Starting phenix.real_space_refine on Sun Sep 29 18:18:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9arf_43780/09_2024/9arf_43780.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9arf_43780/09_2024/9arf_43780.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9arf_43780/09_2024/9arf_43780.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9arf_43780/09_2024/9arf_43780.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9arf_43780/09_2024/9arf_43780.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9arf_43780/09_2024/9arf_43780.cif" } resolution = 3.13 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= 0.001 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 298 atoms to isotropic. 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 120 5.16 5 C 14800 2.51 5 N 3810 2.21 5 O 4302 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 23032 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 796, 5775 Classifications: {'peptide': 796} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'PTRANS': 34, 'TRANS': 761} Chain breaks: 2 Unresolved non-hydrogen bonds: 533 Unresolved non-hydrogen angles: 649 Unresolved non-hydrogen dihedrals: 448 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 13, 'TYR:plan': 2, 'ASN:plan1': 9, 'TRP:plan': 1, 'HIS:plan': 5, 'PHE:plan': 4, 'GLU:plan': 21, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 367 Chain: "B" Number of atoms: 5684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 5684 Classifications: {'peptide': 785} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'PTRANS': 27, 'TRANS': 757} Chain breaks: 2 Unresolved non-hydrogen bonds: 541 Unresolved non-hydrogen angles: 662 Unresolved non-hydrogen dihedrals: 471 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 17, 'TYR:plan': 6, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 7, 'PHE:plan': 6, 'GLU:plan': 29, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 385 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: D, C, F Time building chain proxies: 23.82, per 1000 atoms: 1.03 Number of scatterers: 23032 At special positions: 0 Unit cell: (126.567, 148.953, 175.644, 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 120 16.00 O 4302 8.00 N 3810 7.00 C 14800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 798 " distance=2.02 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG B 901 " - " ASN B 491 " " NAG D 901 " - " ASN D 491 " " NAG E 1 " - " ASN B 688 " " NAG F 1 " - " ASN D 688 " Time building additional restraints: 5.96 Conformation dependent library (CDL) restraints added in 2.9 seconds 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5912 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 28 sheets defined 41.7% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.71 Creating SS restraints... Processing helix chain 'A' and resid 35 through 51 removed outlier: 3.829A pdb=" N LYS A 51 " --> pdb=" O ASN A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 86 Processing helix chain 'A' and resid 104 through 113 removed outlier: 3.529A pdb=" N SER A 108 " --> pdb=" O PRO A 104 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR A 109 " --> pdb=" O THR A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 130 removed outlier: 3.556A pdb=" N ASP A 130 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 147 removed outlier: 3.573A pdb=" N GLN A 147 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 158 Processing helix chain 'A' and resid 170 through 186 Processing helix chain 'A' and resid 204 through 212 removed outlier: 4.086A pdb=" N GLU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 236 removed outlier: 3.913A pdb=" N ALA A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N THR A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL A 231 " --> pdb=" O ASP A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 259 removed outlier: 3.883A pdb=" N ALA A 258 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU A 259 " --> pdb=" O GLY A 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 255 through 259' Processing helix chain 'A' and resid 277 through 296 removed outlier: 3.515A pdb=" N SER A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL A 287 " --> pdb=" O ASP A 283 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 291 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU A 294 " --> pdb=" O GLN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 327 removed outlier: 3.629A pdb=" N VAL A 324 " --> pdb=" O LEU A 320 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER A 327 " --> pdb=" O ARG A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 470 removed outlier: 3.839A pdb=" N LEU A 463 " --> pdb=" O CYS A 459 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE A 464 " --> pdb=" O ILE A 460 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS A 465 " --> pdb=" O ASP A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 506 removed outlier: 3.718A pdb=" N LEU A 505 " --> pdb=" O MET A 501 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU A 506 " --> pdb=" O MET A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 525 removed outlier: 3.823A pdb=" N GLN A 525 " --> pdb=" O GLU A 522 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 522 through 525' Processing helix chain 'A' and resid 559 through 583 removed outlier: 3.877A pdb=" N LEU A 564 " --> pdb=" O SER A 560 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N HIS A 571 " --> pdb=" O GLY A 567 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG A 582 " --> pdb=" O TYR A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 612 Processing helix chain 'A' and resid 628 through 655 removed outlier: 4.236A pdb=" N LEU A 632 " --> pdb=" O SER A 628 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N MET A 634 " --> pdb=" O ARG A 630 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A 640 " --> pdb=" O TRP A 636 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET A 641 " --> pdb=" O ALA A 637 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE A 642 " --> pdb=" O GLY A 638 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE A 643 " --> pdb=" O PHE A 639 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A 653 " --> pdb=" O ALA A 649 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE A 654 " --> pdb=" O ASN A 650 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU A 655 " --> pdb=" O LEU A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 689 through 694 Processing helix chain 'A' and resid 699 through 708 removed outlier: 3.940A pdb=" N HIS A 705 " --> pdb=" O THR A 701 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS A 708 " --> pdb=" O ARG A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 723 removed outlier: 3.654A pdb=" N ALA A 717 " --> pdb=" O SER A 713 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE A 718 " --> pdb=" O ALA A 714 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN A 719 " --> pdb=" O ALA A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 743 removed outlier: 4.394A pdb=" N PHE A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 770 removed outlier: 4.248A pdb=" N GLN A 770 " --> pdb=" O PRO A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 777 removed outlier: 3.642A pdb=" N LEU A 777 " --> pdb=" O SER A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 781 removed outlier: 3.574A pdb=" N GLU A 781 " --> pdb=" O LYS A 778 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 778 through 781' Processing helix chain 'A' and resid 783 through 793 removed outlier: 3.898A pdb=" N ASP A 787 " --> pdb=" O GLY A 783 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU A 788 " --> pdb=" O PHE A 784 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TRP A 792 " --> pdb=" O LEU A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 812 No H-bonds generated for 'chain 'A' and resid 810 through 812' Processing helix chain 'A' and resid 813 through 841 removed outlier: 4.100A pdb=" N PHE A 817 " --> pdb=" O MET A 813 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A 819 " --> pdb=" O GLY A 815 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL A 820 " --> pdb=" O VAL A 816 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE A 833 " --> pdb=" O PHE A 829 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG A 839 " --> pdb=" O ILE A 835 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 removed outlier: 4.324A pdb=" N GLU B 55 " --> pdb=" O LYS B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 92 removed outlier: 4.176A pdb=" N ARG B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 119 removed outlier: 4.158A pdb=" N GLN B 110 " --> pdb=" O GLU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 132 removed outlier: 3.597A pdb=" N MET B 132 " --> pdb=" O GLY B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 164 removed outlier: 3.584A pdb=" N GLN B 153 " --> pdb=" O SER B 149 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR B 164 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 190 Processing helix chain 'B' and resid 212 through 221 removed outlier: 3.605A pdb=" N LYS B 221 " --> pdb=" O GLN B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 248 removed outlier: 4.014A pdb=" N SER B 246 " --> pdb=" O GLU B 242 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL B 247 " --> pdb=" O VAL B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 264 removed outlier: 4.250A pdb=" N ALA B 263 " --> pdb=" O PRO B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 310 removed outlier: 3.709A pdb=" N GLU B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 330 removed outlier: 4.417A pdb=" N