Starting phenix.real_space_refine on Sun Jul 5 23:52:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z9g_14572/07_2026/7z9g_14572_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z9g_14572/07_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_14572/07_2026/7z9g_14572.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z9g_14572/07_2026/7z9g_14572.map" model { file = "/net/cci-nas-00/data/ceres_data/7z9g_14572/07_2026/7z9g_14572_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z9g_14572/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 5.81, 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: 3.17 Conformation dependent library (CDL) restraints added in 914.9 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: 5.26 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: 7.53 Time building geometry restraints manager: 4.35 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=" C3' DC H 24 " pdb=" C2' DC H 24 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.14e+00 bond pdb=" C3' DA F 7 " pdb=" O3' DA F 7 " ideal model delta sigma weight residual 1.435 1.473 -0.038 1.30e-02 5.92e+03 8.55e+00 ... (remaining 31734 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 56819 1.97 - 3.95: 590 3.95 - 5.92: 72 5.92 - 7.89: 10 7.89 - 9.86: 2 Bond angle restraints: 57493 Sorted by residual: angle pdb=" N3 DT H 26 " pdb=" C4 DT H 26 " pdb=" O4 DT H 26 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.76e+01 angle pdb=" N3 DT H 20 " pdb=" C4 DT H 20 " pdb=" O4 DT H 20 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT E 8 " pdb=" C4 DT E 8 " pdb=" O4 DT E 8 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 angle pdb=" N3 DT H 18 " pdb=" C4 DT H 18 " pdb=" O4 DT H 18 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 angle pdb=" N3 DT E 6 " pdb=" C4 DT E 6 " pdb=" O4 DT E 6 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 ... (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: 1906 0.043 - 0.087: 391 0.087 - 0.130: 141 0.130 - 0.173: 63 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.190 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 34.860 Find NCS groups from input model: 0.430 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: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 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 : 0.005 0.182 16362 Z= 0.337 Angle : 0.627 9.864 22392 Z= 0.394 Chirality : 0.046 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/Z covalent geometry : bond 0.00423 / 0.27 (16360) covalent geometry : angle 0.62684 / 0.39 (22392) hydrogen bonds : bond 0.15553 / 10.54 ( 726) hydrogen bonds : angle 5.51394 / 3.95 ( 2069) Misc. bond : bond 0.18032 / 9.06 ( 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 : 0.807 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: 0.3911 time to fit residues: 140.8928 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 : 0.720 ------------------------------------------------------------------------------- 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... A 471 HIS B 721 GLN D 657 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.159628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.121795 restraints weight = 61159.722| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.25 r_work: 0.3173 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16362 Z= 0.176 Angle : 0.534 5.747 22392 Z= 0.310 Chirality : 0.041 0.204 2503 Planarity : 0.004 0.059 2710 Dihedral : 15.813 134.072 2791 Min Nonbonded Distance : 1.682 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.58 % Allowed : 5.74 % Favored : 93.68 % 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: 0.84 (0.20), residues: 1824 helix: 2.54 (0.18), residues: 844 sheet: -0.10 (0.38), residues: 181 loop : -1.59 (0.21), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 438 TYR 0.011 0.001 TYR C 266 PHE 0.012 0.001 PHE B 681 TRP 0.005 0.001 TRP C 415 HIS 0.010 0.001 HIS B 679 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 (16360) covalent geometry : angle 0.53404 / 0.31 (22392) hydrogen bonds : bond 0.06343 / 4.30 ( 726) hydrogen bonds : angle 4.69714 / 3.38 ( 2069) Misc. bond : bond 0.00400 / 0.21 ( 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 153 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 144 time to evaluate : 0.864 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: B 586 GLU cc_start: 0.7667 (tt0) cc_final: 0.7298 (tm-30) REVERT: D 415 PRO cc_start: 0.7468 (Cg_endo) cc_final: 0.7086 (Cg_exo) REVERT: D 552 MET cc_start: 0.8169 (tpt) cc_final: 0.7521 (tpt) outliers start: 9 outliers final: 7 residues processed: 152 average time/residue: 0.3223 time to fit residues: 70.7819 Evaluate side-chains 135 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain D residue 708 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 159 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 82 optimal weight: 7.9990 chunk 119 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 163 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 151 optimal weight: 1.9990 chunk 182 optimal weight: 8.