9286 (mm) cc_final: 0.9080 (tp) REVERT: C 920 TYR cc_start: 0.9333 (m-80) cc_final: 0.9030 (m-80) REVERT: A 245 PHE cc_start: 0.8982 (m-80) cc_final: 0.8405 (m-10) REVERT: A 381 VAL cc_start: 0.9644 (t) cc_final: 0.9410 (m) REVERT: A 388 SER cc_start: 0.9541 (m) cc_final: 0.9140 (t) REVERT: A 406 ASP cc_start: 0.8785 (OUTLIER) cc_final: 0.8243 (p0) REVERT: A 434 MET cc_start: 0.9130 (mmm) cc_final: 0.8908 (mmm) REVERT: A 464 ASN cc_start: 0.8812 (t0) cc_final: 0.8556 (t0) REVERT: A 466 TYR cc_start: 0.9054 (m-80) cc_final: 0.8736 (m-80) REVERT: A 538 TRP cc_start: 0.8326 (m100) cc_final: 0.8009 (m-90) REVERT: A 711 MET cc_start: 0.8199 (ppp) cc_final: 0.7904 (ppp) REVERT: A 721 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8678 (mm) REVERT: A 757 MET cc_start: 0.7876 (tpp) cc_final: 0.7397 (tpt) REVERT: A 922 LYS cc_start: 0.9157 (mttt) cc_final: 0.8879 (mtmm) REVERT: A 931 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8913 (mp) outliers start: 97 outliers final: 38 residues processed: 589 average time/residue: 0.1405 time to fit residues: 134.2823 Evaluate side-chains 486 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 441 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 904 LEU Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 1005 VAL Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 721 ILE Chi-restraints excluded: chain C residue 729 LYS Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 875 VAL Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 908 LEU Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 323 ASN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 851 HIS Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 958 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 154 optimal weight: 3.9990 chunk 201 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 51 optimal weight: 0.3980 chunk 119 optimal weight: 9.9990 chunk 180 optimal weight: 4.9990 chunk 278 optimal weight: 10.0000 chunk 178 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 274 optimal weight: 0.0070 chunk 199 optimal weight: 5.9990 overall best weight: 1.6802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 638 HIS C 598 HIS C 836 GLN C 851 HIS ** C 955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.086985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.067810 restraints weight = 79944.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.069931 restraints weight = 40063.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.071303 restraints weight = 25177.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.072179 restraints weight = 18356.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.072696 restraints weight = 14896.175| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 23492 Z= 0.175 Angle : 0.652 8.623 31928 Z= 0.336 Chirality : 0.043 0.237 3751 Planarity : 0.005 0.075 4106 Dihedral : 4.864 52.473 3318 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.87 % Favored : 96.09 % Rotamer: Outliers : 4.37 % Allowed : 16.38 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.16), residues: 3021 helix: 1.77 (0.12), residues: 1743 sheet: -1.14 (0.26), residues: 372 loop : -0.80 (0.22), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 964 TYR 0.023 0.002 TYR A 315 PHE 0.039 0.002 PHE C 975 TRP 0.015 0.001 TRP B 186 HIS 0.012 0.001 HIS C 209 Details of bonding type rmsd covalent geometry : bond 0.00381 (23492) covalent geometry : angle 0.65203 (31928) hydrogen bonds : bond 0.05104 ( 1510) hydrogen bonds : angle 5.53920 ( 4500) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 485 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 VAL cc_start: 0.9422 (OUTLIER) cc_final: 0.9145 (p) REVERT: B 77 TYR cc_start: 0.8405 (p90) cc_final: 0.8022 (p90) REVERT: B 123 ARG cc_start: 0.8102 (mmt90) cc_final: 0.7870 (mmt90) REVERT: B 183 MET cc_start: 0.6188 (tpt) cc_final: 0.5526 (tpp) REVERT: B 271 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7747 (mt0) REVERT: B 394 MET cc_start: 0.9157 (mmp) cc_final: 0.8950 (mmp) REVERT: B 552 LEU cc_start: 0.9617 (mp) cc_final: 0.9382 (mp) REVERT: B 568 ASP cc_start: 0.8597 (p0) cc_final: 0.8307 (p0) REVERT: B 626 LEU cc_start: 0.9444 (mt) cc_final: 0.9215 (mt) REVERT: B 904 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9061 (tp) REVERT: B 965 LEU cc_start: 0.9530 (tp) cc_final: 0.9241 (tp) REVERT: C 177 TRP cc_start: 0.8232 (m-10) cc_final: 0.7694 (m-10) REVERT: C 283 MET cc_start: 0.8097 (tpt) cc_final: 0.7697 (tpt) REVERT: C 288 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8244 (tt) REVERT: C 404 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9160 (mt) REVERT: C 514 ASN cc_start: 0.8282 (m-40) cc_final: 0.8038 (m-40) REVERT: C 538 TRP cc_start: 0.8915 (m100) cc_final: 0.8665 (m100) REVERT: C 552 LEU cc_start: 0.9604 (mt) cc_final: 0.9359 (mt) REVERT: C 556 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9185 (mt) REVERT: C 566 GLN cc_start: 0.8702 (mm-40) cc_final: 0.8465 (mm110) REVERT: C 656 ARG cc_start: 0.7890 (mtp180) cc_final: 0.7469 (mmp80) REVERT: C 835 MET cc_start: 0.9028 (mtp) cc_final: 0.8221 (mtp) REVERT: C 853 TRP cc_start: 0.8283 (m100) cc_final: 0.7791 (m100) REVERT: C 874 SER cc_start: 0.9481 (t) cc_final: 0.9251 (p) REVERT: C 919 ILE cc_start: 0.9252 (mm) cc_final: 0.8980 (tp) REVERT: A 69 MET cc_start: 0.9243 (mmm) cc_final: 0.9013 (mmm) REVERT: A 82 SER cc_start: 0.9150 (OUTLIER) cc_final: 0.8651 (t) REVERT: A 248 ILE cc_start: 0.8600 (mt) cc_final: 0.8391 (mt) REVERT: A 273 GLU cc_start: 0.7365 (tp30) cc_final: 0.6947 (tp30) REVERT: A 360 ASN cc_start: 0.8569 (t0) cc_final: 0.8266 (t0) REVERT: A 381 VAL cc_start: 0.9622 (t) cc_final: 0.9322 (p) REVERT: A 388 SER cc_start: 0.9560 (m) cc_final: 0.9117 (t) REVERT: A 464 ASN cc_start: 0.8839 (t0) cc_final: 0.8579 (t0) REVERT: A 466 TYR cc_start: 0.9060 (m-80) cc_final: 0.8858 (m-80) REVERT: A 538 TRP cc_start: 0.8453 (m100) cc_final: 0.8151 (m-90) REVERT: A 572 MET cc_start: 0.7723 (mtm) cc_final: 0.6854 (mtm) REVERT: A 711 MET cc_start: 0.8257 (ppp) cc_final: 0.7955 (ppp) REVERT: A 757 MET cc_start: 0.7833 (tpp) cc_final: 0.7396 (tpt) REVERT: A 836 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8267 (pt0) REVERT: A 938 LEU cc_start: 0.9182 (tp) cc_final: 0.8505 (tp) outliers start: 105 outliers final: 51 residues processed: 552 average time/residue: 0.1358 time to fit residues: 122.9228 Evaluate side-chains 470 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 411 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 904 LEU Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 1005 VAL Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 747 MET Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 908 LEU Chi-restraints excluded: chain C residue 1025 LEU Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 803 TRP Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 835 MET Chi-restraints excluded: chain A residue 836 GLN Chi-restraints excluded: chain A residue 851 HIS Chi-restraints excluded: chain A residue 951 MET Chi-restraints excluded: chain A residue 958 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 69 optimal weight: 0.9980 chunk 207 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 79 optimal weight: 9.9990 chunk 260 optimal weight: 7.9990 chunk 126 optimal weight: 9.9990 chunk 301 optimal weight: 0.5980 chunk 262 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 128 optimal weight: 6.9990 chunk 182 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 558 GLN ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 680 GLN ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.086371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.067291 restraints weight = 80220.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.069360 restraints weight = 40503.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.070706 restraints weight = 25513.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.071582 restraints weight = 18664.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.072098 restraints weight = 15126.438| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 23492 Z= 0.185 Angle : 0.656 11.597 31928 Z= 0.337 Chirality : 0.043 0.239 3751 Planarity : 0.004 0.037 4106 Dihedral : 4.683 43.961 3314 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.84 % Favored : 96.13 % Rotamer: Outliers : 4.07 % Allowed : 18.59 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.16), residues: 3021 helix: 1.63 (0.12), residues: 1754 sheet: -0.97 (0.27), residues: 360 loop : -0.87 (0.22), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 727 TYR 0.023 0.001 TYR B 524 PHE 0.042 0.002 PHE C 975 TRP 0.011 0.001 TRP B 186 HIS 0.025 0.001 HIS C 209 Details of bonding type rmsd covalent geometry : bond 0.00410 (23492) covalent geometry : angle 0.65552 (31928) hydrogen bonds : bond 0.04976 ( 1510) hydrogen bonds : angle 5.39618 ( 4500) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 453 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 VAL cc_start: 0.9448 (OUTLIER) cc_final: 0.9172 (p) REVERT: B 105 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8303 (tp30) REVERT: B 123 ARG cc_start: 0.8007 (mmt90) cc_final: 0.7685 (mmt90) REVERT: B 183 MET cc_start: 0.6098 (tpt) cc_final: 0.5326 (tpp) REVERT: B 394 MET cc_start: 0.9202 (mmp) cc_final: 0.8968 (mmp) REVERT: B 524 TYR cc_start: 0.8987 (t80) cc_final: 0.8776 (t80) REVERT: B 568 ASP cc_start: 0.8720 (p0) cc_final: 0.8416 (p0) REVERT: B 626 LEU cc_start: 0.9466 (mt) cc_final: 0.9263 (mt) REVERT: B 711 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8193 (ppp) REVERT: B 851 HIS cc_start: 0.8350 (p90) cc_final: 0.7915 (p90) REVERT: B 965 LEU cc_start: 0.9529 (tp) cc_final: 0.9313 (tp) REVERT: C 30 LEU cc_start: 0.9517 (tp) cc_final: 0.9151 (mp) REVERT: C 69 MET cc_start: 0.8911 (mmp) cc_final: 0.8647 (mmm) REVERT: C 177 TRP cc_start: 0.8220 (m-10) cc_final: 0.7719 (m-10) REVERT: C 195 MET cc_start: 0.7709 (OUTLIER) cc_final: 0.6996 (pmm) REVERT: C 283 MET cc_start: 0.8142 (tpt) cc_final: 0.7816 (tpt) REVERT: C 288 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8464 (tt) REVERT: C 404 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9111 (mt) REVERT: C 514 ASN cc_start: 0.8373 (m-40) cc_final: 0.8090 (m-40) REVERT: C 538 TRP cc_start: 0.8935 (m100) cc_final: 0.8690 (m100) REVERT: C 566 GLN cc_start: 0.8702 (mm-40) cc_final: 0.8467 (mm110) REVERT: C 570 MET cc_start: 0.7644 (ttt) cc_final: 0.6567 (ttt) REVERT: C 656 ARG cc_start: 0.8021 (mtp180) cc_final: 0.7505 (mmp80) REVERT: C 874 SER cc_start: 0.9452 (t) cc_final: 0.9250 (p) REVERT: C 934 LYS cc_start: 0.9167 (ttpt) cc_final: 0.8946 (ttpt) REVERT: C 975 PHE cc_start: 0.8927 (t80) cc_final: 0.8716 (t80) REVERT: A 82 SER cc_start: 0.9283 (OUTLIER) cc_final: 0.8690 (t) REVERT: A 183 MET cc_start: 0.8415 (tpp) cc_final: 0.8107 (tpp) REVERT: A 245 PHE cc_start: 0.9065 (m-80) cc_final: 0.8533 (m-10) REVERT: A 248 ILE cc_start: 0.8678 (mt) cc_final: 0.8452 (mt) REVERT: A 273 GLU cc_start: 0.7592 (tp30) cc_final: 0.7099 (tp30) REVERT: A 388 SER cc_start: 0.9588 (m) cc_final: 0.9181 (t) REVERT: A 458 PHE cc_start: 0.8629 (m-80) cc_final: 0.8140 (m-10) REVERT: A 464 ASN cc_start: 0.8933 (t0) cc_final: 0.8660 (t0) REVERT: A 585 MET cc_start: 0.9060 (mmm) cc_final: 0.8566 (mmm) REVERT: A 711 MET cc_start: 0.8412 (ppp) cc_final: 0.8094 (ppp) REVERT: A 747 MET cc_start: 0.8217 (tpp) cc_final: 0.7976 (tpp) REVERT: A 752 TYR cc_start: 0.6267 (m-80) cc_final: 0.5675 (m-80) REVERT: A 757 MET cc_start: 0.7901 (tpp) cc_final: 0.7514 (tpt) REVERT: A 836 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8276 (pt0) REVERT: A 922 LYS cc_start: 0.9114 (mttt) cc_final: 0.8744 (mttp) REVERT: A 938 LEU cc_start: 0.8926 (tp) cc_final: 0.8717 (tp) outliers start: 98 outliers final: 60 residues processed: 519 average time/residue: 0.1283 time to fit residues: 109.9357 Evaluate side-chains 467 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 399 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 539 MET Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 711 MET Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 904 LEU Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 1005 VAL Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 444 ILE Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 908 LEU Chi-restraints excluded: chain C residue 923 VAL Chi-restraints excluded: chain C residue 980 VAL Chi-restraints excluded: chain C residue 1025 LEU Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 835 MET Chi-restraints excluded: chain A residue 836 GLN Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 939 ILE Chi-restraints excluded: chain A residue 951 MET Chi-restraints excluded: chain A residue 958 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 51 optimal weight: 7.9990 chunk 37 optimal weight: 0.6980 chunk 179 optimal weight: 3.9990 chunk 231 optimal weight: 9.9990 chunk 19 optimal weight: 20.0000 chunk 159 optimal weight: 0.9980 chunk 153 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 199 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 ASN C 359 GLN C 514 ASN ** C 955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.085693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.066416 restraints weight = 80862.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.068415 restraints weight = 41946.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.069654 restraints weight = 26935.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.070546 restraints weight = 20136.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.071048 restraints weight = 16409.047| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 23492 Z= 0.179 Angle : 0.640 8.843 31928 Z= 0.329 Chirality : 0.042 0.236 3751 Planarity : 0.004 0.040 4106 Dihedral : 4.629 38.161 3312 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.14 % Favored : 95.83 % Rotamer: Outliers : 4.37 % Allowed : 19.38 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.15), residues: 3021 helix: 1.59 (0.12), residues: 1758 sheet: -0.84 (0.28), residues: 353 loop : -0.87 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 727 TYR 0.015 0.001 TYR B 524 PHE 0.029 0.002 PHE C 975 TRP 0.021 0.001 TRP A 538 HIS 0.019 0.001 HIS C 209 Details of bonding type rmsd covalent geometry : bond 0.00397 (23492) covalent geometry : angle 0.63955 (31928) hydrogen bonds : bond 0.04891 ( 1510) hydrogen bonds : angle 5.29397 ( 4500) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 439 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 VAL cc_start: 0.9445 (OUTLIER) cc_final: 0.9169 (p) REVERT: B 77 TYR cc_start: 0.8541 (p90) cc_final: 0.8142 (p90) REVERT: B 105 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8255 (tp30) REVERT: B 394 MET cc_start: 0.9181 (mmp) cc_final: 0.8953 (mmp) REVERT: B 524 TYR cc_start: 0.9019 (t80) cc_final: 0.8796 (t80) REVERT: B 552 LEU cc_start: 0.9657 (mt) cc_final: 0.9370 (mp) REVERT: B 568 ASP cc_start: 0.8726 (p0) cc_final: 0.8402 (p0) REVERT: B 711 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.8297 (ppp) REVERT: B 851 HIS cc_start: 0.8356 (p90) cc_final: 0.7912 (p90) REVERT: B 904 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.9002 (tp) REVERT: B 965 LEU cc_start: 0.9528 (tp) cc_final: 0.9307 (tp) REVERT: C 69 MET cc_start: 0.8914 (mmp) cc_final: 0.8476 (mmm) REVERT: C 177 TRP cc_start: 0.8273 (m-10) cc_final: 0.7751 (m-10) REVERT: C 195 MET cc_start: 0.7640 (OUTLIER) cc_final: 0.6904 (pmm) REVERT: C 283 MET cc_start: 0.8234 (tpt) cc_final: 0.7907 (tpt) REVERT: C 288 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8332 (tt) REVERT: C 331 PHE cc_start: 0.8640 (t80) cc_final: 0.8320 (t80) REVERT: C 538 TRP cc_start: 0.8893 (m100) cc_final: 0.8652 (m100) REVERT: C 566 GLN cc_start: 0.8747 (mm-40) cc_final: 0.8218 (mm-40) REVERT: C 570 MET cc_start: 0.7529 (ttt) cc_final: 0.6888 (ttt) REVERT: C 764 LYS cc_start: 0.8261 (mtpt) cc_final: 0.8027 (mmmt) REVERT: C 845 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8482 (mp) REVERT: C 874 SER cc_start: 0.9476 (t) cc_final: 0.9270 (p) REVERT: A 175 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8351 (mm-30) REVERT: A 183 MET cc_start: 0.7980 (tpp) cc_final: 0.7738 (tpp) REVERT: A 207 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8718 (ptp-170) REVERT: A 245 PHE cc_start: 0.9080 (m-80) cc_final: 0.8771 (m-80) REVERT: A 248 ILE cc_start: 0.8668 (mt) cc_final: 0.8466 (mt) REVERT: A 273 GLU cc_start: 0.7755 (tp30) cc_final: 0.7012 (tp30) REVERT: A 381 VAL cc_start: 0.9627 (t) cc_final: 0.9331 (p) REVERT: A 388 SER cc_start: 0.9580 (m) cc_final: 0.9122 (t) REVERT: A 464 ASN cc_start: 0.8944 (t0) cc_final: 0.8702 (t0) REVERT: A 711 MET cc_start: 0.8450 (ppp) cc_final: 0.8037 (ppp) REVERT: A 757 MET cc_start: 0.7882 (tpp) cc_final: 0.7524 (tpt) REVERT: A 836 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8355 (pt0) REVERT: A 922 LYS cc_start: 0.9094 (mttt) cc_final: 0.8807 (mttp) REVERT: A 928 ILE cc_start: 0.9648 (tp) cc_final: 0.9448 (tp) REVERT: A 938 LEU cc_start: 0.8963 (tp) cc_final: 0.8760 (tp) outliers start: 105 outliers final: 68 residues processed: 504 average time/residue: 0.1354 time to fit residues: 112.1993 Evaluate