TYR B 330 " --> pdb=" O LYS B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 339 Processing helix chain 'B' and resid 459 through 472 removed outlier: 3.655A pdb=" N ASP B 463 " --> pdb=" O GLY B 459 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE B 464 " --> pdb=" O PHE B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 503 Processing helix chain 'B' and resid 555 through 577 removed outlier: 4.058A pdb=" N TRP B 559 " --> pdb=" O SER B 555 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N MET B 565 " --> pdb=" O MET B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 612 removed outlier: 3.562A pdb=" N ALA B 605 " --> pdb=" O THR B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 656 removed outlier: 3.745A pdb=" N SER B 628 " --> pdb=" O LYS B 624 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR B 647 " --> pdb=" O LEU B 643 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA B 648 " --> pdb=" O ALA B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 673 Processing helix chain 'B' and resid 674 through 677 removed outlier: 3.945A pdb=" N PHE B 677 " --> pdb=" O PRO B 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 674 through 677' Processing helix chain 'B' and resid 689 through 699 removed outlier: 3.830A pdb=" N ARG B 693 " --> pdb=" O GLY B 689 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN B 698 " --> pdb=" O ASN B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 708 Processing helix chain 'B' and resid 713 through 723 Processing helix chain 'B' and resid 733 through 742 Processing helix chain 'B' and resid 772 through 787 Processing helix chain 'B' and resid 787 through 797 removed outlier: 3.721A pdb=" N GLU B 791 " --> pdb=" O GLY B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 845 removed outlier: 4.162A pdb=" N PHE B 822 " --> pdb=" O MET B 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 51 removed outlier: 3.829A pdb=" N LYS C 51 " --> pdb=" O ASN C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 86 Processing helix chain 'C' and resid 104 through 113 removed outlier: 3.529A pdb=" N SER C 108 " --> pdb=" O PRO C 104 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR C 109 " --> pdb=" O THR C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 130 removed outlier: 3.556A pdb=" N ASP C 130 " --> pdb=" O ILE C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 147 removed outlier: 3.573A pdb=" N GLN C 147 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 158 Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 204 through 212 removed outlier: 4.086A pdb=" N GLU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA C 211 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 236 removed outlier: 3.913A pdb=" N ALA C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N THR C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL C 231 " --> pdb=" O ASP C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 259 removed outlier: 3.883A pdb=" N ALA C 258 " --> pdb=" O SER C 255 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU C 259 " --> pdb=" O GLY C 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 255 through 259' Processing helix chain 'C' and resid 277 through 296 removed outlier: 3.515A pdb=" N SER C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY C 286 " --> pdb=" O SER C 282 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL C 287 " --> pdb=" O ASP C 283 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN C 290 " --> pdb=" O GLY C 286 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA C 291 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU C 294 " --> pdb=" O GLN C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 327 removed outlier: 3.630A pdb=" N VAL C 324 " --> pdb=" O LEU C 320 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER C 327 " --> pdb=" O ARG C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 470 removed outlier: 3.840A pdb=" N LEU C 463 " --> pdb=" O CYS C 459 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE C 464 " --> pdb=" O ILE C 460 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS C 465 " --> pdb=" O ASP C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 506 removed outlier: 3.717A pdb=" N LEU C 505 " --> pdb=" O MET C 501 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU C 506 " --> pdb=" O MET C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 525 removed outlier: 3.824A pdb=" N GLN C 525 " --> pdb=" O GLU C 522 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 522 through 525' Processing helix chain 'C' and resid 559 through 583 removed outlier: 3.877A pdb=" N LEU C 564 " --> pdb=" O SER C 560 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N HIS C 571 " --> pdb=" O GLY C 567 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL C 572 " --> pdb=" O