Starting phenix.real_space_refine on Fri Mar 6 13:26:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z9g_14572/03_2026/7z9g_14572_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z9g_14572/03_2026/7z9g_14572.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z9g_14572/03_2026/7z9g_14572.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z9g_14572/03_2026/7z9g_14572.map" model { file = "/net/cci-nas-00/data/ceres_data/7z9g_14572/03_2026/7z9g_14572_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z9g_14572/03_2026/7z9g_14572_trim.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 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: 7 Type Number sf(0) Gaussians P 64 5.49 5 Mg 2 5.21 5 S 58 5.16 5 C 9825 2.51 5 N 2839 2.21 5 O 3184 1.98 5 H 15379 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31351 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 8216 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 21, 'TRANS': 495} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 6406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 6406 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 15, 'TRANS': 386} Chain: "C" Number of atoms: 8216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 8216 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 21, 'TRANS': 495} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 6406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 6406 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 15, 'TRANS': 386} Chain: "E" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 450 Classifications: {'DNA': 14} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 13} Chain: "F" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 448 Classifications: {'DNA': 14} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 13} Chain: "G" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 561 Classifications: {'DNA': 18} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 17} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "H" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 568 Classifications: {'DNA': 18} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 17} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 68 Unusual residues: {'IM0': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.83, per 1000 atoms: 0.19 Number of scatterers: 31351 At special positions: 0 Unit cell: (129, 135.88, 138.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 58 16.00 P 64 15.00 Mg 2 11.99 O 3184 8.00 N 2839 7.00 C 9825 6.00 H 15379 1.00 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.65 Conformation dependent library (CDL) restraints added in 855.7 milliseconds 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3440 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 23 sheets defined 51.0% alpha, 10.7% beta 6 base pairs and 51 stacking pairs defined. Time for finding SS restraints: 5.02 Creating SS restraints... Processing helix chain 'A' and resid 13 through 30 removed outlier: 3.680A pdb=" N VAL A 30 " --> pdb=" O MET A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 55 Processing helix chain 'A' and resid 66 through 77 Processing helix chain 'A' and resid 81 through 92 removed outlier: 3.828A pdb=" N VAL A 85 " --> pdb=" O GLY A 81 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 122 Processing helix chain 'A' and resid 130 through 135 removed outlier: 3.858A pdb=" N LEU A 134 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 130 through 135' Processing helix chain 'A' and resid 164 through 170 Processing helix chain 'A' and resid 186 through 200 Processing helix chain 'A' and resid 204 through 210 Processing helix chain 'A' and resid 226 through 236 removed outlier: 4.101A pdb=" N GLU A 230 " --> pdb=" O ARG A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 283 Processing helix chain 'A' and resid 312 through 324 removed outlier: 3.603A pdb=" N VAL A 316 " --> pdb=" O VAL A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 388 removed outlier: 3.586A pdb=" N ALA A 382 " --> pdb=" O HIS A 378 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 400 Processing helix chain 'A' and resid 402 through 413 removed outlier: 4.028A pdb=" N ASN A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 427 removed outlier: 3.708A pdb=" N LEU A 424 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 427 " --> pdb=" O MET A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 460 Processing helix chain 'A' and resid 462 through 466 Processing helix chain 'A' and resid 467 through 494 removed outlier: 3.695A pdb=" N LEU A 474 " --> pdb=" O GLU A 470 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU A 475 " --> pdb=" O HIS A 471 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER A 494 " --> pdb=" O ARG A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 514 Processing helix chain 'B' and resid 426 through 436 Processing helix chain 'B' and resid 457 