Starting phenix.real_space_refine on Mon Sep 14 14:57:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z9g_14572/09_2026/7z9g_14572_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z9g_14572/09_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_14572/09_2026/7z9g_14572.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z9g_14572/09_2026/7z9g_14572.map" model { file = "/net/cci-nas-00/data/ceres_data/7z9g_14572/09_2026/7z9g_14572_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z9g_14572/09_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-2.2.1-6174/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: 6.40, per 1000 atoms: 0.20 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: 3.33 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 5.68 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: 8.63 Time building geometry restraints manager: 4.46 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.240 Extract box with map and model: 0.560 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 37.800 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.080 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.070 ------------------------------------------------------------------------------- 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 : 0.628 9.864 22392 Z= 0.396 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 0.62824 / 0.40 (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 : 0.878 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: 0.3993 time to fit residues: 144.6802 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 : 0.888 ------------------------------------------------------------------------------- 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 = 0.3955 r_free = 0.3955 target = 0.159680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.120379 restraints weight = 61146.457| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.74 r_work: 0.3179 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16362 Z= 0.172 Angle : 0.532 5.954 22392 Z= 0.307 Chirality : 0.041 0.216 2503 Planarity : 0.004 0.058 2710 Dihedral : 15.821 134.395 2791 Min Nonbonded Distance : 1.693 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.58 % Allowed : 5.68 % Favored : 93.74 % 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: 0.85 (0.20), residues: 1824 helix: 2.55 (0.18), residues: 844 sheet: -0.09 (0.38), residues: 181 loop : -1.58 (0.21), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 438 TYR 0.011 0.001 TYR C 266 PHE 0.010 0.001 PHE B 791 TRP 0.005 0.001 TRP C 415 HIS 0.008 0.001 HIS B 679 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (16360) covalent geometry : angle 0.53207 / 0.31 (22392) hydrogen bonds : bond 0.06451 / 4.38 ( 726) hydrogen bonds : angle 4.70993 / 3.39 ( 2069) Misc. bond : bond 0.00757 / 0.37 ( 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 152 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 143 time to evaluate : 0.822 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: 0.7706 (tt0) cc_final: 0.7282 (tm-30) REVERT: D 415 PRO cc_start: 0.7611 (Cg_endo) cc_final: 0.7228 (Cg_exo) REVERT: D 552 MET cc_start: 0.8222 (tpt) cc_final: 0.7594 (tpt) REVERT: D 761 ARG cc_start: 0.7763 (ttm110) cc_final: 0.7453 (tpm170) outliers start: 9 outliers final: 7 residues processed: 151 average time/residue: 0.3361 time to fit residues: 73.4203 Evaluate side-chains 138 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 131 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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: 0.1980 chunk 42 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 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: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 471 HIS A 524 ASN B 679 HIS C 45 HIS D 569 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.158203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.118504 restraints weight = 60907.809| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.55 r_work: 0.3156 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16362 Z= 0.160 Angle : 0.506 5.680 22392 Z= 0.292 Chirality : 0.040 0.194 2503 Planarity : 0.004 0.059 2710 Dihedral : 15.952 137.284 2791 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.77 % Allowed : 5.61 % 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: 0.75 (0.20), residues: 1824 helix: 2.51 (0.18), residues: 842 sheet: -0.09 (0.38), residues: 181 loop : -1.69 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 68 TYR 0.023 0.001 TYR B 687 PHE 0.009 0.001 PHE A 368 TRP 0.007 0.001 TRP C 415 HIS 0.004 0.001 HIS B 679 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (16360) covalent geometry : angle 0.50635 / 0.29 (22392) hydrogen bonds : bond 0.06164 / 4.19 ( 726) hydrogen bonds : angle 4.52106 / 3.26 ( 2069) Misc. bond : bond 0.00556 / 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 148 