LEU C 568 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG C 582 " --> pdb=" O TYR C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 612 Processing helix chain 'C' and resid 628 through 655 removed outlier: 4.236A pdb=" N LEU C 632 " --> pdb=" O SER C 628 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N MET C 634 " --> pdb=" O ARG C 630 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA C 640 " --> pdb=" O TRP C 636 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET C 641 " --> pdb=" O ALA C 637 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE C 642 " --> pdb=" O GLY C 638 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE C 643 " --> pdb=" O PHE C 639 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA C 653 " --> pdb=" O ALA C 649 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE C 654 " --> pdb=" O ASN C 650 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU C 655 " --> pdb=" O LEU C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 689 through 694 Processing helix chain 'C' and resid 699 through 708 removed outlier: 3.940A pdb=" N HIS C 705 " --> pdb=" O THR C 701 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS C 708 " --> pdb=" O ARG C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 723 removed outlier: 3.654A pdb=" N ALA C 717 " --> pdb=" O SER C 713 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE C 718 " --> pdb=" O ALA C 714 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN C 719 " --> pdb=" O ALA C 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 743 removed outlier: 4.394A pdb=" N PHE C 738 " --> pdb=" O ALA C 734 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 766 through 770 removed outlier: 4.248A pdb=" N GLN C 770 " --> pdb=" O PRO C 767 " (cutoff:3.500A) Processing helix chain 'C' and resid 772 through 777 removed outlier: 3.642A pdb=" N LEU C 777 " --> pdb=" O SER C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 778 through 781 removed outlier: 3.575A pdb=" N GLU C 781 " --> pdb=" O LYS C 778 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 778 through 781' Processing helix chain 'C' and resid 783 through 793 removed outlier: 3.898A pdb=" N ASP C 787 " --> pdb=" O GLY C 783 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU C 788 " --> pdb=" O PHE C 784 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TRP C 792 " --> pdb=" O LEU C 788 " (cutoff:3.500A) Processing helix chain 'C' and resid 810 through 812 No H-bonds generated for 'chain 'C' and resid 810 through 812' Processing helix chain 'C' and resid 813 through 841 removed outlier: 4.101A pdb=" N PHE C 817 " --> pdb=" O MET C 813 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU C 819 " --> pdb=" O GLY C 815 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL C 820 " --> pdb=" O VAL C 816 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE C 833 " --> pdb=" O PHE C 829 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG C 839 " --> pdb=" O ILE C 835 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 55 removed outlier: 4.324A pdb=" N GLU D 55 " --> pdb=" O LYS D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 92 removed outlier: 4.177A pdb=" N ARG D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 119 removed outlier: 4.158A pdb=" N GLN D 110 " --> pdb=" O GLU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 132 removed outlier: 3.597A pdb=" N MET D 132 " --> pdb=" O GLY D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 164 removed outlier: 3.584A pdb=" N GLN D 153 " --> pdb=" O SER D 149 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR D 164 " --> pdb=" O ILE D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 190 Processing helix chain 'D' and resid 212 through 221 removed outlier: 3.606A pdb=" N LYS D 221 " --> pdb=" O GLN D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 248 removed outlier: 4.014A pdb=" N SER D 246 " --> pdb=" O GLU D 242 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL D 247 " --> pdb=" O VAL D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 264 removed outlier: 4.250A pdb=" N ALA D 263 " --> pdb=" O PRO D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 310 removed outlier: 3.710A pdb=" N GLU D 310 " --> pdb=" O ASP D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 330 removed outlier: 4.416A pdb=" N TYR D 330 " --> pdb=" O LYS D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 339 Processing helix chain 'D' and resid 459 through 472 removed outlier: 3.655A pdb=" N ASP D 463 " --> pdb=" O GLY D 459 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE D 464 " --> pdb=" O PHE D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 503 Processing helix chain 'D' and resid 555 through 577 removed outlier: 4.058A pdb=" N TRP D 559 " --> pdb=" O SER D 555 