through 464 removed outlier: 3.564A pdb=" N MET B 461 " --> pdb=" O ARG B 457 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU B 462 " --> pdb=" O PHE B 458 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER B 463 " --> pdb=" O ASP B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 475 Processing helix chain 'B' and resid 500 through 518 Processing helix chain 'B' and resid 518 through 525 removed outlier: 3.597A pdb=" N VAL B 522 " --> pdb=" O MET B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 561 removed outlier: 4.140A pdb=" N ALA B 551 " --> pdb=" O LYS B 547 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET B 552 " --> pdb=" O ASP B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 597 removed outlier: 3.514A pdb=" N MET B 597 " --> pdb=" O MET B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 610 removed outlier: 3.583A pdb=" N LEU B 606 " --> pdb=" O PRO B 602 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE B 610 " --> pdb=" O LEU B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 639 removed outlier: 3.925A pdb=" N TRP B 629 " --> pdb=" O THR B 625 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL B 630 " --> pdb=" O VAL B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 684 removed outlier: 3.517A pdb=" N ILE B 682 " --> pdb=" O ASP B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 697 removed outlier: 3.660A pdb=" N ARG B 688 " --> pdb=" O GLY B 684 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS B 696 " --> pdb=" O THR B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 731 Processing helix chain 'B' and resid 732 through 734 No H-bonds generated for 'chain 'B' and resid 732 through 734' Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 769 through 782 removed outlier: 3.704A pdb=" N ALA B 773 " --> pdb=" O ASP B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 795 removed outlier: 3.779A pdb=" N ARG B 788 " --> pdb=" O ALA B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 796 through 801 Processing helix chain 'C' and resid 13 through 32 Processing helix chain 'C' and resid 42 through 55 Processing helix chain 'C' and resid 66 through 77 Processing helix chain 'C' and resid 81 through 92 removed outlier: 4.059A pdb=" N VAL C 85 " --> pdb=" O GLY C 81 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET C 92 " --> pdb=" O THR C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 122 Processing helix chain 'C' and resid 130 through 135 removed outlier: 3.768A pdb=" N LEU C 134 " --> pdb=" O ILE C 130 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET C 135 " --> pdb=" O ALA C 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 130 through 135' Processing helix chain 'C' and resid 164 through 170 Processing helix chain 'C' and resid 186 through 200 Processing helix chain 'C' and resid 204 through 212 removed outlier: 3.554A pdb=" N GLU C 210 " --> pdb=" O GLU C 206 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N HIS C 211 " --> pdb=" O GLY C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 236 removed outlier: 3.566A pdb=" N GLU C 230 " --> pdb=" O ARG C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 283 Processing helix chain 'C' and resid 312 through 324 removed outlier: 3.547A pdb=" N VAL C 316 " --> pdb=" O VAL C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 389 removed outlier: 3.632A pdb=" N ILE C 379 " --> pdb=" O ASP C 375 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN C 389 " --> pdb=" O VAL C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 399 removed outlier: 3.768A pdb=" N HIS C 399 " --> pdb=" O GLU C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 412 Processing helix chain 'C' and resid 420 through 426 removed outlier: 3.515A pdb=" N LEU C 424 " --> pdb=" O VAL C 420 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 460 Processing helix chain 'C' and resid 462 through 466 removed outlier: 3.511A pdb=" N LYS C 465 " --> pdb=" O ARG C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 493 removed outlier: 3.718A pdb=" N LEU C 474 " --> pdb=" O GLU C 470 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU C 475 " --> pdb=" O HIS C 471 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP C 483 " --> pdb=" O LYS C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 514 Processing helix chain 'D' and resid 425 through 435 removed outlier: 3.682A pdb=" N GLN D 434 " --> pdb=" O GLY D 430 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY D 435 " --> pdb=" O SER D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 464 Processing helix chain 'D' and resid 464 through 475 removed outlier: 3.545A pdb=" N ALA D 468 " --> pdb=" O SER D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 518 Processing helix chain 'D' and resid 518 through 525 removed outlier: 3.646A pdb=" N VAL D 522 " --> pdb=" O MET D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 561 Processing helix chain 