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 471 HIS A 524 ASN C 45 HIS D 569 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.155254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.116129 restraints weight = 61123.580| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.35 r_work: 0.3108 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 16362 Z= 0.233 Angle : 0.573 5.486 22392 Z= 0.328 Chirality : 0.043 0.184 2503 Planarity : 0.005 0.061 2710 Dihedral : 16.126 136.030 2791 Min Nonbonded Distance : 1.698 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.77 % Allowed : 5.94 % Favored : 93.29 % 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: 0.43 (0.20), residues: 1824 helix: 2.25 (0.18), residues: 842 sheet: -0.19 (0.38), residues: 181 loop : -1.89 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 46 TYR 0.021 0.002 TYR B 687 PHE 0.013 0.002 PHE A 368 TRP 0.008 0.001 TRP C 415 HIS 0.005 0.001 HIS B 679 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.23 (16360) covalent geometry : angle 0.57322 / 0.33 (22392) hydrogen bonds : bond 0.07178 / 4.87 ( 726) hydrogen bonds : angle 4.69290 / 3.38 ( 2069) Misc. bond : bond 0.00521 / 0.27 ( 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 149 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 0.609 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: 0.8251 (tpt) cc_final: 0.7638 (tpt) outliers start: 12 outliers final: 11 residues processed: 147 average time/residue: 0.2866 time to fit residues: 59.9497 Evaluate side-chains 138 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 235 THR 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 82 ASP 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: 3.9990 chunk 0 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 174 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 chunk 68 optimal weight: 9.9990 chunk 171 optimal weight: 7.9990 chunk 129 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 471 HIS C 346 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.154422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.113719 restraints weight = 60824.210| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.77 r_work: 0.3093 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16362 Z= 0.227 Angle : 0.562 5.425 22392 Z= 0.323 Chirality : 0.042 0.185 2503 Planarity : 0.005 0.059 2710 Dihedral : 16.196 136.514 2788 Min Nonbonded Distance : 1.681 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 1.03 % Allowed : 6.84 % Favored : 92.13 % 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: 0.22 (0.19), residues: 1824 helix: 2.12 (0.17), residues: 842 sheet: -0.22 (0.38), residues: 181 loop : -2.06 (0.19), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 46 TYR 0.019 0.002 TYR B 687 PHE 0.018 0.002 PHE B 681 TRP 0.008 0.001 TRP C 415 HIS 0.005 0.001 HIS A 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.23 (16360) covalent geometry : angle 0.56170 / 0.32 (22392) hydrogen bonds : bond 0.07104 / 4.83 ( 726) hydrogen bonds : angle 4.67452 / 3.37 ( 2069) Misc. bond : bond 0.00264 / 0.13 ( 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 148 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 461 MET cc_start: 0.8686 (ttp) cc_final: 0.8470 (ttp) REVERT: D 552 MET cc_start: 0.8217 (tpt) cc_final: 0.7546 (tpt) REVERT: D 761 ARG cc_start: 0.7681 (tpt170) cc_final: 0.7420 (tpm170) outliers start: 16 outliers final: 15 residues processed: 144 average time/residue: 0.3055 time to fit residues: 63.3672 Evaluate side-chains 143 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 399 HIS 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 82 ASP 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 Chi-restraints excluded: chain D residue 794 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 168 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 166 optimal weight: 5.9990 chunk 176 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 162 optimal weight: 6.9990 chunk 131 optimal weight: 0.0470 chunk 46 optimal weight: 3.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 471 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.157387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.118835 restraints weight = 60684.347| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.31 r_work: 0.3144 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16362 Z= 0.112 Angle : 0.478 5.158 22392 Z= 0.276 Chirality : 0.039 0.178 2503 Planarity : 0.004 0.056 2710 Dihedral : 16.053 138.441 2788 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.77 % Allowed : 7.23 % Favored : 92.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.20), residues: 1824 helix: 2.40 (0.18), residues: 842 sheet: -0.12 (0.38), residues: 180 loop : -1.93 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 489 TYR 0.010 0.001 TYR A 266 PHE 0.006 0.001 PHE D 719 TRP 0.007 0.001 TRP D 629 HIS 0.004 0.001 HIS B 679 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.11 (16360) covalent geometry : angle 0.47843 / 0.28 (22392) hydrogen bonds : bond 0.05663 / 3.87 ( 726) hydrogen bonds : angle 4.39694 / 3.18 ( 2069) Misc. bond : bond 0.00145 / 0.08 ( 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 142 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.628 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: 0.8258 (tpt) cc_final: 0.7590 (tpt) outliers start: 12 outliers final: 10 residues processed: 137 average time/residue: 0.3159 time to fit residues: 62.1262 Evaluate side-chains 134 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.809 ------------------------------------------------------------------------------- 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 D residue 598 GLU Chi-restraints excluded: chain D residue 605 MET Chi-restraints excluded: chain D residue 734 LEU Chi-restraints excluded: chain D residue 762 MET 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: 8.9990 chunk 97 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 153 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 HIS A 471 HIS D 646 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.157430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.119164 restraints weight = 60431.330| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.25 r_work: 0.3150 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 16362 Z= 0.120 Angle : 0.470 5.192 22392 Z= 0.271 Chirality : 0.039 0.175 2503 Planarity : 0.004 0.053 2710 Dihedral : 16.054 138.730 2788 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.58 % Allowed : 7.35 % Favored : 92.06 % 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: 0.64 (0.20), residues: 1824 helix: 2.50 (0.18), residues: 843 sheet: -0.09 (0.38), residues: 180 loop : -1.87 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 600 TYR 0.011 0.001 TYR C 266 PHE 0.007 0.001 PHE D 706 TRP 0.006 0.001 TRP D 629 HIS 0.003 0.001 HIS B 679 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (16360) covalent geometry : angle 0.46985 / 0.27 (22392) hydrogen bonds : bond 0.05511 / 3.76 ( 726) hydrogen bonds : angle 4.29051 / 3.11 ( 2069) Misc. bond : bond 0.00046 / 0.02 ( 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 137 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 0.846 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: 0.8253 (tpt) cc_final: 0.7648 (tpt) REVERT: D 732 ARG cc_start: 0.7694 (ttm-80) cc_final: 0.7194 (mtm110) outliers start: 9 outliers final: 9 residues processed: 134 average time/residue: 0.3057 time to fit residues: 59.2456 Evaluate side-chains 134 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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 D residue 605 MET Chi-restraints excluded: chain D residue 734 LEU Chi-restraints excluded: chain D residue 762 MET 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: 0.4980 chunk 70 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 147 optimal weight: 0.6980 chunk 67 optimal weight: 8.9990 chunk 160 optimal weight: 8.9990 chunk 117 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.156003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.115669 restraints weight = 60702.401| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.41 r_work: 0.3120 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2704 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= 0.160 Angle : 0.496 5.351 22392 Z= 0.284 Chirality : 0.040 0.179 2503 Planarity : 0.004 0.050 2710 Dihedral : 16.176 137.665 2788 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.58 % Allowed : 7.81 % Favored : 91.61 % 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: 0.59 (0.20), residues: 1824 helix: 2.47 (0.18), residues: 843 sheet: -0.02 (0.38), residues: 180 loop : -1.94 (0.20), 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 0.012 0.001 PHE B 719 TRP 0.006 0.001 TRP C 415 HIS 0.003 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (16360) covalent geometry : angle 0.49554 / 0.28 (22392) hydrogen bonds : bond 0.06058 / 4.13 ( 726) hydrogen bonds : angle 4.33761 / 3.13 ( 2069) Misc. bond : bond 0.00048 / 0.02 ( 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 137 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 0.842 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: 0.8321 (tpt) cc_final: 0.7682 (tpt) REVERT: D 732 ARG cc_start: 0.7690 (ttm-80) cc_final: 0.7145 (mtm110) outliers start: 9 outliers final: 8 residues processed: 135 average time/residue: 0.3318 time to fit residues: 64.1027 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 : 0.824 ------------------------------------------------------------------------------- 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 D residue 605 MET 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: 4.9990 chunk 128 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 65 optimal weight: 0.0770 chunk 13 optimal weight: 0.7980 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 471 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.157910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.119496 restraints weight = 60482.524| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.25 r_work: 0.3159 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16362 Z= 0.107 Angle : 0.458 5.246 22392 Z= 0.263 Chirality : 0.039 0.176 2503 Planarity : 0.004 0.046 2710 Dihedral : 16.149 138.806 2788 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.58 % Allowed : 7.94 % Favored : 91.48 % 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: 2.61 (0.18), residues: 843 sheet: 0.02 (0.38), residues: 180 loop : -1.83 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 600 TYR 0.010 0.001 TYR A 266 PHE 0.011 0.001 PHE B 719 TRP 0.006 0.001 TRP D 629 HIS 0.003 0.001 HIS A 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.11 (16360) covalent geometry : angle 0.45828 / 0.26 (22392) hydrogen bonds : bond 0.05218 / 3.57 ( 726) hydrogen bonds : angle 4.18311 / 3.03 ( 2069) Misc. bond : bond 0.00012 / 0.01 ( 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 141 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 132 time to evaluate : 0.848 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: 0.8266 (tpt) cc_final: 0.7605 (tpt) REVERT: D 732 ARG cc_start: 0.7636 (ttm-80) cc_final: 0.7139 (mtm110) outliers start: 9 outliers final: 8 residues