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N MET D 565 " --> pdb=" O MET D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 612 removed outlier: 3.562A pdb=" N ALA D 605 " --> pdb=" O THR D 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 656 removed outlier: 3.745A pdb=" N SER D 628 " --> pdb=" O LYS D 624 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR D 647 " --> pdb=" O LEU D 643 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA D 648 " --> pdb=" O ALA D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 673 Processing helix chain 'D' and resid 674 through 677 removed outlier: 3.945A pdb=" N PHE D 677 " --> pdb=" O PRO D 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 674 through 677' Processing helix chain 'D' and resid 689 through 699 removed outlier: 3.830A pdb=" N ARG D 693 " --> pdb=" O GLY D 689 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN D 698 " --> pdb=" O ASN D 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 700 through 708 Processing helix chain 'D' and resid 713 through 723 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 772 through 787 Processing helix chain 'D' and resid 787 through 797 removed outlier: 3.721A pdb=" N GLU D 791 " --> pdb=" O GLY D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 818 through 845 removed outlier: 4.162A pdb=" N PHE D 822 " --> pdb=" O MET D 818 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 63 removed outlier: 3.617A pdb=" N THR A 63 " --> pdb=" O ILE A 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 197 removed outlier: 7.266A pdb=" N ILE A 163 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N LEU A 195 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU A 165 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N PHE A 197 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL A 167 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE A 164 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N SER A 222 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU A 166 " --> pdb=" O SER A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 271 removed outlier: 3.742A pdb=" N TYR A 351 " --> pdb=" O TYR A 367 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ASN A 355 " --> pdb=" O GLN A 363 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N GLN A 363 " --> pdb=" O ASN A 355 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLN A 357 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LEU A 361 " --> pdb=" O GLN A 357 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE A 366 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE A 373 " --> pdb=" O ILE A 366 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 476 through 478 removed outlier: 6.034A pdb=" N ILE A 400 " --> pdb=" O HIS A 477 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N VAL A 401 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 9.661A pdb=" N ILE A 513 " --> pdb=" O ARG A 763 " (cutoff:3.500A) removed outlier: 9.287A pdb=" N ARG A 763 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ALA A 515 " --> pdb=" O GLY A 761 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N GLY A 761 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU A 517 " --> pdb=" O GLY A 759 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 410 through 413 removed outlier: 3.821A pdb=" N GLY A 438 " --> pdb=" O VAL A 451 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 487 through 489 removed outlier: 3.615A pdb=" N GLU A 497 " --> pdb=" O GLU A 488 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 681 through 682 removed outlier: 7.029A pdb=" N ALA A 682 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 9.607A pdb=" N ASP A 732 " --> pdb=" O ALA A 682 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 67 through 73 removed outlier: 3.585A pdb=" N GLU B 69 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLY B 36 " --> pdb=" O ILE B 94 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL B 42 " --> pdb=" O ALA B 100 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 198 through 199 removed outlier: 7.152A pdb=" N ILE B 168 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N LEU B 229 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER B 170 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N TYR B 231 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N VAL B 172 " --> pdb=" O TYR B 231 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N TRP B 256 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N VAL B 280 " --> pdb=" O TRP B 256 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N VAL B 258 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N TYR B 282 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU B 362 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LYS B 378 " --> pdb=" O LEU B 362 