'D' and resid 577 through 596 removed outlier: 3.635A pdb=" N ARG D 596 " --> pdb=" O LYS D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 602 through 610 removed outlier: 4.167A pdb=" N ILE D 610 " --> pdb=" O LEU D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 616 through 621 removed outlier: 4.245A pdb=" N SER D 621 " --> pdb=" O GLU D 617 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 640 removed outlier: 3.832A pdb=" N LYS D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 684 removed outlier: 3.520A pdb=" N ILE D 682 " --> pdb=" O ASP D 678 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 697 removed outlier: 3.695A pdb=" N ARG D 688 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS D 696 " --> pdb=" O THR D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 718 through 731 Processing helix chain 'D' and resid 741 through 745 Processing helix chain 'D' and resid 746 through 754 Processing helix chain 'D' and resid 769 through 782 Processing helix chain 'D' and resid 784 through 795 removed outlier: 3.827A pdb=" N ARG D 788 " --> pdb=" O ALA D 784 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 12 removed outlier: 5.491A pdb=" N VAL B 527 " --> pdb=" O VAL B 765 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE B 493 " --> pdb=" O TYR B 528 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ALA B 530 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU B 420 " --> pdb=" O ILE B 494 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 65 Processing sheet with id=AA3, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AA4, first strand: chain 'A' and resid 171 through 174 Processing sheet with id=AA5, first strand: chain 'A' and resid 327 through 333 removed outlier: 4.426A pdb=" N TYR A 241 " --> pdb=" O ASN A 224 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 245 through 250 removed outlier: 3.731A pdb=" N GLU A 263 " --> pdb=" O ARG A 245 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N GLU A 247 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N VAL A 261 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N GLU A 249 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ILE A 259 " --> pdb=" O GLU A 249 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N GLU A 257 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL A 307 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL A 304 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU A 292 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLU A 306 " --> pdb=" O SER A 290 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 335 through 337 Processing sheet with id=AA8, first strand: chain 'A' and resid 415 through 416 removed outlier: 3.552A pdb=" N TYR A 449 " --> pdb=" O GLY A 442 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY A 442 " --> pdb=" O TYR A 449 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 542 through 546 removed outlier: 3.829A pdb=" N GLN B 542 " --> pdb=" O LYS B 539 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 567 through 568 Processing sheet with id=AB2, first strand: chain 'B' and resid 646 through 648 Processing sheet with id=AB3, first strand: chain 'B' and resid 651 through 653 Processing sheet with id=AB4, first strand: chain 'C' and resid 9 through 12 removed outlier: 3.862A pdb=" N THR C 9 " --> pdb=" O MET D 762 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N VAL D 527 " --> pdb=" O VAL D 765 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE D 493 " --> pdb=" O TYR D 528 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ALA D 530 " --> pdb=" O ILE D 493 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU D 420 " --> pdb=" O ILE D 494 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 64 through 65 Processing sheet with id=AB6, first strand: chain 'C' and resid 145 through 147 Processing sheet with id=AB7, first strand: chain 'C' and resid 171 through 174 Processing sheet with id=AB8, first strand: chain 'C' and resid 327 through 333 removed outlier: 4.032A pdb=" N TYR C 241 " --> pdb=" O ASN C 224 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 245 through 250 removed outlier: 6.966A pdb=" N ARG C 245 " --> pdb=" O HIS C 262 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N GLU C 257 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL C 307 " --> pdb=" O GLU C 257 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 335 through 337 Processing sheet with id=AC2, first strand: chain 'C' and resid 415 through 416 Processing sheet with id=AC3, first strand: chain 'D' and resid 543 through 546 Processing sheet with id=AC4, first strand: chain 'D' and resid 566 through 568 removed outlier: 3.546A pdb=" N GLU D 708 " --> pdb=" O LEU D 566 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE D 706 " --> pdb=" O THR D 568 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN D 714 " --> pdb=" O ILE D 707 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 646 through 652 713 hydrogen bonds defined for protein. 