Starting phenix.real_space_refine on Sat Jan 25 05:59:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e9f_47796/01_2025/9e9f_47796.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e9f_47796/01_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_47796/01_2025/9e9f_47796.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e9f_47796/01_2025/9e9f_47796.map" model { file = "/net/cci-nas-00/data/ceres_data/9e9f_47796/01_2025/9e9f_47796.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e9f_47796/01_2025/9e9f_47796.cif" } resolution = 3.63 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG: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: 13.36, per 1000 atoms: 0.58 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: 5.72 Conformation dependent library (CDL) restraints added in 3.1 seconds 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: 2.53 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: 9.42 Time building geometry restraints manager: 6.63 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: 4.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.800 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 51.130 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.110 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: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.710 ------------------------------------------------------------------------------- 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= 0.203 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 : 15.43 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.016 0.001 TRP B 186 HIS 0.002 0.001 HIS B 598 PHE 0.022 0.001 PHE C 469 TYR 0.017 0.001 TYR C 181 ARG 0.008 0.000 ARG C 417 *********************** 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 : 2.481 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: 0.3843 time to fit residues: 497.1233 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 : 2.391 ------------------------------------------------------------------------------- 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 255 optimal weight: 3.9990 chunk 229 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 154 optimal weight: 20.0000 chunk 122 optimal weight: 10.0000 chunk 237 optimal weight: 0.7980 chunk 91 optimal weight: 9.9990 chunk 144 optimal weight: 7.9990 chunk 176 optimal weight: 20.0000 chunk 275 optimal weight: 9.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 GLN B 136 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 297 ASN A 390 ASN A 414 ASN A 436 GLN A 696 GLN ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 758 HIS A 866 GLN A 948 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.086574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.067046 restraints weight = 80830.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.069117 restraints weight = 41038.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.070434 restraints weight = 25867.070| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 23492 Z= 0.343 Angle : 0.708 8.628 31928 Z= 0.368 Chirality : 0.043 0.192 3751 Planarity : 0.005 0.066 4106 Dihedral : 5.016 53.620 3331 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.10 % Favored : 95.83 % Rotamer: Outliers : 4.20 % Allowed : 16.01 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.16), residues: 3021 helix: 1.79 (0.12), residues: 1729 sheet: -1.17 (0.26), residues: 367 loop : -0.85 (0.22), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 803 HIS 0.016 0.002 HIS B 504 PHE 0.026 0.002 PHE B 5 TYR 0.027 0.002 TYR B 605 ARG 0.009 0.001 ARG C 649 *********************** 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 