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE B 364 " --> pdb=" O VAL B 376 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 408 through 409 removed outlier: 3.608A pdb=" N VAL B 409 " --> pdb=" O MET B 508 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 765 " --> pdb=" O ALA B 509 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 418 through 420 Processing sheet with id=AB3, first strand: chain 'B' and resid 489 through 490 Processing sheet with id=AB4, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AB5, first strand: chain 'B' and resid 683 through 684 removed outlier: 6.711A pdb=" N GLY B 684 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 9.323A pdb=" N ASP B 732 " --> pdb=" O GLY B 684 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 62 through 63 removed outlier: 3.618A pdb=" N THR C 63 " --> pdb=" O ILE C 29 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 193 through 197 removed outlier: 7.267A pdb=" N ILE C 163 " --> pdb=" O LYS C 193 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N LEU C 195 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU C 165 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N PHE C 197 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N VAL C 167 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE C 164 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N SER C 222 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU C 166 " --> pdb=" O SER C 222 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 269 through 271 removed outlier: 3.743A pdb=" N TYR C 351 " --> pdb=" O TYR C 367 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASN C 355 " --> pdb=" O GLN C 363 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLN C 363 " --> pdb=" O ASN C 355 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLN C 357 " --> pdb=" O LEU C 361 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LEU C 361 " --> pdb=" O GLN C 357 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE C 366 " --> pdb=" O ILE C 373 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE C 373 " --> pdb=" O ILE C 366 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 476 through 478 removed outlier: 6.035A pdb=" N ILE C 400 " --> pdb=" O HIS C 477 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N VAL C 401 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 9.661A pdb=" N ILE C 513 " --> pdb=" O ARG C 763 " (cutoff:3.500A) removed outlier: 9.287A pdb=" N ARG C 763 " --> pdb=" O ILE C 513 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ALA C 515 " --> pdb=" O GLY C 761 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N GLY C 761 " --> pdb=" O ALA C 515 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU C 517 " --> pdb=" O GLY C 759 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 410 through 413 removed outlier: 3.820A pdb=" N GLY C 438 " --> pdb=" O VAL C 451 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 487 through 489 removed outlier: 3.614A pdb=" N GLU C 497 " --> pdb=" O GLU C 488 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 681 through 682 removed outlier: 7.029A pdb=" N ALA C 682 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 9.607A pdb=" N ASP C 732 " --> pdb=" O ALA C 682 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 67 through 73 removed outlier: 3.586A pdb=" N GLU D 69 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLY D 36 " --> pdb=" O ILE D 94 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL D 42 " --> pdb=" O ALA D 100 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 198 through 199 removed outlier: 7.152A pdb=" N ILE D 168 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N LEU D 229 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER D 170 " --> pdb=" O LEU D 229 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N TYR D 231 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N VAL D 172 " --> pdb=" O TYR D 231 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N TRP D 256 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N VAL D 280 " --> pdb=" O TRP D 256 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N VAL D 258 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N TYR D 282 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU D 362 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LYS D 378 " --> pdb=" O LEU D 362 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE D 364 " --> pdb=" O VAL D 376 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 408 through 409 removed outlier: 3.608A pdb=" N VAL D 409 " --> pdb=" O MET D 508 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA D 765 " --> pdb=" O ALA D 509 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 418 through 420 Processing sheet with id=AC8, first strand: chain 'D' and resid 489 through 490 Processing sheet with id=AC9, first strand: chain 'D' and resid 531 through 532 Processing sheet with id=AD1, first strand: chain 'D' and resid 683 through 684 removed outlier: 6.711A pdb=" N GLY D 684 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 9.323A pdb=" N ASP D 732 " --> pdb=" O GLY D 684 " (cutoff:3.500A) 898 hydrogen bonds defined for protein. 