2043 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 13 hydrogen bonds 26 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 51 stacking parallelities Total time for adding SS restraints: 7.72 Time building geometry restraints manager: 3.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 15371 1.03 - 1.23: 36 1.23 - 1.42: 6711 1.42 - 1.61: 9513 1.61 - 1.81: 108 Bond restraints: 31739 Sorted by residual: bond pdb=" OH PTR C 122 " pdb=" P PTR C 122 " ideal model delta sigma weight residual 1.769 1.609 0.160 2.00e-02 2.50e+03 6.36e+01 bond pdb=" OH PTR A 122 " pdb=" P PTR A 122 " ideal model delta sigma weight residual 1.769 1.612 0.157 2.00e-02 2.50e+03 6.15e+01 bond pdb=" C31 IM0 C 901 " pdb=" O2 IM0 C 901 " ideal model delta sigma weight residual 1.243 1.304 -0.061 2.00e-02 2.50e+03 9.22e+00 bond pdb=" N GLY B 405 " pdb=" CA GLY B 405 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.31e+00 bond pdb=" N GLY D 405 " pdb=" CA GLY D 405 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.15e+00 ... (remaining 31734 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 56889 1.97 - 3.95: 521 3.95 - 5.92: 73 5.92 - 7.89: 8 7.89 - 9.86: 2 Bond angle restraints: 57493 Sorted by residual: angle pdb=" OH PTR A 122 " pdb=" P PTR A 122 " pdb=" O2P PTR A 122 " ideal model delta sigma weight residual 99.92 109.78 -9.86 3.00e+00 1.11e-01 1.08e+01 angle pdb=" O3' DA F 7 " pdb=" C3' DA F 7 " pdb=" C2' DA F 7 " ideal model delta sigma weight residual 111.50 115.92 -4.42 1.50e+00 4.44e-01 8.70e+00 angle pdb=" O3' DG E 7 " pdb=" C3' DG E 7 " pdb=" C2' DG E 7 " ideal model delta sigma weight residual 111.50 115.91 -4.41 1.50e+00 4.44e-01 8.64e+00 angle pdb=" OH PTR C 122 " pdb=" P PTR C 122 " pdb=" O2P PTR C 122 " ideal model delta sigma weight residual 99.92 108.14 -8.22 3.00e+00 1.11e-01 7.51e+00 angle pdb=" CA GLU B 711 " pdb=" CB GLU B 711 " pdb=" CG GLU B 711 " ideal model delta sigma weight residual 114.10 119.24 -5.14 2.00e+00 2.50e-01 6.61e+00 ... (remaining 57488 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.76: 13843 26.76 - 53.53: 559 53.53 - 80.29: 109 80.29 - 107.05: 7 107.05 - 133.82: 2 Dihedral angle restraints: 14520 sinusoidal: 8546 harmonic: 5974 Sorted by residual: dihedral pdb=" CA ARG A 32 " pdb=" C ARG A 32 " pdb=" N ALA A 33 " pdb=" CA ALA A 33 " ideal model delta harmonic sigma weight residual -180.00 -159.25 -20.75 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA GLY D 577 " pdb=" C GLY D 577 " pdb=" N GLU D 578 " pdb=" CA GLU D 578 " ideal model delta harmonic sigma weight residual 180.00 -160.21 -19.79 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA ASP B 674 " pdb=" C ASP B 674 " pdb=" N TYR B 675 " pdb=" CA TYR B 675 " ideal model delta harmonic sigma weight residual 180.00 161.76 18.24 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 14517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1938 0.043 - 0.087: 420 0.087 - 0.130: 121 0.130 - 0.173: 22 0.173 - 0.216: 2 Chirality restraints: 2503 Sorted by residual: chirality pdb=" CA PTR A 122 " pdb=" N PTR A 122 " pdb=" C PTR A 122 " pdb=" CB PTR A 122 " both_signs ideal model delta sigma weight residual False 2.35 2.57 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA PTR C 122 " pdb=" N PTR C 122 " pdb=" C PTR C 122 " pdb=" CB PTR C 122 " both_signs ideal model delta sigma weight residual False 2.35 2.54 -0.18 2.00e-01 2.50e+01 8.44e-01 chirality pdb=" CA ILE C 182 " pdb=" N ILE C 182 " pdb=" C ILE C 182 " pdb=" CB ILE C 182 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.92e-01 ... (remaining 2500 not shown) Planarity restraints: 4517 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C27 IM0 C 901 " -0.050 2.00e-02 2.50e+03 8.64e-02 1.86e+02 pdb=" C28 IM0 C 901 " 0.013 2.00e-02 2.50e+03 pdb=" C29 IM0 C 901 " 0.044 2.00e-02 2.50e+03 pdb=" C30 IM0 C 901 " 0.013 2.00e-02 2.50e+03 pdb=" C31 IM0 C 901 " 0.061 2.00e-02 2.50e+03 pdb=" C32 IM0 C 901 " -0.060 2.00e-02 2.50e+03 pdb=" C33 IM0 C 901 " -0.095 2.00e-02 2.50e+03 pdb=" N7 IM0 C 901 " -0.038 2.00e-02 2.50e+03 pdb=" O3 IM0 C 901 " -0.095 2.00e-02 2.50e+03 pdb=" O4 IM0 C 901 " 0.207 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PTR A 122 " -0.036 2.00e-02 2.50e+03 7.15e-02 5.11e+01 pdb=" C PTR A 122 " 0.124 2.00e-02 2.50e+03 pdb=" O PTR A 122 " -0.046 2.00e-02 2.50e+03 pdb=" N THR A 123 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 IM0 C 901 " -0.058 2.00e-02 2.50e+03 6.34e-02 5.03e+01 pdb=" C11 IM0 C 901 " 0.019 2.00e-02 2.50e+03 pdb=" C12 IM0 C 901 " -0.077 2.00e-02 2.50e+03 pdb=" N1 IM0 C 901 " 0.101 2.00e-02 2.50e+03 pdb=" O10 IM0 C 901 " 0.015 2.00e-02 2.50e+03 ... (remaining 4514 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 6358 2.32 - 2.89: 69311 2.89 - 3.46: 71377 3.46 - 4.03: 99477 4.03 - 4.60: 153806 Nonbonded interactions: 400329 Sorted by model distance: nonbonded pdb=" HE ARG C 121 " pdb=" O1P PTR C 122 " model vdw 1.750 2.450 nonbonded pdb=" OD1 ASN A 165 " pdb="HD21 ASN A 169 " model vdw 1.753 2.450 nonbonded pdb=" OE1 GLU B 720 " pdb=" H GLU B 720 " model vdw 1.760 2.450 nonbonded pdb=" O GLU A 314 " pdb="HD21 ASN A 318 " model vdw 1.760 2.450 nonbonded pdb=" OE1 GLN B 646 " pdb="HH21 ARG B 665 " model vdw 1.760 2.450 ... (remaining 400324 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' and resid 8 through 524) } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.540 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: 0.210 Extract box with map and model: 0.620 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 32.880 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.182 16362 Z= 0.270 Angle : 0.590 9.864 22392 Z= 0.310 Chirality : 0.041 0.216 2503 Planarity : 0.004 0.086 2710 Dihedral : 13.503 133.816 6440 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.13 % Allowed : 2.13 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.20), residues: 1824 helix: 2.46 (0.18), residues: 833 sheet: 0.04 (0.38), residues: 184 loop : -1.55 (0.20), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 47 TYR 0.011 0.001 TYR A 266 PHE 0.006 0.001 PHE C 330 TRP 0.004 0.001 TRP B 751 HIS 0.003 0.001 HIS C 339 Details of bonding type rmsd covalent geometry : bond 0.00386 (16360) covalent geometry : angle 0.58992 (22392) hydrogen bonds : bond 0.15553 ( 726) hydrogen bonds : angle 5.51394 ( 2069) Misc. bond : bond 0.18032 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 264 time to evaluate : 0.889 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: D 415 PRO cc_start: 0.7086 (Cg_endo) cc_final: 0.6704 (Cg_exo) REVERT: D 552 MET cc_start: 0.8057 (tpt) cc_final: 0.7721 (tpt) outliers start: 2 outliers final: 1 residues processed: 265 average time/residue: 0.4266 time to fit residues: 150.8354 Evaluate side-chains 143 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 708 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 HIS B 721 GLN C 45 HIS D 569 ASN D 657 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.158511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.118831 restraints weight = 61080.859| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.40 r_work: 0.3161 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16362 Z= 0.168 Angle : 0.522 4.297 22392 Z= 0.294 Chirality : 0.041 0.147 2503 Planarity : 0.004 0.048 2710 Dihedral : 15.976 138.038 2791 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.71 % Allowed : 5.68 % Favored : 93.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.20), residues: 1824 helix: 2.56 (0.18), residues: 842 sheet: -0.03 (0.38), residues: 181 loop : -1.58 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 46 TYR 0.013 0.001 TYR C 266 PHE 0.011 0.001 PHE D 649 TRP 0.006 0.001 TRP C 415 HIS 0.012 0.001 HIS B 679 Details of bonding type rmsd covalent geometry : bond 0.00394 (16360) covalent geometry : angle 0.52182 (22392) hydrogen bonds : bond 0.06137 ( 726) hydrogen bonds : angle 4.53170 ( 2069) Misc. bond : bond 0.00107 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 0.850 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: D 415 PRO cc_start: 0.7460 (Cg_endo) cc_final: 0.7039 (Cg_exo) REVERT: D 794 GLU cc_start: 0.7504 (tt0) cc_final: 0.7276 (tt0) outliers start: 11 outliers final: 9 residues processed: 152 average time/residue: 0.3480 time to fit residues: 74.6209 Evaluate side-chains 135 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 126 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain B residue 660 PHE Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain D residue 708 GLU Chi-restraints excluded: chain D residue 734 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 159 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 82 optimal weight: 0.0870 chunk 119 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 151 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 HIS A 524 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.156610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.118050 restraints weight = 60687.120| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.28 r_work: 0.3132 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16362 Z= 0.163 Angle : 0.511 4.377 22392 Z= 0.287 Chirality : 0.041 0.151 2503 Planarity : 0.004 0.048 2710 Dihedral : 16.126 139.348 2791 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 1.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.65 % Allowed : 6.32 % Favored : 93.