Starting phenix.real_space_refine on Mon Sep 14 15:08:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z9k_14573/09_2026/7z9k_14573_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z9k_14573/09_2026/7z9k_14573.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/7z9k_14573/09_2026/7z9k_14573.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z9k_14573/09_2026/7z9k_14573.map" model { file = "/net/cci-nas-00/data/ceres_data/7z9k_14573/09_2026/7z9k_14573_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z9k_14573/09_2026/7z9k_14573_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= 0.002 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 9821 2.51 5 N 2840 2.21 5 O 3171 1.98 5 H 15371 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 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: 31327 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 8213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 8213 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: 6405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 6405 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 15, 'TRANS': 386} Chain: "C" Number of atoms: 8213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 8213 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: 6405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 6405 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: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'IL1': 1} Classifications: {'undetermined': 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: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.89, per 1000 atoms: 0.16 Number of scatterers: 31327 At special positions: 0 Unit cell: (128.14, 138.46, 135.02, 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 3171 8.00 N 2840 7.00 C 9821 6.00 H 15371 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.97 Conformation dependent library (CDL) restraints added in 1.1 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: 73 helices and 23 sheets defined 51.1% alpha, 10.7% beta 9 base pairs and 51 stacking pairs defined. Time for finding SS restraints: 5.09 Creating SS restraints... Processing helix chain 'A' and resid 13 through 30 removed outlier: 3.597A 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: 3.956A pdb=" N VAL A 85 " --> pdb=" O GLY A 81 " (cutoff:3.500A) removed outlier: 3.514A 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: 3.974A pdb=" N LEU A 134 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 4.025A 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 212 removed outlier: 4.178A pdb=" N HIS A 211 " --> pdb=" O GLY A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 236 removed outlier: 4.211A pdb=" N GLU A 230 " --> pdb=" O ARG A 226 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU A 231 " --> pdb=" O ARG A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 283 Processing helix chain 'A' and resid 312 through 324 removed outlier: 3.679A pdb=" N VAL A 316 " --> pdb=" O VAL A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 388 removed outlier: 3.526A pdb=" N ALA A 382 " --> pdb=" O HIS A 378 " (cutoff:3.500A) removed outlier: 3.705A 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: 3.784A pdb=" N ASN A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 425 removed outlier: 3.622A pdb=" N LEU A 424 " --> pdb=" O VAL A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 460 Processing helix chain 'A' and resid 462 through 466 removed outlier: 3.520A pdb=" N LYS A 465 " --> pdb=" O ARG A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 494 removed outlier: 3.590A pdb=" N LEU A 474 " --> pdb=" O GLU A 470 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A 475 " --> pdb=" O HIS A 471 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER A 494 " --> pdb=" O ARG A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 514 removed outlier: 4.198A pdb=" N MET A 499 " --> pdb=" O ALA A 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 436 Processing helix chain 'B' and resid 457 through 464 removed outlier: 3.733A pdb=" N LEU B 462 " --> pdb=" O PHE B 458 " (cutoff:3.500A) removed outlier: 3.611A 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: 3.606A pdb=" N VAL B 522 " --> pdb=" O MET B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 561 removed outlier: 4.192A pdb=" N ALA B 551 " --> pdb=" O LYS B 547 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET B 552 " --> pdb=" O ASP B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 597 removed outlier: 3.539A pdb=" N MET B 597 " --> pdb=" O MET B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 610 removed outlier: 3.555A pdb=" N LEU B 606 " --> pdb=" O