2598 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: 8.19 Time building geometry restraints manager: 6.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.04 - 1.20: 128 1.20 - 1.35: 7316 1.35 - 1.51: 6822 1.51 - 1.67: 9044 1.67 - 1.82: 202 Bond restraints: 23512 Sorted by residual: bond pdb=" C MET C 512 " pdb=" O MET C 512 " ideal model delta sigma weight residual 1.234 1.038 0.196 1.24e-02 6.50e+03 2.49e+02 bond pdb=" C MET A 512 " pdb=" O MET A 512 " ideal model delta sigma weight residual 1.234 1.038 0.195 1.24e-02 6.50e+03 2.48e+02 bond pdb=" C MET B 508 " pdb=" O MET B 508 " ideal model delta sigma weight residual 1.234 1.044 0.190 1.26e-02 6.30e+03 2.27e+02 bond pdb=" C MET D 508 " pdb=" O MET D 508 " ideal model delta sigma weight residual 1.234 1.044 0.190 1.26e-02 6.30e+03 2.27e+02 bond pdb=" C ALA D 509 " pdb=" O ALA D 509 " ideal model delta sigma weight residual 1.236 1.062 0.174 1.20e-02 6.94e+03 2.09e+02 ... (remaining 23507 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.29: 31958 6.29 - 12.58: 150 12.58 - 18.87: 14 18.87 - 25.17: 2 25.17 - 31.46: 2 Bond angle restraints: 32126 Sorted by residual: angle pdb=" C ASN B 495 " pdb=" CA ASN B 495 " pdb=" CB ASN B 495 " ideal model delta sigma weight residual 113.15 81.69 31.46 2.38e+00 1.77e-01 1.75e+02 angle pdb=" C ASN D 495 " pdb=" CA ASN D 495 " pdb=" CB ASN D 495 " ideal model delta sigma weight residual 113.15 81.70 31.45 2.38e+00 1.77e-01 1.75e+02 angle pdb=" C ASP C 690 " pdb=" CA ASP C 690 " pdb=" CB ASP C 690 " ideal model delta sigma weight residual 110.79 89.10 21.69 1.66e+00 3.63e-01 1.71e+02 angle pdb=" C ASP A 690 " pdb=" CA ASP A 690 " pdb=" CB ASP A 690 " ideal model delta sigma weight residual 110.79 89.11 21.68 1.66e+00 3.63e-01 1.71e+02 angle pdb=" C GLU B 500 " pdb=" CA GLU B 500 " pdb=" CB GLU B 500 " ideal model delta sigma weight residual 110.85 95.10 15.75 1.70e+00 3.46e-01 8.59e+01 ... (remaining 32121 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.87: 13427 22.87 - 45.73: 392 45.73 - 68.60: 75 68.60 - 91.46: 8 91.46 - 114.33: 6 Dihedral angle restraints: 13908 sinusoidal: 4750 harmonic: 9158 Sorted by residual: dihedral pdb=" C ASN B 495 " pdb=" N ASN B 495 " pdb=" CA ASN B 495 " pdb=" CB ASN B 495 " ideal model delta harmonic sigma weight residual -122.60 -89.15 -33.45 0 2.50e+00 1.60e-01 1.79e+02 dihedral pdb=" C ASN D 495 " pdb=" N ASN D 495 " pdb=" CA ASN D 495 " pdb=" CB ASN D 495 " ideal model delta harmonic sigma weight residual -122.60 -89.16 -33.44 0 2.50e+00 1.60e-01 1.79e+02 dihedral pdb=" C ASP C 690 " pdb=" N ASP C 690 " pdb=" CA ASP C 690 " pdb=" CB ASP C 690 " ideal model delta harmonic sigma weight residual -122.60 -98.01 -24.59 0 2.50e+00 1.60e-01 9.68e+01 ... (remaining 13905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.175: 3728 0.175 - 0.350: 112 0.350 - 0.525: 22 0.525 - 0.700: 4 0.700 - 0.875: 4 Chirality restraints: 3870 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.53 -0.87 2.00e-02 2.50e+03 1.91e+03 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.53 -0.87 2.00e-02 2.50e+03 1.91e+03 chirality pdb=" CA TYR D 507 " pdb=" N TYR D 507 " pdb=" C TYR D 507 " pdb=" CB TYR D 507 " both_signs ideal model delta sigma weight residual False 2.51 1.77 0.74 2.00e-01 2.50e+01 1.36e+01 ... (remaining 3867 not shown) Planarity restraints: 4074 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP A 792 " 0.031 2.00e-02 2.50e+03 6.52e-02 4.25e+01 pdb=" C TRP A 792 " -0.113 2.00e-02 2.50e+03 pdb=" O TRP A 792 " 0.043 2.00e-02 2.50e+03 pdb=" N VAL A 793 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP C 792 " 0.031 2.00e-02 2.50e+03 6.51e-02 4.24e+01 pdb=" C TRP C 792 " -0.112 2.00e-02 2.50e+03 pdb=" O TRP C 792 " 0.043 2.00e-02 2.50e+03 pdb=" N VAL C 793 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 500 " 0.026 2.00e-02 2.50e+03 5.45e-02 2.97e+01 pdb=" C GLU D 500 " -0.094 2.00e-02 2.50e+03 pdb=" O GLU D 500 " 0.036 2.00e-02 2.50e+03 pdb=" N VAL D 501 " 0.032 2.00e-02 2.50e+03 ... (remaining 4071 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 144 2.57 - 3.15: 18092 3.15 - 3.73: 32718 3.73 - 4.32: 43831 4.32 - 4.90: 74299 Nonbonded interactions: 169084 Sorted by model distance: nonbonded pdb=" O ILE B 297 " pdb=" CG2 THR B 301 " model vdw 1.985 3.460 nonbonded pdb=" O ILE D 297 " pdb=" CG2 THR D 301 " model vdw 1.986 3.460 nonbonded pdb=" SG CYS C 744 " pdb=" SG CYS C 798 " model vdw 2.019 3.760 nonbonded pdb=" SG CYS D 429 " pdb=" SG CYS D 