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.20), residues: 1824 helix: 2.44 (0.18), residues: 843 sheet: -0.04 (0.38), residues: 181 loop : -1.75 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 46 TYR 0.015 0.001 TYR C 266 PHE 0.008 0.001 PHE B 681 TRP 0.007 0.001 TRP D 629 HIS 0.004 0.001 HIS C 78 Details of bonding type rmsd covalent geometry : bond 0.00383 (16360) covalent geometry : angle 0.51140 (22392) hydrogen bonds : bond 0.06242 ( 726) hydrogen bonds : angle 4.38841 ( 2069) Misc. bond : bond 0.00016 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 0.754 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: D 552 MET cc_start: 0.8312 (tpt) cc_final: 0.7642 (tpt) outliers start: 10 outliers final: 8 residues processed: 142 average time/residue: 0.3510 time to fit residues: 70.3175 Evaluate side-chains 135 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain B residue 660 PHE Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain D residue 734 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 144 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 174 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 171 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS A 471 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.154842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.114705 restraints weight = 59992.539| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.38 r_work: 0.3109 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16362 Z= 0.168 Angle : 0.513 6.509 22392 Z= 0.288 Chirality : 0.041 0.153 2503 Planarity : 0.004 0.051 2710 Dihedral : 16.217 139.536 2788 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.90 % Allowed : 7.16 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.20), residues: 1824 helix: 2.45 (0.18), residues: 841 sheet: -0.00 (0.38), residues: 180 loop : -1.84 (0.20), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 46 TYR 0.014 0.001 TYR C 266 PHE 0.011 0.001 PHE B 719 TRP 0.006 0.001 TRP D 629 HIS 0.004 0.001 HIS C 78 Details of bonding type rmsd covalent geometry : bond 0.00398 (16360) covalent geometry : angle 0.51318 (22392) hydrogen bonds : bond 0.06198 ( 726) hydrogen bonds : angle 4.34714 ( 2069) Misc. bond : bond 0.00034 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.815 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: D 552 MET cc_start: 0.8336 (tpt) cc_final: 0.7661 (tpt) outliers start: 14 outliers final: 10 residues processed: 149 average time/residue: 0.3720 time to fit residues: 77.0314 Evaluate side-chains 144 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain B residue 660 PHE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain D residue 605 MET Chi-restraints excluded: chain D residue 734 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 168 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 chunk 176 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 HIS B 556 GLN C 454 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.153832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.114344 restraints weight = 60405.385| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.32 r_work: 0.3093 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16362 Z= 0.176 Angle : 0.518 4.916 22392 Z= 0.291 Chirality : 0.041 0.154 2503 Planarity : 0.004 0.052 2710 Dihedral : 16.324 141.131 2788 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.70 % Favored : 94.24 % Rotamer: Outliers : 1.03 % Allowed : 7.68 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.20), residues: 1824 helix: 2.40 (0.18), residues: 841 sheet: -0.02 (0.38), residues: 185 loop : -1.91 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 46 TYR 0.014 0.001 TYR C 266 PHE 0.009 0.001 PHE A 368 TRP 0.006 0.001 TRP C 415 HIS 0.004 0.001 HIS C 78 Details of bonding type rmsd covalent geometry : bond 0.00421 (16360) covalent geometry : angle 0.51763 (22392) hydrogen bonds : bond 0.06376 ( 726) hydrogen bonds : angle 4.35829 ( 2069) Misc. bond : bond 0.00032 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 1.107 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: B 689 ARG cc_start: 0.6505 (ptp-110) cc_final: 0.6282 (ptm160) REVERT: D 552 MET cc_start: 0.8348 (tpt) cc_final: 0.7675 (tpt) outliers start: 16 outliers final: 12 residues processed: 146 average time/residue: 0.3695 time to fit residues: 75.9924 Evaluate side-chains 142 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain B residue 660 PHE Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain D residue 481 ASP Chi-restraints excluded: chain D residue 598 GLU Chi-restraints excluded: chain D residue 734 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 105 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 166 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 153 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.154939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.115544 restraints weight = 60115.551| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.28 r_work: 0.3106 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16362 Z= 0.142 Angle : 0.489 6.397 22392 Z= 0.274 Chirality : 0.040 0.149 2503 Planarity : 0.004 0.049 2710 Dihedral : 16.265 141.271 2788 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.54 % Favored : 94.41 % Rotamer: Outliers : 1.16 % Allowed : 7.94 % Favored : 90.