609 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 508 time to evaluate : 2.993 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: 0.9388 (OUTLIER) cc_final: 0.9109 (p) REVERT: B 183 MET cc_start: 0.6350 (tpt) cc_final: 0.5988 (tpp) REVERT: B 283 MET cc_start: 0.7723 (mtp) cc_final: 0.7357 (mpp) REVERT: B 409 ILE cc_start: 0.9740 (mt) cc_final: 0.9409 (mt) REVERT: B 524 TYR cc_start: 0.9021 (t80) cc_final: 0.8802 (t80) REVERT: B 552 LEU cc_start: 0.9573 (mt) cc_final: 0.9279 (mp) REVERT: B 874 SER cc_start: 0.9546 (m) cc_final: 0.9199 (p) REVERT: B 965 LEU cc_start: 0.9512 (tp) cc_final: 0.9212 (tp) REVERT: C 65 ILE cc_start: 0.9345 (mt) cc_final: 0.9139 (mt) REVERT: C 69 MET cc_start: 0.8943 (mmm) cc_final: 0.8673 (mmm) REVERT: C 90 THR cc_start: 0.9326 (m) cc_final: 0.9099 (p) REVERT: C 94 ARG cc_start: 0.8807 (ttp-170) cc_final: 0.8413 (ttp-110) REVERT: C 177 TRP cc_start: 0.8317 (m-10) cc_final: 0.7786 (m-10) REVERT: C 288 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8350 (tt) REVERT: C 292 MET cc_start: 0.7890 (mpp) cc_final: 0.7659 (mmm) REVERT: C 331 PHE cc_start: 0.8557 (t80) cc_final: 0.7886 (t80) REVERT: C 514 ASN cc_start: 0.8400 (m-40) cc_final: 0.8060 (m-40) REVERT: C 538 TRP cc_start: 0.8976 (m100) cc_final: 0.8730 (m100) REVERT: C 552 LEU cc_start: 0.9551 (mt) cc_final: 0.9308 (mt) REVERT: C 572 MET cc_start: 0.7839 (ptm) cc_final: 0.7558 (ptm) REVERT: C 723 LEU cc_start: 0.8944 (tt) cc_final: 0.8704 (pt) REVERT: C 729 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7610 (ttpt) REVERT: C 835 MET cc_start: 0.9071 (mtp) cc_final: 0.8317 (mtp) REVERT: C 853 TRP cc_start: 0.8228 (m100) cc_final: 0.7793 (m100) REVERT: C 920 TYR cc_start: 0.9377 (m-80) cc_final: 0.9044 (m-80) REVERT: A 245 PHE cc_start: 0.8951 (m-80) cc_final: 0.8402 (m-10) REVERT: A 381 VAL cc_start: 0.9666 (t) cc_final: 0.9431 (m) REVERT: A 388 SER cc_start: 0.9548 (m) cc_final: 0.9132 (t) REVERT: A 406 ASP cc_start: 0.8847 (OUTLIER) cc_final: 0.8380 (p0) REVERT: A 434 MET cc_start: 0.9216 (mmm) cc_final: 0.8981 (mmm) REVERT: A 464 ASN cc_start: 0.8943 (t0) cc_final: 0.8650 (t0) REVERT: A 466 TYR cc_start: 0.9130 (m-80) cc_final: 0.8810 (m-80) REVERT: A 538 TRP cc_start: 0.8410 (m100) cc_final: 0.8032 (m-90) REVERT: A 585 MET cc_start: 0.8945 (mmm) cc_final: 0.8429 (mmm) REVERT: A 711 MET cc_start: 0.8222 (ppp) cc_final: 0.7821 (ppp) REVERT: A 922 LYS cc_start: 0.9195 (mttt) cc_final: 0.8901 (mtmm) outliers start: 101 outliers final: 43 residues processed: 574 average time/residue: 0.3291 time to fit residues: 303.4893 Evaluate side-chains 475 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 428 time to evaluate : 2.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 115 SER 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 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 938 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 767 VAL 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 14 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 340 VAL 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 663 SER Chi-restraints excluded: chain A residue 851 HIS 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 193 optimal weight: 0.7980 chunk 236 optimal weight: 0.9990 chunk 255 optimal weight: 1.9990 chunk 289 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 chunk 234 optimal weight: 3.9990 chunk 223 optimal weight: 0.1980 chunk 185 optimal weight: 1.9990 chunk 265 optimal weight: 9.9990 chunk 301 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 A 720 GLN A 741 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.087873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.068662 restraints weight = 78977.