456 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS C 420 " pdb=" SG CYS C 454 " model vdw 2.031 3.760 ... (remaining 169079 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' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.020 Extract box with map and model: 1.040 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 61.600 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.070 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.196 23512 Z= 0.678 Angle : 1.157 31.458 32126 Z= 0.756 Chirality : 0.077 0.875 3870 Planarity : 0.007 0.065 4070 Dihedral : 11.195 114.326 7972 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.56 % Favored : 95.32 % Rotamer: Outliers : 5.16 % Allowed : 6.04 % Favored : 88.80 % Cbeta Deviations : 1.42 % 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: -3.34 (0.13), residues: 3138 helix: -1.25 (0.14), residues: 1202 sheet: -2.19 (0.23), residues: 430 loop : -3.08 (0.13), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 636 HIS 0.005 0.001 HIS C 280 PHE 0.058 0.002 PHE C 529 TYR 0.064 0.001 TYR D 507 ARG 0.008 0.000 ARG C 763 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 411 time to evaluate : 2.504 Fit side-chains REVERT: B 386 MET cc_start: 0.8867 (mmm) cc_final: 0.8449 (mmm) REVERT: B 513 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.7733 (mt) REVERT: B 515 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8643 (mt) REVERT: B 654 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8524 (mtt) REVERT: D 513 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.7738 (mt) outliers start: 116 outliers final: 66 residues processed: 512 average time/residue: 0.3513 time to fit residues: 279.1668 Evaluate side-chains 361 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 291 time to evaluate : 2.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 663 ARG Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 722 ARG Chi-restraints excluded: chain A residue 725 LYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 795 TYR Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 437 GLN Chi-restraints excluded: chain B residue 485 LYS Chi-restraints excluded: chain B residue 504 LYS Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 654 MET Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 663 ARG Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 722 ARG Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 795 TYR Chi-restraints excluded: chain C residue 798 CYS Chi-restraints excluded: chain C residue 819 LEU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 185 LYS Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 437 GLN Chi-restraints excluded: chain D residue 485 LYS Chi-restraints excluded: chain D residue 504 LYS Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 617 SER Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 626 THR Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 642 PHE Chi-restraints excluded: chain D residue 686 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.157 > 50: distance: 31 - 97: 32.291 distance: 66 - 71: 18.257 distance: 71 - 72: 13.791 distance: 72 - 73: 49.696 distance: 72 - 75: 18.099 distance: 73 - 74: 24.093 distance: 73 - 76: 44.024 distance: 76 - 77: 29.374 distance: 77 - 78: 26.583 distance: 77 - 80: 11.679 distance: 78 - 79: 37.713 distance: 78 - 84: 13.363 distance: 80 - 81: 24.959 distance: 81 - 82: 5.670 distance: 81 - 83: 25.164 distance: 84 - 85: 24.513 distance: 85 - 86: 26.097 distance: 85 - 88: 17.255 distance: 86 - 89: 28.931 distance: 89 - 90: 39.436 distance: 90 - 91: 16.838 distance: 90 - 93: 46.491 distance: 91 - 92: 18.389 distance: 91 - 94: 20.497 distance: 94 - 95: 42.755 distance: 95 - 96: 17.365 distance: 95 - 98: 25.480 distance: 96 - 97: 17.041 distance: 96 - 101: 31.877 distance: 98 - 99: 30.552 distance: 98 - 100: 11.228 distance: 101 - 102: 25.880 distance: 102 - 103: 21.224 distance: 102 - 105: 24.648 distance: 103 - 104: 17.123 distance: 103 - 107: 30.164 distance: 105 - 106: 35.444 distance: 107 - 108: 30.881 distance: 108 - 109: 34.245 distance: 108 - 111: 33.279 distance: 109 - 110: 30.680 distance: 109 - 114: 25.518 distance: 111 - 112: 12.325 distance: 111 - 113: 16.642 distance: 114 - 115: 43.094 distance: 115 - 116: 15.717 distance: 115 - 118: 30.170 distance: 116 - 121: 38.857 distance: 118 - 119: 45.570 distance: 118 - 120: 17.142 distance: 121 - 122: 44.990 distance: 122 - 123: 13.648 distance: 122 - 125: 28.524 distance: 123 - 124: 46.702 distance: 123 - 131: 17.664 distance: 125 - 126: 37.492 distance: 126 - 127: 29.647 distance: 126 - 128: 14.162 distance: 127 - 129: 16.660 distance: 128 - 130: 32.861 distance: 129 - 130: 27.599 distance: 131 - 132: 28.474 distance: 132 - 133: 21.928 distance: 132 - 135: 45.671 distance: 133 - 134: 15.376 distance: 133 - 136: 23.623