side-chains 470 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 393 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 539 MET Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 655 ASN Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 711 MET Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 897 LEU Chi-restraints excluded: chain B residue 904 LEU Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain B residue 970 MET Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 675 PHE Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 804 THR Chi-restraints excluded: chain C residue 845 LEU Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 908 LEU Chi-restraints excluded: chain C residue 923 VAL Chi-restraints excluded: chain C residue 980 VAL Chi-restraints excluded: chain C residue 1025 LEU Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 835 MET Chi-restraints excluded: chain A residue 836 GLN Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 939 ILE Chi-restraints excluded: chain A residue 951 MET Chi-restraints excluded: chain A residue 958 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 86 optimal weight: 0.9990 chunk 156 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 190 optimal weight: 5.9990 chunk 147 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 284 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 chunk 259 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 ASN ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 ASN B 761 GLN C 281 ASN C 955 GLN A 866 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.086408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.067298 restraints weight = 80496.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.069329 restraints weight = 41433.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.070674 restraints weight = 26278.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.071542 restraints weight = 19228.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.072064 restraints weight = 15569.218| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 23492 Z= 0.148 Angle : 0.642 10.595 31928 Z= 0.328 Chirality : 0.043 0.295 3751 Planarity : 0.004 0.045 4106 Dihedral : 4.585 34.281 3312 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.84 % Favored : 96.13 % Rotamer: Outliers : 3.78 % Allowed : 20.58 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.16), residues: 3021 helix: 1.64 (0.12), residues: 1758 sheet: -0.69 (0.28), residues: 346 loop : -0.85 (0.21), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 763 TYR 0.025 0.001 TYR A 315 PHE 0.039 0.001 PHE C 975 TRP 0.016 0.001 TRP B 186 HIS 0.016 0.001 HIS C 209 Details of bonding type rmsd covalent geometry : bond 0.00324 (23492) covalent geometry : angle 0.64247 (31928) hydrogen bonds : bond 0.04733 ( 1510) hydrogen bonds : angle 5.18359 ( 4500) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 437 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 VAL cc_start: 0.9373 (OUTLIER) cc_final: 0.9059 (p) REVERT: B 77 TYR cc_start: 0.8500 (p90) cc_final: 0.8044 (p90) REVERT: B 123 ARG cc_start: 0.8215 (mmt90) cc_final: 0.7974 (mmt-90) REVERT: B 183 MET cc_start: 0.5906 (tpp) cc_final: 0.5181 (tpp) REVERT: B 524 TYR cc_start: 0.8990 (t80) cc_final: 0.8749 (t80) REVERT: B 568 ASP cc_start: 0.8683 (p0) cc_final: 0.8360 (p0) REVERT: B 621 MET cc_start: 0.8236 (tpp) cc_final: 0.7705 (tpp) REVERT: B 711 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8279 (ppp) REVERT: B 842 MET cc_start: 0.9205 (ttp) cc_final: 0.8823 (ttp) REVERT: B 851 HIS cc_start: 0.8296 (p90) cc_final: 0.7911 (p90) REVERT: B 965 LEU cc_start: 0.9478 (tp) cc_final: 0.9242 (tp) REVERT: C 76 LEU cc_start: 0.9382 (mt) cc_final: 0.8818 (mt) REVERT: C 92 THR cc_start: 0.9252 (m) cc_final: 0.8699 (p) REVERT: C 114 GLU cc_start: 0.8756 (tm-30) cc_final: 0.8555 (tm-30) REVERT: C 177 TRP cc_start: 0.8259 (m-10) cc_final: 0.7739 (m-10) REVERT: C 283 MET cc_start: 0.8221 (tpt) cc_final: 0.7901 (tpt) REVERT: C 288 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8360 (tt) REVERT: C 320 VAL cc_start: 0.8356 (OUTLIER) cc_final: 0.8108 (t) REVERT: C 570 MET cc_start: 0.7521 (ttt) cc_final: 0.6812 (ttt) REVERT: C 764 LYS cc_start: 0.8074 (mtpt) cc_final: 0.7764 (mmmt) REVERT: C 835 MET cc_start: 0.8828 (ptp) cc_final: 0.8024 (ptp) REVERT: C 842 MET cc_start: 0.8428 (ttt) cc_final: 0.8095 (ttp) REVERT: C 959 GLU cc_start: 0.8102 (tt0) cc_final: 0.7771 (tt0) REVERT: A 183 MET cc_start: 0.7889 (tpp) cc_final: 0.7668 (tpp) REVERT: A 245 PHE cc_start: 0.9101 (m-80) cc_final: 0.8774 (m-80) REVERT: A 273 GLU cc_start: 0.7743 (tp30) cc_final: 0.7299 (tp30) REVERT: A 388 SER cc_start: 0.9560 (m) cc_final: 0.9145 (t) REVERT: A 585 MET cc_start: 0.9031 (tpp) cc_final: 0.8784 (tpp) REVERT: A 711 MET cc_start: 0.8558 (ppp) cc_final: 0.8223 (ppp) REVERT: A 747 MET cc_start: 0.8060 (tpp) cc_final: 0.7810 (tpp) REVERT: A 757 MET cc_start: 0.7834 (tpp) cc_final: 0.7556 (tpt) REVERT: A 792 MET cc_start: 0.8084 (mpp) cc_final: 0.7597 (ttt) REVERT: A 922 LYS cc_start: 0.9062 (mttt) cc_final: 0.8782 (mttp) outliers start: 91 outliers final: 56 residues processed: 492 average time/residue: 0.1356 time to fit residues: 110.3558 Evaluate side-chains 458 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 398 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 539 MET Chi-restraints excluded: chain B residue 655 ASN Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 711 MET Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 904 LEU Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 675 PHE Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 804 THR Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 923 VAL Chi-restraints excluded: chain C residue 980 VAL Chi-restraints excluded: chain C residue 1005 VAL Chi-restraints excluded: chain C residue 1025 LEU Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 951 MET Chi-restraints excluded: chain A residue 958 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 48 optimal weight: 6.9990 chunk 225 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 chunk 240 optimal weight: 0.0970 chunk 58 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 153 optimal weight: 0.0870 chunk 233 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 9.9990 overall best weight: 1.4362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 ASN A 210 ASN A 414 ASN A 789 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.086250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.067211 restraints weight = 80537.