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.070772 restraints weight = 39765.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.072066 restraints weight = 24897.405| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23492 Z= 0.203 Angle : 0.646 11.693 31928 Z= 0.331 Chirality : 0.043 0.241 3751 Planarity : 0.004 0.037 4106 Dihedral : 4.711 48.611 3316 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.74 % Favored : 96.19 % Rotamer: Outliers : 3.99 % Allowed : 16.59 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.16), residues: 3021 helix: 1.80 (0.12), residues: 1748 sheet: -1.12 (0.27), residues: 369 loop : -0.77 (0.22), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 803 HIS 0.012 0.001 HIS C 209 PHE 0.036 0.002 PHE C 975 TYR 0.024 0.002 TYR A 315 ARG 0.005 0.000 ARG C 763 *********************** 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 601 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 505 time to evaluate : 2.431 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: B 77 TYR cc_start: 0.8408 (p90) cc_final: 0.7996 (p90) REVERT: B 123 ARG cc_start: 0.8082 (mmt90) cc_final: 0.7840 (mmt90) REVERT: B 183 MET cc_start: 0.6069 (tpt) cc_final: 0.5537 (tpp) REVERT: B 626 LEU cc_start: 0.9417 (mt) cc_final: 0.9203 (mt) REVERT: B 737 MET cc_start: 0.6115 (mmm) cc_final: 0.5589 (mmm) REVERT: B 842 MET cc_start: 0.9148 (ttp) cc_final: 0.8943 (ttp) REVERT: B 874 SER cc_start: 0.9491 (m) cc_final: 0.9158 (p) REVERT: B 904 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9048 (tp) REVERT: B 965 LEU cc_start: 0.9530 (tp) cc_final: 0.9229 (tp) REVERT: C 177 TRP cc_start: 0.8257 (m-10) cc_final: 0.7733 (m-10) REVERT: C 288 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8156 (tt) REVERT: C 292 MET cc_start: 0.7912 (mpp) cc_final: 0.7677 (mmm) REVERT: C 514 ASN cc_start: 0.8289 (m-40) cc_final: 0.8022 (m-40) REVERT: C 538 TRP cc_start: 0.8904 (m100) cc_final: 0.8700 (m100) REVERT: C 572 MET cc_start: 0.7710 (ptm) cc_final: 0.7409 (ptm) REVERT: C 835 MET cc_start: 0.8992 (mtp) cc_final: 0.8180 (mtp) REVERT: C 853 TRP cc_start: 0.8223 (m100) cc_final: 0.7730 (m100) REVERT: C 874 SER cc_start: 0.9475 (t) cc_final: 0.9234 (p) REVERT: A 69 MET cc_start: 0.9222 (mmm) cc_final: 0.8979 (mmm) REVERT: A 82 SER cc_start: 0.9132 (OUTLIER) cc_final: 0.8640 (t) REVERT: A 183 MET cc_start: 0.8277 (tpp) cc_final: 0.7162 (tpp) REVERT: A 273 GLU cc_start: 0.7389 (tp30) cc_final: 0.6871 (tp30) REVERT: A 360 ASN cc_start: 0.8523 (t0) cc_final: 0.8205 (t0) REVERT: A 381 VAL cc_start: 0.9617 (t) cc_final: 0.9309 (p) REVERT: A 388 SER cc_start: 0.9524 (m) cc_final: 0.9072 (t) REVERT: A 406 ASP cc_start: 0.8812 (OUTLIER) cc_final: 0.8353 (p0) REVERT: A 434 MET cc_start: 0.9276 (mmm) cc_final: 0.9072 (mmm) REVERT: A 458 PHE cc_start: 0.8768 (m-80) cc_final: 0.8505 (m-80) REVERT: A 464 ASN cc_start: 0.8915 (t0) cc_final: 0.8654 (t0) REVERT: A 466 TYR cc_start: 0.9112 (m-80) cc_final: 0.8832 (m-80) REVERT: A 538 TRP cc_start: 0.8421 (m100) cc_final: 0.8150 (m-90) REVERT: A 572 MET cc_start: 0.7735 (mtm) cc_final: 0.6969 (mtm) REVERT: A 711 MET cc_start: 0.8247 (ppp) cc_final: 0.7962 (ppp) REVERT: A 757 MET cc_start: 0.7809 (tpp) cc_final: 0.7245 (tpt) REVERT: A 922 LYS cc_start: 0.9174 (mttt) cc_final: 0.8800 (mttp) outliers start: 96 outliers final: 44 residues processed: 563 average time/residue: 0.3150 time to fit residues: 288.7456 Evaluate side-chains 476 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 428 time to evaluate : 2.