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 0.772 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: 0.7391 (Cg_endo) cc_final: 0.6989 (Cg_exo) outliers start: 12 outliers final: 10 residues processed: 147 average time/residue: 0.3200 time to fit residues: 68.3560 Evaluate side-chains 136 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.821 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- 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: 1.9990 chunk 73 optimal weight: 10.0000 chunk 174 optimal weight: 0.8980 chunk 119 optimal weight: 4.9990 chunk 68 optimal weight: 9.9990 chunk 171 optimal weight: 8.9990 chunk 129 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 471 HIS D 646 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.155873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.116232 restraints weight = 60707.113| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.53 r_work: 0.3117 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16362 Z= 0.189 Angle : 0.526 5.598 22392 Z= 0.302 Chirality : 0.041 0.193 2503 Planarity : 0.004 0.055 2710 Dihedral : 16.124 137.392 2791 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.84 % Allowed : 6.39 % Favored : 92.77 % 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: 0.55 (0.20), residues: 1824 helix: 2.38 (0.18), residues: 842 sheet: -0.14 (0.38), residues: 181 loop : -1.86 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 46 TYR 0.020 0.001 TYR B 687 PHE 0.025 0.002 PHE B 681 TRP 0.007 0.001 TRP C 415 HIS 0.005 0.001 HIS C 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 (16360) covalent geometry : angle 0.52624 / 0.30 (22392) hydrogen bonds : bond 0.06484 / 4.41 ( 726) hydrogen bonds : angle 4.51023 / 3.25 ( 2069) Misc. bond : bond 0.00081 / 0.04 ( 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 146 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.862 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 415 PRO cc_start: 0.7538 (Cg_endo) cc_final: 0.7132 (Cg_exo) REVERT: D 552 MET cc_start: 0.8178 (tpt) cc_final: 0.7501 (tpt) outliers start: 13 outliers final: 12 residues processed: 143 average time/residue: 0.3266 time to fit residues: 67.8297 Evaluate side-chains 139 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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 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 708 GLU 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: 0.0570 chunk 31 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 166 optimal weight: 0.6980 chunk 176 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 162 optimal weight: 6.9990 chunk 131 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- 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 = 0.3941 r_free = 0.3941 target = 0.158515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.120755 restraints weight = 60712.517| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.33 r_work: 0.3163 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 16362 Z= 0.111 Angle : 0.468 5.460 22392 Z= 0.270 Chirality : 0.039 0.188 2503 Planarity : 0.004 0.052 2710 Dihedral : 16.040 138.646 2791 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.77 % Allowed : 6.77 % Favored : 92.45 % 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: 0.76 (0.20), residues: 1824 helix: 2.58 (0.18), residues: 842 sheet: -0.11 (0.38), residues: 181 loop : -1.75 (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 0.006 0.001 PHE D 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 0.00220 / 0.11 (16360) covalent geometry : angle 0.46809 / 0.27 (22392) hydrogen bonds : bond 0.05435 / 3.72 ( 726) hydrogen bonds : angle 4.29323 / 3.11 ( 2069) Misc. bond : bond 0.00060 / 0.03 ( 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 : 1.021 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: 0.8241 (tpt) cc_final: 0.7651 (tpt) outliers start: 12 outliers final: 12 residues processed: 138 average time/residue: 0.3346 time to fit residues: 66.7034 Evaluate side-chains 140 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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 598 GLU Chi-restraints excluded: chain D residue 605 MET Chi-restraints excluded: chain D residue 708 GLU 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: 0.6980 chunk 182 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 166 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 153 optimal weight: 0.0870 overall best weight: 0.9162 ------------------------------------------------------------------------------- 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 = 0.3939 r_free = 0.3939 target = 0.158389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.119903 restraints weight = 60483.544| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.27 r_work: 0.3165 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16362 Z= 0.118 Angle : 0.462 5.518 22392 Z= 0.266 Chirality : 