PRO B 602 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE B 610 " --> pdb=" O LEU B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 639 removed outlier: 4.104A pdb=" N TRP B 629 " --> pdb=" O THR B 625 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL B 630 " --> pdb=" O VAL B 626 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP B 639 " --> pdb=" O SER B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 684 removed outlier: 3.501A pdb=" N ILE B 682 " --> pdb=" O ASP B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 697 removed outlier: 3.637A pdb=" N ARG B 688 " --> pdb=" O GLY B 684 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS B 696 " --> pdb=" O THR B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 731 removed outlier: 3.789A pdb=" N ALA B 722 " --> pdb=" O SER B 718 " (cutoff:3.500A) 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: 3.836A pdb=" N ALA B 773 " --> pdb=" O ASP B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 795 removed outlier: 4.024A 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 93 removed outlier: 4.119A pdb=" N VAL C 85 " --> pdb=" O GLY C 81 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA C 93 " --> pdb=" O ILE C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 135 removed outlier: 3.741A pdb=" N LEU C 134 " --> pdb=" O ILE C 130 " (cutoff:3.500A) removed outlier: 3.600A 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: 4.249A pdb=" N HIS C 211 " --> pdb=" O GLY C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 236 removed outlier: 3.548A 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: 3.709A pdb=" N TYR C 321 " --> pdb=" O LEU C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 389 removed outlier: 3.535A pdb=" N ILE C 379 " --> pdb=" O ASP C 375 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA C 382 " --> pdb=" O HIS C 378 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN C 389 " --> pdb=" O VAL C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 399 removed outlier: 3.960A 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 427 removed outlier: 3.662A 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 Processing helix chain 'C' and resid 467 through 493 removed outlier: 3.558A pdb=" N LEU C 474 " --> pdb=" O GLU C 470 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU C 475 " --> pdb=" O HIS C 471 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP C 483 " --> pdb=" O LYS C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 514 removed outlier: 3.557A pdb=" N MET C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 435 removed outlier: 3.647A pdb=" N GLN D 434 " --> pdb=" O GLY D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 464 Processing helix chain 'D' and resid 465 through 475 Processing helix chain 'D' and resid 500 through 518 Processing helix chain 'D' and resid 518 through 525 removed outlier: 3.619A 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: 3.585A pdb=" N ARG D 596 " --> pdb=" O LYS D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 602 through 612 removed outlier: 3.580A pdb=" N LEU D 606 " --> pdb=" O PRO D 602 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE D 610 " --> pdb=" O LEU D 606 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TYR D 611 " --> pdb=" O LYS D 607 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN D 612 " --> pdb=" O GLU D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 640 removed outlier: 4.368A pdb=" N ARG D 628 " --> pdb=" O GLN D 624 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 684 Processing helix chain 'D' and resid 684 through 697 removed outlier: 3.549A pdb=" N ARG D 688 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 3.721A 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 removed outlier: 3.759A pdb=" N ALA D 773 " --> pdb=" O ASP D 769 " (cutoff:3.500A) Processing helix chain 'D' and resid 784 through 795 removed outlier: 3.675A pdb=" N ARG D 788 " --> pdb=" O ALA D 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 796 through 801 removed outlier: 3.624A pdb=" N ASN D 801 " --> pdb=" O LEU D 797 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 12 removed outlier: 5.862A pdb=" N VAL A 11 " --> pdb=" O THR B 766 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N VAL B 527 " --> pdb=" O VAL B 765 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ILE B 493 " --> pdb=" O TYR B 528 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ALA B 530 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 6.232A 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: 4.737A 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: 3.746A pdb=" N GLU A 263 " --> pdb=" O ARG A 245 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N GLU A 247 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N VAL A 261 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N GLU A 249 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ILE A 259 " --> pdb=" O GLU A 249 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N GLU A 257 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 307 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL A 304 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LEU A 292 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 6.531A 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: 3.676A pdb=" N TYR A 449 " --> pdb=" O GLY A 442 " (cutoff:3.500A) removed outlier: 3.879A 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: 4.088A 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: 6.633A pdb=" N THR C 9 " --> pdb=" O ARG D 764 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N THR D 766 " --> pdb=" O THR C 9 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N VAL C 11 " --> pdb=" O THR D 766 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N VAL D 527 " --> pdb=" O VAL D 765 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ILE D 493 " --> pdb=" O TYR D 528 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ALA D 530 " --> pdb=" O ILE D 493 " (cutoff:3.500A) removed outlier: 6.290A 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: 3.902A pdb=" N TYR C 241 " --> pdb=" O ASN C 224 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 246 through 250 removed outlier: 6.198A pdb=" N GLU C 257 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 3.916A 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: 3.543A pdb=" N PHE D 706 " --> pdb=" O THR D 568 " (cutoff:3.500A) removed outlier: 3.915A 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 652 708 hydrogen bonds defined for protein. 2028 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 18 hydrogen bonds 36 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 51 stacking parallelities Total time for adding SS restraints: 7.45 Time building geometry restraints manager: 3.98 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: 15363 1.03 - 1.23: 31 1.23 - 1.42: 6710 1.42 - 1.61: 9511 1.61 - 1.81: 109 Bond restraints: 31724 Sorted by residual: bond pdb=" OH PTR C 122 " pdb=" P PTR C 122 " ideal model delta sigma weight residual 1.769 1.612 0.157 2.00e-02 2.50e+03 6.18e+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=" C3' DA F 7 " pdb=" O3' DA F 7 " ideal model delta sigma weight residual 1.435 1.477 -0.042 1.30e-02 5.92e+03 1.03e+01 bond pdb=" C1' DT F 12 " pdb=" N1 DT F 12 " ideal model delta sigma weight residual 1.468 1.511 -0.043 1.40e-02 5.10e+03 9.57e+00 bond pdb=" C3' DG E 7 " pdb=" O3' DG E 7 " ideal model delta sigma weight residual 1.435 1.475 -0.040 1.30e-02 5.92e+03 9.55e+00 ... (remaining 31719 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 56759 1.93 - 3.87: 626 3.87 - 5.80: 73 5.80 - 7.73: 8 7.73 - 9.67: 2 Bond angle restraints: 57468 Sorted by residual: angle pdb=" N3 DT G 32 " pdb=" C4 DT G 32 " pdb=" O4 DT G 32 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT H 19 " pdb=" C4 DT H 19 " pdb=" O4 DT H 19 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.65e+01 angle pdb=" N3 DT E 8 " pdb=" C4 DT E 8 " pdb=" O4 DT E 8 " ideal model delta sigma weight residual 119.90 122.33 -2.43 6.00e-01 2.78e+00 1.64e+01 angle pdb=" N3 DT H 20 " pdb=" C4 DT H 20 " pdb=" O4 DT H 20 " ideal model delta sigma weight residual 119.90 122.33 -2.43 6.00e-01 2.78e+00 1.64e+01 angle pdb=" N3 DT H 17 " pdb=" C4 DT H 17 " pdb=" O4 DT H 17 " ideal model delta sigma weight residual 119.90 122.32 -2.42 6.00e-01 2.78e+00 1.62e+01 ... (remaining 57463 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.29: 13796 25.29 - 50.58: 555 50.58 - 75.86: 155 75.86 - 101.15: 2 101.15 - 126.44: 2 Dihedral angle restraints: 14510 sinusoidal: 8536 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 -157.79 -22.21 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA ARG C 32 " pdb=" C ARG C 32 " pdb=" N ALA C 33 " pdb=" CA ALA C 33 " ideal model delta harmonic sigma weight residual -180.00 -161.49 -18.51 0 5.00e+00 4.00e-02 1.37e+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 -161.77 -18.23 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 14507 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1655 0.033 - 0.066: 574 0.066 - 0.100: 111 0.100 - 0.133: 120 0.133 - 0.166: 43 Chirality restraints: 2503 Sorted by residual: chirality pdb=" CA ILE C 163 " pdb=" N ILE C 163 " pdb=" C ILE C 163 " pdb=" CB ILE C 163 