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 518 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 1022 VAL Chi-restraints excluded: chain C residue 112 ILE 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 398 VAL Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 747 MET 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 70 ASN Chi-restraints excluded: chain A residue 82 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 406 ASP 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 835 MET Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 851 HIS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 104 optimal weight: 2.9990 chunk 276 optimal weight: 5.9990 chunk 235 optimal weight: 0.3980 chunk 274 optimal weight: 0.5980 chunk 180 optimal weight: 10.0000 chunk 272 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 199 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 287 optimal weight: 3.9990 chunk 173 optimal weight: 20.0000 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 160 ASN B 271 GLN 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 566 GLN C 575 GLN C 587 ASN ** C 955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 993 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.086039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.066955 restraints weight = 80732.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.068968 restraints weight = 41490.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.070277 restraints weight = 26480.104| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 23492 Z= 0.283 Angle : 0.653 10.379 31928 Z= 0.338 Chirality : 0.043 0.248 3751 Planarity : 0.004 0.037 4106 Dihedral : 4.671 43.397 3314 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.24 % Favored : 95.73 % Rotamer: Outliers : 3.87 % Allowed : 19.25 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.16), residues: 3021 helix: 1.62 (0.12), residues: 1753 sheet: -1.02 (0.27), residues: 371 loop : -0.76 (0.22), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 186 HIS 0.010 0.001 HIS C 209 PHE 0.045 0.002 PHE C 975 TYR 0.027 0.002 TYR A 315 ARG 0.007 0.000 ARG C 656 *********************** 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 528 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 435 time to evaluate : 2.551 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: B 5 PHE cc_start: 0.9315 (m-10) cc_final: 0.8972 (m-80) REVERT: B 56 VAL cc_start: 0.9432 (OUTLIER) cc_final: 0.9150 (p) REVERT: B 105 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8250 (tp30) REVERT: B 123 ARG cc_start: 0.8073 (mmt90) cc_final: 0.7765 (mmt90) REVERT: B 137 LEU cc_start: 0.9021 (tp) cc_final: 0.8820 (tp) REVERT: B 183 MET cc_start: 0.6024 (tpt) cc_final: 0.5534 (tpp) REVERT: B 552 LEU cc_start: 0.9638 (mp) cc_final: 0.9433 (mp) REVERT: B 568 ASP cc_start: 0.8620 (p0) cc_final: 0.8397 (p0) REVERT: B 570 MET cc_start: 0.8108 (ptt) cc_final: 0.7624 (ptt) REVERT: B 711 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8283 (ppp) REVERT: B 842 MET cc_start: 0.9144 (ttp) cc_final: 0.8852 (ttp) REVERT: B 851 HIS cc_start: 0.8266 (p90) cc_final: 0.7983 (p90) REVERT: B 965 LEU cc_start: 0.9494 (tp) cc_final: 0.9277 (tp) REVERT: C 30 LEU cc_start: 0.9531 (tp) cc_final: 0.9155 (mp) REVERT: C 177 TRP cc_start: 0.8205 (m-10) cc_final: 0.7720 (m-10) REVERT: C 195 MET cc_start: 0.7711 (OUTLIER) cc_final: 0.7003 (pmm) REVERT: C 283 MET cc_start: 0.8096 (tpt) cc_final: 0.7738 (tpt) REVERT: C 288 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8520 (tt) REVERT: C 292 MET cc_start: 0.8054 (mpp) cc_final: 0.7769 (mmm) REVERT: C 514 ASN cc_start: 0.8374 (m-40) cc_final: 0.8097 (m-40) REVERT: C 538 TRP cc_start: 0.8905 (m100) cc_final: 0.8655 (m100) REVERT: C 570 MET cc_start: 0.7759 (ttt) cc_final: 0.6965 (ttt) REVERT: C 