processed: 137 average time/residue: 0.3038 time to fit residues: 59.5186 Evaluate side-chains 137 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 129 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain D residue 605 MET Chi-restraints excluded: chain D residue 734 LEU Chi-restraints excluded: chain D residue 762 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 79 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 471 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.156678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.120360 restraints weight = 60538.076| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.16 r_work: 0.3139 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16362 Z= 0.145 Angle : 0.478 5.390 22392 Z= 0.274 Chirality : 0.040 0.179 2503 Planarity : 0.004 0.044 2710 Dihedral : 16.195 138.735 2788 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.32 % Favored : 94.63 % Rotamer: Outliers : 0.52 % Allowed : 8.06 % Favored : 91.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.73 (0.20), residues: 1824 helix: 2.60 (0.18), residues: 843 sheet: 0.04 (0.38), residues: 180 loop : -1.89 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 46 TYR 0.012 0.001 TYR C 266 PHE 0.009 0.001 PHE B 719 TRP 0.005 0.001 TRP D 629 HIS 0.003 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (16360) covalent geometry : angle 0.47828 / 0.27 (22392) hydrogen bonds : bond 0.05667 / 3.87 ( 726) hydrogen bonds : angle 4.22158 / 3.05 ( 2069) Misc. bond : bond 0.00028 / 0.01 ( 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 141 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 133 time to evaluate : 0.873 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: 0.8222 (tpt) cc_final: 0.7605 (tpt) REVERT: D 732 ARG cc_start: 0.7647 (ttm-80) cc_final: 0.7124 (mtm110) outliers start: 8 outliers final: 7 residues processed: 139 average time/residue: 0.3309 time to fit residues: 66.2089 Evaluate side-chains 137 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 130 time to evaluate : 0.825 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain D residue 605 MET Chi-restraints excluded: chain D residue 734 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: 0.3980 chunk 30 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 130 optimal weight: 0.4980 chunk 37 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 471 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.157445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.118915 restraints weight = 60317.792| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.25 r_work: 0.3152 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 16362 Z= 0.114 Angle : 0.461 5.381 22392 Z= 0.264 Chirality : 0.039 0.178 2503 Planarity : 0.004 0.042 2710 Dihedral : 16.185 139.144 2788 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.52 % Allowed : 8.32 % Favored : 91.16 % 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: 2.65 (0.18), residues: 841 sheet: 0.06 (0.38), residues: 180 loop : -1.84 (0.20), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 600 TYR 0.010 0.001 TYR C 266 PHE 0.009 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/Z covalent geometry : bond 0.00239 / 0.11 (16360) covalent geometry : angle 0.46070 / 0.26 (22392) hydrogen bonds : bond 0.05294 / 3.62 ( 726) hydrogen bonds : angle 4.15622 / 3.01 ( 2069) Misc. bond : bond 0.00023 / 0.01 ( 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 138 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 0.836 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: 0.8262 (tpt) cc_final: 0.7658 (tpt) REVERT: D 732 ARG cc_start: 0.7614 (ttm-80) cc_final: 0.7130 (mtm110) outliers start: 8 outliers final: 8 residues processed: 136 average time/residue: 0.3222 time to fit residues: 63.0063 Evaluate side-chains 137 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 129 time to evaluate : 0.779 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain D residue 605 MET Chi-restraints excluded: chain D residue 734 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: 3.9990 chunk 32 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 165 optimal weight: 0.7980 chunk 176 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 110 optimal weight: 0.0070 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 471 HIS B 556 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.158704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.120450 restraints weight = 60490.215| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.24 r_work: 0.3169 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 16362 Z= 0.105 Angle : 0.449 5.458 22392 Z= 0.257 Chirality : 0.039 0.179 2503 Planarity : 0.004 0.042 2710 Dihedral : 16.155 140.062 2788 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.45 % Allowed : 8.32 % Favored : 91.23 % 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: 2.71 (0.18), residues: 843 sheet: 0.08 (0.38), residues: 180 loop : -1.79 (0.20), residues: 801 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 0.006 0.001 TRP D 725 HIS 0.002 0.001 HIS A 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.11 (16360) covalent geometry : angle 0.44935 / 0.26 (22392) hydrogen bonds : bond 0.04916 / 3.37 ( 726) hydrogen bonds : angle 4.07104 / 2.95 ( 2069) Misc. bond : bond 0.00008 / 0.00 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6338.38 seconds wall clock time: 108 minutes 9.13 seconds (6489.13 seconds total)