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.069238 restraints weight = 41671.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.070570 restraints weight = 26450.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.071458 restraints weight = 19358.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.071899 restraints weight = 15667.791| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 23492 Z= 0.155 Angle : 0.652 9.435 31928 Z= 0.331 Chirality : 0.043 0.313 3751 Planarity : 0.004 0.037 4106 Dihedral : 4.570 34.035 3312 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.67 % Favored : 96.29 % Rotamer: Outliers : 3.74 % Allowed : 21.41 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.16), residues: 3021 helix: 1.63 (0.12), residues: 1759 sheet: -0.66 (0.28), residues: 346 loop : -0.89 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 167 TYR 0.013 0.001 TYR A 466 PHE 0.046 0.001 PHE C 975 TRP 0.021 0.001 TRP B 186 HIS 0.014 0.001 HIS C 209 Details of bonding type rmsd covalent geometry : bond 0.00347 (23492) covalent geometry : angle 0.65235 (31928) hydrogen bonds : bond 0.04699 ( 1510) hydrogen bonds : angle 5.16221 ( 4500) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 430 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 VAL cc_start: 0.9394 (OUTLIER) cc_final: 0.9111 (p) REVERT: B 77 TYR cc_start: 0.8514 (p90) cc_final: 0.8065 (p90) REVERT: B 123 ARG cc_start: 0.8222 (mmt90) cc_final: 0.7957 (mmt-90) REVERT: B 183 MET cc_start: 0.5413 (tpp) cc_final: 0.4934 (tpp) REVERT: B 292 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.8611 (mtm) REVERT: B 394 MET cc_start: 0.9090 (mmp) cc_final: 0.8816 (mmp) REVERT: B 524 TYR cc_start: 0.9003 (t80) cc_final: 0.8766 (t80) REVERT: B 552 LEU cc_start: 0.9641 (mt) cc_final: 0.9339 (mp) REVERT: B 568 ASP cc_start: 0.8721 (p0) cc_final: 0.8330 (p0) REVERT: B 621 MET cc_start: 0.8272 (tpp) cc_final: 0.7556 (tpp) REVERT: B 661 MET cc_start: 0.7677 (pmm) cc_final: 0.7344 (pmm) REVERT: B 711 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.8248 (ppp) REVERT: B 851 HIS cc_start: 0.8305 (p90) cc_final: 0.7944 (p90) REVERT: B 965 LEU cc_start: 0.9488 (tp) cc_final: 0.9260 (tp) REVERT: C 76 LEU cc_start: 0.9361 (mt) cc_final: 0.8785 (mt) REVERT: C 92 THR cc_start: 0.9269 (m) cc_final: 0.8739 (p) REVERT: C 114 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8517 (tm-30) REVERT: C 177 TRP cc_start: 0.8239 (m-10) cc_final: 0.7782 (m-10) REVERT: C 283 MET cc_start: 0.8245 (tpt) cc_final: 0.7922 (tpt) REVERT: C 288 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8351 (tt) REVERT: C 320 VAL cc_start: 0.8353 (OUTLIER) cc_final: 0.7850 (t) REVERT: C 331 PHE cc_start: 0.8383 (t80) cc_final: 0.7745 (t80) REVERT: C 566 GLN cc_start: 0.8955 (mm-40) cc_final: 0.8538 (mm110) REVERT: C 570 MET cc_start: 0.7586 (ttt) cc_final: 0.6907 (ttt) REVERT: C 574 MET cc_start: 0.8598 (mmp) cc_final: 0.7279 (tmm) REVERT: C 680 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.7205 (pp30) REVERT: C 764 LYS cc_start: 0.7975 (mtpt) cc_final: 0.7683 (mmmt) REVERT: C 835 MET cc_start: 0.8836 (ptp) cc_final: 0.8031 (ptp) REVERT: C 842 MET cc_start: 0.8383 (ttt) cc_final: 0.7909 (ttp) REVERT: C 959 GLU cc_start: 0.8092 (tt0) cc_final: 0.7786 (tt0) REVERT: A 183 MET cc_start: 0.7865 (tpp) cc_final: 0.7656 (tpp) REVERT: A 207 ARG cc_start: 0.8947 (ptp-170) cc_final: 0.8683 (ptp90) REVERT: A 245 PHE cc_start: 0.9106 (m-80) cc_final: 0.8800 (m-80) REVERT: A 273 GLU cc_start: 0.7794 (tp30) cc_final: 0.7361 (tp30) REVERT: A 388 SER cc_start: 0.9540 (m) cc_final: 0.9146 (t) REVERT: A 572 MET cc_start: 0.7417 (mpp) cc_final: 0.7004 (mpp) REVERT: A 585 MET cc_start: 0.9099 (tpp) cc_final: 0.8822 (tpp) REVERT: A 605 TYR cc_start: 0.8808 (t80) cc_final: 0.8384 (t80) REVERT: A 621 MET cc_start: 0.9375 (tpp) cc_final: 0.9037 (mmt) REVERT: A 711 MET cc_start: 0.8595 (ppp) cc_final: 0.8251 (ppp) REVERT: A 757 MET cc_start: 0.7754 (tpp) cc_final: 0.7506 (tpt) REVERT: A 792 MET cc_start: 0.8073 (mpp) cc_final: 0.7574 (ttt) REVERT: A 842 MET cc_start: 0.8835 (ttp) cc_final: 0.8571 (ttt) outliers start: 90 outliers final: 61 residues processed: 491 average time/residue: 0.1349 time to fit residues: 108.8084 Evaluate side-chains 464 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 397 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 539 MET Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 655 ASN Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 711 MET Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 904 LEU Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 167 ARG Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 675 PHE Chi-restraints excluded: chain C residue 680 GLN Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 804 THR Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 908 LEU Chi-restraints excluded: chain C residue 923 VAL Chi-restraints excluded: chain C residue 980 VAL Chi-restraints excluded: chain C residue 1025 LEU Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 951 MET Chi-restraints excluded: chain A residue 958 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 258 optimal weight: 0.8980 chunk 219 optimal weight: 6.9990 chunk 80 optimal weight: 0.6980 chunk 14 optimal weight: 7.9990 chunk 131 optimal weight: 2.9990 chunk 160 optimal weight: 10.0000 chunk 162 optimal weight: 0.0870 chunk 40 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 125 optimal weight: 6.