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.90e-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 6.86e-01 chirality pdb=" CA ILE A 163 " pdb=" N ILE A 163 " pdb=" C ILE A 163 " pdb=" CB ILE A 163 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.75e-01 ... (remaining 2500 not shown) Planarity restraints: 4515 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C13 IL1 A 901 " -0.076 2.00e-02 2.50e+03 4.42e-02 3.90e+01 pdb=" C14 IL1 A 901 " 0.018 2.00e-02 2.50e+03 pdb=" C15 IL1 A 901 " 0.030 2.00e-02 2.50e+03 pdb=" C16 IL1 A 901 " 0.028 2.00e-02 2.50e+03 pdb=" C17 IL1 A 901 " 0.017 2.00e-02 2.50e+03 pdb=" C37 IL1 A 901 " 0.030 2.00e-02 2.50e+03 pdb=" N10 IL1 A 901 " 0.029 2.00e-02 2.50e+03 pdb=" N2 IL1 A 901 " -0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C IL1 A 901 " 0.022 2.00e-02 2.50e+03 3.72e-02 3.46e+01 pdb=" O IL1 A 901 " 0.031 2.00e-02 2.50e+03 pdb=" C1 IL1 A 901 " 0.007 2.00e-02 2.50e+03 pdb=" C10 IL1 A 901 " 0.021 2.00e-02 2.50e+03 pdb=" C11 IL1 A 901 " 0.033 2.00e-02 2.50e+03 pdb=" C12 IL1 A 901 " 0.021 2.00e-02 2.50e+03 pdb=" C2 IL1 A 901 " -0.075 2.00e-02 2.50e+03 pdb=" C38 IL1 A 901 " 0.023 2.00e-02 2.50e+03 pdb=" N1 IL1 A 901 " -0.059 2.00e-02 2.50e+03 pdb=" O8 IL1 A 901 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 IL1 A 901 " -0.069 2.00e-02 2.50e+03 3.15e-02 2.23e+01 pdb=" C29 IL1 A 901 " 0.017 2.00e-02 2.50e+03 pdb=" C30 IL1 A 901 " 0.024 2.00e-02 2.50e+03 pdb=" C31 IL1 A 901 " 0.021 2.00e-02 2.50e+03 pdb=" C32 IL1 A 901 " 0.014 2.00e-02 2.50e+03 pdb=" C33 IL1 A 901 " -0.015 2.00e-02 2.50e+03 pdb=" C34 IL1 A 901 " 0.021 2.00e-02 2.50e+03 pdb=" C35 IL1 A 901 " 0.024 2.00e-02 2.50e+03 pdb=" N8 IL1 A 901 " -0.037 2.00e-02 2.50e+03 ... (remaining 4512 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.30: 4889 2.30 - 2.88: 69671 2.88 - 3.45: 71616 3.45 - 4.03: 99802 4.03 - 4.60: 155578 Nonbonded interactions: 401556 Sorted by model distance: nonbonded pdb="HD21 ASN D 569 " pdb=" O LEU D 700 " model vdw 1.725 2.450 nonbonded pdb=" O GLN D 749 " pdb=" HG1 THR D 753 " model vdw 1.730 2.450 nonbonded pdb=" OD1 ASP D 498 " pdb=" H ALA D 499 " model vdw 1.739 2.450 nonbonded pdb=" OE2 GLU D 424 " pdb="HO3' DA F 14 " model vdw 1.742 2.450 nonbonded pdb=" O GLN D 612 " pdb="HH12 ARG D 698 " model vdw 1.749 2.450 ... (remaining 401551 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 8 through 524) selection = chain 'C' } 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: 5.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.150 Extract box with map and model: 0.530 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 33.140 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 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 16355 Z= 0.335 Angle : 0.630 9.667 22381 Z= 0.399 Chirality : 0.045 0.166 2503 Planarity : 0.004 0.048 2710 Dihedral : 13.104 126.440 6438 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.13 % Allowed : 2.26 % Favored : 97.61 % 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: 0.91 (0.20), residues: 1824 helix: 2.61 (0.18), residues: 841 sheet: 0.00 (0.41), residues: 169 loop : -1.54 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 689 TYR 0.010 0.001 TYR C 266 PHE 0.007 0.001 PHE C 96 TRP 0.006 0.001 TRP B 647 HIS 0.003 0.001 HIS A 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.27 (16353) covalent geometry : angle 0.63004 / 0.40 (22381) hydrogen bonds : bond 0.16300 / 10.51 ( 726) hydrogen bonds : angle 5.48063 / 3.90 ( 2064) Misc. bond : bond 0.18152 / 9.11 ( 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 291 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 289 time to evaluate : 0.830 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 406 LYS cc_start: 0.6868 (mmtp) cc_final: 0.6644 (mtmt) REVERT: B 552 MET cc_start: 0.8346 (tpt) cc_final: 0.7857 (tpt) REVERT: B 598 GLU cc_start: 0.7858 (tt0) cc_final: 0.7649 (tt0) REVERT: C 258 THR cc_start: 0.8920 (p) cc_final: 0.8607 (p) REVERT: C 402 THR cc_start: 0.7311 (p) cc_final: 0.6534 (p) REVERT: D 415 PRO cc_start: 0.8236 (Cg_endo) cc_final: 0.7929 (Cg_exo) outliers start: 2 outliers final: 0 residues processed: 291 average time/residue: 0.3613 time to fit residues: 143.7343 Evaluate side-chains 148 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 0.4980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 484 GLN B 531 GLN B 567 HIS C 484 GLN D 657 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.150166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.104219 restraints weight = 67948.756| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.34 r_work: 0.3154 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16355 Z= 0.161 Angle : 0.542 6.751 22381 Z= 