572 MET cc_start: 0.7931 (ptm) cc_final: 0.7627 (ptm) REVERT: C 874 SER cc_start: 0.9439 (t) cc_final: 0.9229 (p) REVERT: A 273 GLU cc_start: 0.7669 (tp30) cc_final: 0.7186 (tp30) REVERT: A 388 SER cc_start: 0.9550 (m) cc_final: 0.9116 (t) REVERT: A 464 ASN cc_start: 0.8999 (t0) cc_final: 0.8775 (t0) REVERT: A 466 TYR cc_start: 0.9027 (m-80) cc_final: 0.8697 (m-80) REVERT: A 585 MET cc_start: 0.9031 (tpp) cc_final: 0.8822 (tpp) REVERT: A 690 LEU cc_start: 0.9241 (tp) cc_final: 0.8960 (tp) REVERT: A 711 MET cc_start: 0.8337 (ppp) cc_final: 0.7994 (ppp) REVERT: A 752 TYR cc_start: 0.6223 (m-80) cc_final: 0.5657 (m-80) REVERT: A 757 MET cc_start: 0.7827 (tpp) cc_final: 0.7541 (tpp) REVERT: A 836 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.8266 (pt0) REVERT: A 928 ILE cc_start: 0.9629 (tp) cc_final: 0.9414 (tp) REVERT: A 938 LEU cc_start: 0.8924 (tp) cc_final: 0.8722 (tp) outliers start: 93 outliers final: 59 residues processed: 498 average time/residue: 0.3187 time to fit residues: 258.8767 Evaluate side-chains 458 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 393 time to evaluate : 3.277 ------------------------------------------------------------------------------- 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 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 622 ILE 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 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 675 PHE Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 873 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 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 896 ILE 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 66.8645 > 50: distance: 42 - 48: 21.745 distance: 48 - 49: 45.648 distance: 49 - 50: 55.504 distance: 49 - 52: 47.409 distance: 50 - 51: 21.513 distance: 50 - 55: 47.779 distance: 52 - 53: 37.657 distance: 52 - 54: 40.488 distance: 55 - 56: 29.054 distance: 56 - 57: 19.277 distance: 56 - 59: 29.924 distance: 57 - 58: 18.705 distance: 57 - 62: 19.818 distance: 58 - 87: 40.406 distance: 59 - 60: 30.655 distance: 59 - 61: 30.792 distance: 62 - 63: 6.527 distance: 62 - 68: 22.163 distance: 63 - 64: 35.661 distance: 63 - 66: 5.813 distance: 64 - 65: 17.622 distance: 64 - 69: 25.004 distance: 65 - 98: 39.822 distance: 66 - 67: 41.278 distance: 67 - 68: 19.332 distance: 69 - 70: 17.762 distance: 70 - 71: 33.179 distance: 70 - 73: 13.743 distance: 71 - 72: 31.250 distance: 71 - 78: 16.092 distance: 72 - 102: 18.644 distance: 73 - 74: 28.035 distance: 74 - 75: 24.647 distance: 75 - 76: 25.735 distance: 75 - 77: 27.491 distance: 78 - 79: 23.867 distance: 79 - 80: 39.646 distance: 79 - 82: 12.289 distance: 80 - 81: 28.117 distance: 80 - 87: 38.632 distance: 81 - 111: 53.484 distance: 82 - 83: 33.202 distance: 83 - 84: 26.484 distance: 84 - 86: 56.856 distance: 87 - 88: 21.535 distance: 88 - 89: 41.035 distance: 88 - 91: 22.881 distance: 89 - 90: 36.219 distance: 89 - 98: 20.182 distance: 91 - 92: 24.724 distance: 92 - 93: 31.622 distance: 92 - 94: 27.047 distance: 93 - 95: 20.803 distance: 94 - 96: 20.129 distance: 95 - 97: 33.912 distance: 96 - 97: 33.296 distance: 99 - 100: 16.585 distance: 100 - 101: 13.496 distance: 100 - 102: 18.734 distance: 102 - 103: 28.479 distance: 103 - 104: 37.707 distance: 103 - 106: 25.279 distance: 104 - 105: 30.184 distance: 104 - 111: 27.591 distance: 106 - 107: 13.834 distance: 107 - 108: 18.012 distance: 108 - 109: 21.285 distance: 108 - 110: 41.413 distance: 111 - 112: 30.520 distance: 115 - 116: 3.997 distance: 116 - 118: 39.538 distance: 119 - 125: 40.276 distance: 120 - 121: 19.843 distance: 121 - 122: 41.146 distance: 121 - 126: 28.823 distance: 123 - 124: 39.654