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 ASN A 866 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.087477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.068251 restraints weight = 79962.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.070270 restraints weight = 41753.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.071616 restraints weight = 26851.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.072418 restraints weight = 19777.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.073030 restraints weight = 16268.636| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 23492 Z= 0.140 Angle : 0.663 10.598 31928 Z= 0.333 Chirality : 0.043 0.288 3751 Planarity : 0.004 0.038 4106 Dihedral : 4.566 31.294 3311 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.84 % Favored : 96.13 % Rotamer: Outliers : 2.95 % Allowed : 22.62 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.16), residues: 3021 helix: 1.60 (0.12), residues: 1762 sheet: -0.78 (0.27), residues: 367 loop : -0.83 (0.22), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 656 TYR 0.025 0.001 TYR C 466 PHE 0.038 0.001 PHE C 975 TRP 0.024 0.001 TRP B 186 HIS 0.013 0.001 HIS C 209 Details of bonding type rmsd covalent geometry : bond 0.00307 (23492) covalent geometry : angle 0.66277 (31928) hydrogen bonds : bond 0.04622 ( 1510) hydrogen bonds : angle 5.10112 ( 4500) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 444 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 VAL cc_start: 0.9365 (OUTLIER) cc_final: 0.9094 (p) REVERT: B 77 TYR cc_start: 0.8538 (p90) cc_final: 0.8119 (p90) REVERT: B 123 ARG cc_start: 0.8244 (mmt90) cc_final: 0.8034 (mmt90) REVERT: B 183 MET cc_start: 0.5528 (tpp) cc_final: 0.4964 (tpp) REVERT: B 394 MET cc_start: 0.9131 (mmp) cc_final: 0.8808 (mmp) REVERT: B 568 ASP cc_start: 0.8702 (p0) cc_final: 0.8263 (p0) REVERT: B 661 MET cc_start: 0.7680 (pmm) cc_final: 0.7324 (pmm) REVERT: B 711 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8224 (ppp) REVERT: B 965 LEU cc_start: 0.9509 (tp) cc_final: 0.9259 (tp) REVERT: C 76 LEU cc_start: 0.9362 (mt) cc_final: 0.8759 (mt) REVERT: C 92 THR cc_start: 0.9214 (m) cc_final: 0.8723 (p) REVERT: C 114 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8528 (tm-30) REVERT: C 167 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.8062 (mmm-85) REVERT: C 177 TRP cc_start: 0.8308 (m-10) cc_final: 0.7888 (m-10) REVERT: C 283 MET cc_start: 0.8265 (tpt) cc_final: 0.7946 (tpt) REVERT: C 288 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8297 (tt) REVERT: C 320 VAL cc_start: 0.8291 (OUTLIER) cc_final: 0.7780 (t) REVERT: C 331 PHE cc_start: 0.8504 (t80) cc_final: 0.7859 (t80) REVERT: C 570 MET cc_start: 0.7759 (ttt) cc_final: 0.7298 (ttt) REVERT: C 572 MET cc_start: 0.7655 (ptm) cc_final: 0.7452 (ptm) REVERT: C 680 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.7179 (pp30) REVERT: C 764 LYS cc_start: 0.7953 (mtpt) cc_final: 0.7592 (mmmt) REVERT: C 835 MET cc_start: 0.8893 (ptp) cc_final: 0.8087 (ptp) REVERT: C 852 GLU cc_start: 0.8657 (tp30) cc_final: 0.8246 (tp30) REVERT: C 959 GLU cc_start: 0.8149 (tt0) cc_final: 0.7814 (tt0) REVERT: A 68 GLU cc_start: 0.8809 (tp30) cc_final: 0.8322 (tp30) REVERT: A 183 MET cc_start: 0.7831 (tpp) cc_final: 0.7564 (tpp) REVERT: A 207 ARG cc_start: 0.8934 (ptp-170) cc_final: 0.8677 (ptp90) REVERT: A 245 PHE cc_start: 0.9091 (m-80) cc_final: 0.8739 (m-80) REVERT: A 388 SER cc_start: 0.9519 (m) cc_final: 0.9098 (t) REVERT: A 585 MET cc_start: 0.9158 (tpp) cc_final: 0.8858 (tpp) REVERT: A 621 MET cc_start: 0.9360 (tpp) cc_final: 0.8973 (mmt) REVERT: A 711 MET cc_start: 0.8629 (ppp) cc_final: 0.8317 (ppp) REVERT: A 792 MET cc_start: 0.8233 (mpp) cc_final: 0.7727 (ttt) REVERT: A 836 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8380 (pt0) REVERT: A 842 MET cc_start: 0.8863 (ttp) cc_final: 0.8631 (ttt) outliers start: 71 outliers final: 43 residues processed: 487 average time/residue: 0.1320 time to fit residues: 106.3852 Evaluate side-chains 452 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 402 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 655 ASN Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 711 MET Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 904 LEU Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 167 ARG Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 675 PHE Chi-restraints excluded: chain C residue 680 GLN Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 804 THR Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 836 GLN Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 951 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 92 optimal weight: 0.9990 chunk 235 optimal weight: 0.9990 chunk 247 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 290 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 174 optimal weight: 9.9990 chunk 253 optimal weight: 4.9990 chunk 281 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 ASN C 34 GLN C 566 GLN ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.086329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.067191 restraints weight = 81204.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.069153 restraints weight = 42290.