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.20), residues: 1824 helix: 2.47 (0.18), residues: 841 sheet: 0.06 (0.38), residues: 184 loop : -1.92 (0.20), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 600 TYR 0.012 0.001 TYR C 266 PHE 0.007 0.001 PHE B 719 TRP 0.005 0.001 TRP C 415 HIS 0.003 0.001 HIS A 78 Details of bonding type rmsd covalent geometry : bond 0.00328 (16360) covalent geometry : angle 0.48945 (22392) hydrogen bonds : bond 0.05714 ( 726) hydrogen bonds : angle 4.21333 ( 2069) Misc. bond : bond 0.00023 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.816 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: D 552 MET cc_start: 0.8287 (tpt) cc_final: 0.7601 (tpt) REVERT: D 728 LYS cc_start: 0.7319 (tttm) cc_final: 0.7075 (tttp) outliers start: 18 outliers final: 14 residues processed: 145 average time/residue: 0.3603 time to fit residues: 74.0875 Evaluate side-chains 143 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain B residue 660 PHE Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 346 ASN Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain D residue 481 ASP Chi-restraints excluded: chain D residue 598 GLU Chi-restraints excluded: chain D residue 605 MET Chi-restraints excluded: chain D residue 734 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 70 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 147 optimal weight: 0.0570 chunk 67 optimal weight: 20.0000 chunk 160 optimal weight: 7.9990 chunk 117 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 overall best weight: 1.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.154614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.114565 restraints weight = 60929.278| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.35 r_work: 0.3115 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16362 Z= 0.175 Angle : 0.517 6.347 22392 Z= 0.289 Chirality : 0.041 0.156 2503 Planarity : 0.004 0.046 2710 Dihedral : 16.410 140.840 2788 Min Nonbonded Distance : 1.716 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.59 % Favored : 94.30 % Rotamer: Outliers : 1.03 % Allowed : 8.52 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.20), residues: 1824 helix: 2.40 (0.17), residues: 835 sheet: 0.02 (0.38), residues: 185 loop : -1.95 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 46 TYR 0.013 0.001 TYR C 266 PHE 0.014 0.001 PHE D 706 TRP 0.006 0.001 TRP C 415 HIS 0.003 0.001 HIS C 78 Details of bonding type rmsd covalent geometry : bond 0.00418 (16360) covalent geometry : angle 0.51689 (22392) hydrogen bonds : bond 0.06309 ( 726) hydrogen bonds : angle 4.32328 ( 2069) Misc. bond : bond 0.00035 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.751 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: D 552 MET cc_start: 0.8199 (tpt) cc_final: 0.7557 (tpt) REVERT: D 728 LYS cc_start: 0.7353 (tttm) cc_final: 0.7123 (tttp) outliers start: 16 outliers final: 11 residues processed: 145 average time/residue: 0.3529 time to fit residues: 72.3984 Evaluate side-chains 141 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain B residue 660 PHE Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 346 ASN Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain D residue 481 ASP Chi-restraints excluded: chain D residue 734 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 130 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.157328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.118609 restraints weight = 60939.816| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.27 r_work: 0.3163 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16362 Z= 0.115 Angle : 0.470 7.436 22392 Z= 0.263 Chirality : 0.039 0.145 2503 Planarity : 0.004 0.042 2710 Dihedral : 16.237 142.246 2788 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.15 % Favored : 94.74 % Rotamer: Outliers : 0.84 % Allowed : 9.10 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.20), residues: 1824 helix: 2.57 (0.18), residues: 836 sheet: 0.06 (0.38), residues: 185 loop : -1.85 (0.20), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 689 TYR 0.009 0.001 TYR C 266 PHE 0.008 0.001 PHE B 719 TRP 0.005 0.001 TRP D 629 HIS 0.002 0.001 HIS A 78 Details of bonding type rmsd covalent geometry : bond 0.00254 (16360) covalent geometry : angle 0.47006 (22392) hydrogen bonds : bond 0.05185 ( 726) hydrogen bonds : angle 4.09572 ( 2069) Misc. bond : bond 0.00009 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 0.790 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: D 552 MET cc_start: 0.8350 (tpt) cc_final: 0.7777 (tpt) REVERT: D 728 LYS cc_start: 0.7362 (tttm) cc_final: 0.7119 (tttp) outliers start: 13 outliers final: 9 residues processed: 138 average time/residue: 0.3486 time to fit residues: 68.3688 Evaluate side-chains 137 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain B residue 660 PHE Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain D residue 598 GLU Chi-restraints excluded: chain D residue 734 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.153809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.113458 restraints weight = 60996.838| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.45 r_work: 0.3090 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16362 Z= 0.191 Angle : 0.529 6.798 22392 Z= 0.296 Chirality : 0.042 0.157 2503 Planarity : 0.004 0.043 2710 Dihedral : 16.484 140.561 2788 Min Nonbonded Distance : 1.702 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.98 % Favored : 93.97 % Rotamer: Outliers : 0.52 % Allowed : 9.61 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.20), residues: 1824 helix: 2.38 (0.18), residues: 836 sheet: 0.17 (0.39), residues: 182 loop : -1.97 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 46 TYR 0.013 0.001 TYR C 266 PHE 0.011 0.001 PHE A 368 TRP 0.006 0.001 TRP C 415 HIS 0.004 0.001 HIS A 78 Details of bonding type rmsd covalent geometry : bond 0.00462 (16360) covalent geometry : angle 0.52923 (22392) hydrogen bonds : bond 0.06523 ( 726) hydrogen bonds : angle 4.33835 ( 2069) Misc. bond : bond 0.00047 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 0.978 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: D 728 LYS cc_start: 0.7360 (tttm) cc_final: 0.7118 (tttp) outliers start: 8 outliers final: 6 residues processed: 133 average time/residue: 0.3450 time to fit residues: 65.7562 Evaluate side-chains 131 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 125 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain B residue 660 PHE Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 292 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 104 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 30 optimal weight: 0.6980 chunk 164 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.157700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.119356 restraints weight = 60705.188| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.27 r_work: 0.3161 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16362 Z= 0.110 Angle : 0.466 7.348 22392 Z= 0.261 Chirality : 0.039 0.142 2503 Planarity : 0.004 0.040 2710 Dihedral : 16.222 142.904 2788 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.93 % Favored : 95.01 % Rotamer: Outliers : 0.45 % Allowed : 9.94 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.20), residues: 1824 helix: 2.60 (0.18), residues: 836 sheet: 0.24 (0.39), residues: 181 loop : -1.85 (0.20), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 600 TYR 0.009 0.001 TYR C 266 PHE 0.008 0.001 PHE B 719 TRP 0.005 0.001 TRP B 647 HIS 0.002 0.001 HIS A 262 Details of bonding type rmsd covalent geometry : bond 0.00243 (16360) covalent geometry : angle 0.46636 (22392) hydrogen bonds : bond 0.04954 ( 726) hydrogen bonds : angle 4.04443 ( 2069) Misc. bond : bond 0.00013 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 129 time to evaluate : 0.816 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: D 552 MET cc_start: 0.8254 (tpt) cc_final: 0.7650 (tpt) REVERT: D 728 LYS cc_start: 0.7353 (tttm) cc_final: 0.7109 (tttp) outliers start: 7 outliers final: 5 residues processed: 133 average time/residue: 0.3385 time to fit residues: 64.5696 Evaluate side-chains 129 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 124 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain B residue 660 PHE Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 292 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 148 optimal weight: 2.9990 chunk 171 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 164 optimal weight: 0.5980 chunk 165 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.155974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.116903 restraints weight = 61027.688| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.28 r_work: 0.3147 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16362 Z= 0.142 Angle : 0.486 7.052 22392 Z= 0.271 Chirality : 0.040 0.150 2503 Planarity : 0.004 0.040 2710 Dihedral : 16.281 141.153 2788 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.59 % Favored : 94.35 % Rotamer: Outliers : 0.32 % Allowed : 10.06 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.20), residues: 1824 helix: 2.56 (0.18), residues: 836 sheet: 0.29 (0.39), residues: 181 loop : -1.88 (0.20), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 46 TYR 0.011 0.001 TYR B 555 PHE 0.008 0.001 PHE A 368 TRP 0.005 0.001 TRP C 415 HIS 0.003 0.001 HIS B 643 Details of bonding type rmsd covalent geometry : bond 0.00333 (16360) covalent geometry : angle 0.48640 (22392) hydrogen bonds : bond 0.05531 ( 726) hydrogen bonds : angle 4.13658 ( 2069) Misc. bond : bond 0.00031 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7362.17 seconds wall clock time: 125 minutes 27.94 seconds (7527.94 seconds total)