0.039 0.188 2503 Planarity : 0.004 0.049 2710 Dihedral : 16.056 138.648 2791 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.65 % Allowed : 7.16 % Favored : 92.19 % 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: 0.81 (0.20), residues: 1824 helix: 2.62 (0.18), residues: 843 sheet: -0.06 (0.38), residues: 180 loop : -1.75 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 667 TYR 0.010 0.001 TYR C 266 PHE 0.009 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 0.00250 / 0.12 (16360) covalent geometry : angle 0.46204 / 0.27 (22392) hydrogen bonds : bond 0.05333 / 3.65 ( 726) hydrogen bonds : angle 4.22090 / 3.06 ( 2069) Misc. bond : bond 0.00031 / 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 139 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 0.808 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: 0.8256 (tpt) cc_final: 0.7656 (tpt) outliers start: 10 outliers final: 10 residues processed: 136 average time/residue: 0.3257 time to fit residues: 64.1906 Evaluate side-chains 137 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 0.823 ------------------------------------------------------------------------------- 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 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: 0.0170 chunk 70 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 147 optimal weight: 0.5980 chunk 67 optimal weight: 9.9990 chunk 160 optimal weight: 8.9990 chunk 117 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 overall best weight: 1.1224 ------------------------------------------------------------------------------- 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 = 0.3932 r_free = 0.3932 target = 0.157811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.119862 restraints weight = 60584.632| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.31 r_work: 0.3153 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16362 Z= 0.125 Angle : 0.465 5.620 22392 Z= 0.267 Chirality : 0.039 0.190 2503 Planarity : 0.004 0.047 2710 Dihedral : 16.092 138.278 2788 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.77 % Allowed : 7.16 % 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: 0.83 (0.20), residues: 1824 helix: 2.66 (0.18), residues: 843 sheet: -0.03 (0.38), residues: 180 loop : -1.77 (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 0.010 0.001 PHE B 719 TRP 0.005 0.001 TRP D 629 HIS 0.003 0.001 HIS C 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (16360) covalent geometry : angle 0.46520 / 0.27 (22392) hydrogen bonds : bond 0.05383 / 3.68 ( 726) hydrogen bonds : angle 4.18900 / 3.03 ( 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 139 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.879 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: 0.8234 (tpt) cc_final: 0.7632 (tpt) outliers start: 12 outliers final: 12 residues processed: 134 average time/residue: 0.3431 time to fit residues: 66.2318 Evaluate side-chains 138 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.816 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 130 optimal weight: 0.0170 chunk 128 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3950 r_free = 0.3950 target = 0.159377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.121109 restraints weight = 60521.246| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.29 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: 0.8599 moved from start: 0.2629 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= 0.101 Angle : 0.448 5.625 22392 Z= 0.257 Chirality : 0.039 0.191 2503 Planarity : 0.004 0.045 2710 Dihedral : 16.084 139.114 2788 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.71 % Allowed : 7.16 % 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: 0.93 (0.20), residues: 1824 helix: 2.73 (0.18), residues: 845 sheet: 0.01 (0.38), residues: 180 loop : -1.71 (0.20), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 444 TYR 0.009 0.001 TYR A 266 PHE 0.009 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 0.00200 / 0.10 (16360) covalent geometry : angle 0.44778 / 0.26 (22392) hydrogen bonds : bond 0.04858 / 3.33 ( 726) hydrogen bonds : angle 4.07657 / 2.95 ( 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 144 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 0.832 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: 0.8275 (tpt) cc_final: 0.7691 (tpt) outliers start: 11 outliers final: 10 residues processed: 140 average time/residue: 0.3317 time to fit residues: 67.5410 Evaluate side-chains 138 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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 344 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 79 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 161 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3932 r_free = 0.3932 target = 0.157775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.119808 restraints