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.070496 restraints weight = 27296.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.071289 restraints weight = 20133.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.071897 restraints weight = 16549.811| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.5029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 23492 Z= 0.179 Angle : 0.700 11.219 31928 Z= 0.353 Chirality : 0.044 0.303 3751 Planarity : 0.004 0.056 4106 Dihedral : 4.604 34.352 3311 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.94 % Favored : 96.03 % Rotamer: Outliers : 3.12 % Allowed : 22.87 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.16), residues: 3021 helix: 1.59 (0.12), residues: 1760 sheet: -0.70 (0.27), residues: 370 loop : -0.83 (0.22), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 116 TYR 0.036 0.002 TYR A 466 PHE 0.039 0.002 PHE C 975 TRP 0.023 0.001 TRP B 186 HIS 0.020 0.001 HIS C 209 Details of bonding type rmsd covalent geometry : bond 0.00408 (23492) covalent geometry : angle 0.70043 (31928) hydrogen bonds : bond 0.04746 ( 1510) hydrogen bonds : angle 5.16072 ( 4500) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 404 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 VAL cc_start: 0.9365 (OUTLIER) cc_final: 0.9104 (p) REVERT: B 77 TYR cc_start: 0.8520 (p90) cc_final: 0.8090 (p90) REVERT: B 116 ARG cc_start: 0.8121 (mmt-90) cc_final: 0.7866 (mmt-90) REVERT: B 183 MET cc_start: 0.5583 (tpp) cc_final: 0.5232 (tpp) REVERT: B 568 ASP cc_start: 0.8626 (p0) cc_final: 0.8231 (p0) REVERT: B 661 MET cc_start: 0.7826 (pmm) cc_final: 0.7512 (pmm) REVERT: B 711 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.8270 (ppp) REVERT: B 904 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.8923 (tp) REVERT: C 76 LEU cc_start: 0.9372 (mt) cc_final: 0.8795 (mt) REVERT: C 90 THR cc_start: 0.9128 (m) cc_final: 0.8900 (p) REVERT: C 92 THR cc_start: 0.9245 (m) cc_final: 0.8783 (p) REVERT: C 114 GLU cc_start: 0.8707 (tm-30) cc_final: 0.8494 (tm-30) REVERT: C 177 TRP cc_start: 0.8267 (m-10) cc_final: 0.7882 (m-10) REVERT: C 283 MET cc_start: 0.8248 (tpt) cc_final: 0.7950 (tpt) REVERT: C 288 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8369 (tt) REVERT: C 320 VAL cc_start: 0.8334 (OUTLIER) cc_final: 0.7853 (t) REVERT: C 572 MET cc_start: 0.7308 (ptm) cc_final: 0.7056 (ptm) REVERT: C 680 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.7281 (pp30) REVERT: C 764 LYS cc_start: 0.7898 (mtpt) cc_final: 0.7640 (mmmt) REVERT: C 835 MET cc_start: 0.8861 (ptp) cc_final: 0.8051 (ptp) REVERT: C 852 GLU cc_start: 0.8621 (tp30) cc_final: 0.8225 (tp30) REVERT: C 959 GLU cc_start: 0.8041 (tt0) cc_final: 0.7756 (tt0) REVERT: A 68 GLU cc_start: 0.8817 (tp30) cc_final: 0.8431 (tp30) REVERT: A 183 MET cc_start: 0.7846 (tpp) cc_final: 0.7623 (tpp) REVERT: A 207 ARG cc_start: 0.8934 (ptp-170) cc_final: 0.8691 (ptp90) REVERT: A 245 PHE cc_start: 0.9066 (m-80) cc_final: 0.8744 (m-80) REVERT: A 292 MET cc_start: 0.7479 (tmm) cc_final: 0.7239 (tmm) REVERT: A 388 SER cc_start: 0.9528 (m) cc_final: 0.9162 (t) REVERT: A 621 MET cc_start: 0.9298 (tpp) cc_final: 0.9034 (mmt) REVERT: A 661 MET cc_start: 0.7492 (pmm) cc_final: 0.7085 (pmm) REVERT: A 711 MET cc_start: 0.8582 (ppp) cc_final: 0.8264 (ppp) REVERT: A 792 MET cc_start: 0.8104 (mpp) cc_final: 0.7681 (ttt) REVERT: A 836 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8367 (pt0) outliers start: 75 outliers final: 57 residues processed: 451 average time/residue: 0.1327 time to fit residues: 99.0090 Evaluate side-chains 455 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 391 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 539 MET Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 655 ASN Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 711 MET Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 904 LEU Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 167 ARG Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 581 MET Chi-restraints excluded: chain C residue 675 PHE Chi-restraints excluded: chain C residue 680 GLN Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 804 THR Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 908 LEU Chi-restraints excluded: chain C residue 1025 LEU Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 836 GLN Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 951 MET Chi-restraints excluded: chain A residue 958 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 295 optimal weight: 5.9990 chunk 230 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 283 optimal weight: 3.9990 chunk 196 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 289 optimal weight: 0.7980 chunk 277 optimal weight: 30.0000 chunk 193 optimal weight: 0.8980 chunk 177 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 ASN C 575 GLN C 587 ASN A 504 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.087535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.068461 restraints weight = 80259.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.070493 restraints weight = 41392.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.071765 restraints weight = 26365.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.072692 restraints weight = 19484.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.073212 restraints weight = 15767.909| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.5180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 23492 Z= 0.150 Angle : 0.722 12.591 31928 Z= 0.357 Chirality : 0.045 0.434 3751 Planarity : 0.004 0.044 4106 Dihedral : 4.607 31.480 3311 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.71 % Favored : 96.26 % Rotamer: Outliers : 2.58 % Allowed : 23.78 % Favored : 73.64 % Cbeta Deviations : 0.04 % 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: 0.86 (0.16), residues: 3021 helix: 1.58 (0.12), residues: 1759 sheet: -0.66 (0.27), residues: 370 loop : -0.84 (0.22), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 116 TYR 0.032 0.002 TYR C 466 PHE 0.035 0.001 PHE C 975 TRP 0.025 0.001 TRP B 186 HIS 0.018 0.001 HIS C 209 Details of bonding type rmsd covalent geometry : bond 0.00335 (23492) covalent geometry : angle 0.72191 (31928) hydrogen bonds : bond 0.04660 ( 1510) hydrogen bonds : angle 5.10318 ( 4500) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 410 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 VAL cc_start: 0.9353 (OUTLIER) cc_final: 0.9082 (p) REVERT: B 77 TYR cc_start: 0.8524 (p90) cc_final: 0.8103 (p90) REVERT: B 116 ARG cc_start: 0.8144 (mmt-90) cc_final: 0.7791 (mmt-90) REVERT: B 123 ARG cc_start: 0.8350 (mmt90) cc_final: 0.8118 (mmt-90) REVERT: B 183 MET cc_start: 0.5564 (tpp) cc_final: 0.5275 (tpp) REVERT: B 292 MET cc_start: 0.9430 (mmm) cc_final: 0.9194 (mmm) REVERT: B 394 MET cc_start: 0.9088 (mmp) cc_final: 0.8787 (mmp) REVERT: B 568 ASP cc_start: 0.8676 (p0) cc_final: 0.8260 (p0) REVERT: B 621 MET cc_start: 0.8291 (tpp) cc_final: 0.8051 (tpp) REVERT: B 661 MET cc_start: 0.8073 (pmm) cc_final: 0.7636 (pmm) REVERT: B 711 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.8240 (ppp) REVERT: B 835 MET cc_start: 0.9153 (mtm) cc_final: 0.8873 (mtm) REVERT: C 76 LEU cc_start: 0.9352 (mt) cc_final: 0.8741 (mt) REVERT: C 90 THR cc_start: 0.9097 (m) cc_final: 0.8819 (p) REVERT: C 92 THR cc_start: 0.9213 (m) cc_final: 0.8710 (p) REVERT: C 114 GLU cc_start: 0.8757 (tm-30) cc_final: 0.8547 (tm-30) REVERT: C 177 TRP cc_start: 0.8293 (m-10) cc_final: 0.7892 (m-10) REVERT: C 283 MET cc_start: 0.8303 (tpt) cc_final: 0.8001 (tpt) REVERT: C 288 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8156 (tt) REVERT: C 320 VAL cc_start: 0.8326 (OUTLIER) cc_final: 0.7841 (t) REVERT: C 553 PHE cc_start: 0.8119 (t80) cc_final: 0.7672 (t80) REVERT: C 680 GLN cc_start: 0.7540 (OUTLIER) cc_final: 0.7193 (pp30) REVERT: C 747 MET cc_start: 0.7789 (ptm) cc_final: 0.7541 (mtp) REVERT: C 764 LYS cc_start: 0.7883 (mtpt) cc_final: 0.7593 (mmmt) REVERT: C 835 MET cc_start: 0.8906 (ptp) cc_final: 0.8097 (ptp) REVERT: C 852 GLU cc_start: 0.8639 (tp30) cc_final: 0.8228 (tp30) REVERT: C 959 GLU cc_start: 0.8156 (tt0) cc_final: 0.7819 (tt0) REVERT: A 68 GLU cc_start: 0.8811 (tp30) cc_final: 0.8383 (tp30) REVERT: A 183 MET cc_start: 0.7734 (tpp) cc_final: 0.7468 (tpp) REVERT: A 207 ARG cc_start: 0.8914 (ptp-170) cc_final: 0.8670 (ptp90) REVERT: A 245 PHE cc_start: 0.9034 (m-80) cc_final: 0.8712 (m-80) REVERT: A 388 SER cc_start: 0.9519 (m) cc_final: 0.9101 (t) REVERT: A 621 MET cc_start: 0.9316 (tpp) cc_final: 0.9063 (mmt) REVERT: A 661 MET cc_start: 0.7282 (pmm) cc_final: 0.6950 (pmm) REVERT: A 711 MET cc_start: 0.8636 (ppp) cc_final: 0.8364 (ppp) REVERT: A 792 MET cc_start: 0.8228 (mpp) cc_final: 0.7652 (ttt) REVERT: A 836 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8380 (pt0) outliers start: 62 outliers final: 50 residues processed: 447 average time/residue: 0.1299 time to fit residues: 96.2320 Evaluate side-chains 449 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 393 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 655 ASN Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 711 MET Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 904 LEU Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 675 PHE Chi-restraints excluded: chain C residue 680 GLN Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 804 THR Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 908 LEU Chi-restraints excluded: chain C residue 1025 LEU Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 836 GLN Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 951 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 136 optimal weight: 0.9980 chunk 225 optimal weight: 9.9990 chunk 116 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 99 optimal weight: 0.3980 chunk 21 optimal weight: 2.9990 chunk 209 optimal weight: 0.7980 chunk 275 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 ASN C 34 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.086953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.067893 restraints weight = 80360.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.069920 restraints weight = 41826.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.071258 restraints weight = 26750.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.072128 restraints weight = 19667.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.072637 restraints weight = 15967.926| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.5280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 23492 Z= 0.166 Angle : 0.713 11.707 31928 Z= 0.356 Chirality : 0.045 0.323 3751 Planarity : 0.004 0.045 4106 Dihedral : 4.577 31.630 3308 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.94 % Favored : 96.03 % Rotamer: Outliers : 2.83 % Allowed : 23.62 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.16), residues: 3021 helix: 1.57 (0.12), residues: 1757 sheet: -0.61 (0.27), residues: 365 loop : -0.90 (0.22), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 656 TYR 0.030 0.001 TYR B 524 PHE 0.036 0.001 PHE C 975 TRP 0.024 0.001 TRP B 186 HIS 0.017 0.001 HIS C 209 Details of bonding type rmsd covalent geometry : bond 0.00377 (23492) covalent geometry : angle 0.71287 (31928) hydrogen bonds : bond 0.04709 ( 1510) hydrogen bonds : angle 5.12681 ( 4500) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3796.19 seconds wall clock time: 66 minutes 22.73 seconds (3982.73 seconds total)