weight = 60605.705| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.26 r_work: 0.3151 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16362 Z= 0.134 Angle : 0.468 5.777 22392 Z= 0.267 Chirality : 0.039 0.193 2503 Planarity : 0.004 0.043 2710 Dihedral : 16.127 138.932 2788 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.65 % Allowed : 7.35 % 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: 0.89 (0.20), residues: 1824 helix: 2.71 (0.18), residues: 843 sheet: 0.02 (0.38), residues: 181 loop : -1.75 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 46 TYR 0.011 0.001 TYR C 266 PHE 0.008 0.001 PHE B 719 TRP 0.005 0.001 TRP C 415 HIS 0.003 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (16360) covalent geometry : angle 0.46781 / 0.27 (22392) hydrogen bonds : bond 0.05326 / 3.64 ( 726) hydrogen bonds : angle 4.12284 / 2.98 ( 2069) Misc. bond : bond 0.00032 / 0.02 ( 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 139 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 0.905 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: 0.8272 (tpt) cc_final: 0.7688 (tpt) outliers start: 10 outliers final: 10 residues processed: 135 average time/residue: 0.3326 time to fit residues: 65.3337 Evaluate side-chains 138 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.839 ------------------------------------------------------------------------------- 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 344 ILE Chi-restraints excluded: chain D residue 598 GLU Chi-restraints excluded: chain D residue 605 MET Chi-restraints excluded: chain D residue 637 LEU 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: 1.9990 chunk 30 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 77 optimal weight: 0.4980 chunk 36 optimal weight: 0.5980 chunk 99 optimal weight: 0.9980 chunk 115 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3938 r_free = 0.3938 target = 0.158272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.119982 restraints weight = 60457.430| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.28 r_work: 0.3160 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16362 Z= 0.116 Angle : 0.457 5.765 22392 Z= 0.261 Chirality : 0.039 0.192 2503 Planarity : 0.004 0.042 2710 Dihedral : 16.140 139.264 2788 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.65 % Allowed : 7.61 % Favored : 91.74 % 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: 0.93 (0.20), residues: 1824 helix: 2.74 (0.18), residues: 844 sheet: 0.03 (0.38), residues: 181 loop : -1.73 (0.20), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 46 TYR 0.010 0.001 TYR C 266 PHE 0.008 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 0.00250 / 0.12 (16360) covalent geometry : angle 0.45724 / 0.26 (22392) hydrogen bonds : bond 0.05121 / 3.51 ( 726) hydrogen bonds : angle 4.08204 / 2.95 ( 2069) Misc. bond : bond 0.00017 / 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 139 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 0.792 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 552 MET cc_start: 0.8247 (tpt) cc_final: 0.7648 (tpt) outliers start: 10 outliers final: 10 residues processed: 135 average time/residue: 0.3232 time to fit residues: 63.5352 Evaluate side-chains 138 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.812 ------------------------------------------------------------------------------- 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 344 ILE Chi-restraints excluded: chain D residue 598 GLU Chi-restraints excluded: chain D residue 605 MET Chi-restraints excluded: chain D residue 637 LEU 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: 9.9990 chunk 32 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 176 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.156726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.118240 restraints weight = 60749.054| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.32 r_work: 0.3132 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16362 Z= 0.149 Angle : 0.482 5.914 22392 Z= 0.274 Chirality : 0.040 0.194 2503 Planarity : 0.004 0.043 2710 Dihedral : 16.216 139.400 2788 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.43 % Favored : 94.52 % Rotamer: Outliers : 0.77 % Allowed : 7.42 % Favored : 91.81 % 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: 2.67 (0.18), residues: 843 sheet: 0.04 (0.38), residues: 181 loop : -1.80 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 46 TYR 0.012 0.001 TYR C 266 PHE 0.008 0.001 PHE A 368 TRP 0.005 0.001 TRP C 415 HIS 0.003 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (16360) covalent geometry : angle 0.48229 / 0.27 (22392) hydrogen bonds : bond 0.05638 / 3.85 ( 726) hydrogen bonds : angle 4.15405 / 3.00 ( 2069) Misc. bond : bond 0.00016 / 0.01 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6380.51 seconds wall clock time: 109 minutes 3.71 seconds (6543.71 seconds total)