0.310 Chirality : 0.041 0.252 2503 Planarity : 0.004 0.050 2710 Dihedral : 15.375 127.275 2786 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.52 % Allowed : 6.19 % 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: 0.92 (0.20), residues: 1824 helix: 2.69 (0.18), residues: 853 sheet: -0.13 (0.41), residues: 170 loop : -1.67 (0.19), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 599 TYR 0.010 0.001 TYR C 266 PHE 0.020 0.001 PHE B 719 TRP 0.006 0.001 TRP A 415 HIS 0.003 0.001 HIS A 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (16353) covalent geometry : angle 0.54205 / 0.31 (22381) hydrogen bonds : bond 0.06235 / 4.08 ( 726) hydrogen bonds : angle 4.74439 / 3.35 ( 2064) Misc. bond : bond 0.00884 / 0.45 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 147 time to evaluate : 0.768 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: B 406 LYS cc_start: 0.7266 (mmtp) cc_final: 0.6711 (mtmt) REVERT: B 552 MET cc_start: 0.8452 (tpt) cc_final: 0.7793 (tpt) REVERT: B 598 GLU cc_start: 0.8428 (tt0) cc_final: 0.8039 (mt-10) REVERT: D 415 PRO cc_start: 0.8474 (Cg_endo) cc_final: 0.8135 (Cg_exo) outliers start: 8 outliers final: 6 residues processed: 151 average time/residue: 0.2959 time to fit residues: 65.7089 Evaluate side-chains 139 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 133 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 458 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 104 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 174 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 591 GLN C 45 HIS ** D 746 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.147160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.100236 restraints weight = 68430.285| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.36 r_work: 0.3083 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16355 Z= 0.180 Angle : 0.543 8.394 22381 Z= 0.307 Chirality : 0.041 0.202 2503 Planarity : 0.004 0.051 2710 Dihedral : 15.761 131.135 2786 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.77 % Allowed : 6.32 % Favored : 92.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.20), residues: 1824 helix: 2.45 (0.17), residues: 853 sheet: -0.07 (0.40), residues: 176 loop : -1.83 (0.19), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 121 TYR 0.012 0.001 TYR C 266 PHE 0.009 0.001 PHE A 330 TRP 0.007 0.001 TRP A 415 HIS 0.006 0.001 HIS A 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (16353) covalent geometry : angle 0.54252 / 0.31 (22381) hydrogen bonds : bond 0.06020 / 3.99 ( 726) hydrogen bonds : angle 4.62535 / 3.27 ( 2064) Misc. bond : bond 0.00585 / 0.30 ( 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 152 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 0.825 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: B 406 LYS cc_start: 0.7355 (mmtp) cc_final: 0.6777 (mtmt) REVERT: B 598 GLU cc_start: 0.8476 (tt0) cc_final: 0.8074 (mt-10) REVERT: C 209 MET cc_start: 0.8680 (mtp) cc_final: 0.8478 (mtp) REVERT: C 516 LYS cc_start: 0.8310 (pttt) cc_final: 0.8050 (tttm) REVERT: D 758 GLU cc_start: 0.7808 (tp30) cc_final: 0.7436 (tp30) outliers start: 12 outliers final: 8 residues processed: 147 average time/residue: 0.2714 time to fit residues: 59.7555 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 : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 660 PHE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 458 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 70 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 182 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 30 optimal weight: 0.0470 chunk 56 optimal weight: 0.2980 chunk 61 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 150 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.148812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.102341 restraints weight = 67643.311| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.36 r_work: 0.3120 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16355 Z= 0.106 Angle : 0.476 6.490 22381 Z= 0.273 Chirality : 0.039 0.246 2503 Planarity : 0.004 0.048 2710 Dihedral : 15.799 133.522 2786 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % 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: 0.87 (0.20), residues: 1824 helix: 2.61 (0.18), residues: 855 sheet: -0.03 (0.40), residues: 176 loop : -1.71 (0.20), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 503 TYR 0.009 0.001 TYR C 266 PHE 0.020 0.001 PHE B 719 TRP 0.005 0.001 TRP A 415 HIS 0.006 0.001 HIS A 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.11 (16353) covalent geometry : angle 0.47596 / 0.27 (22381) hydrogen bonds : bond 0.04949 / 3.28 ( 726) hydrogen bonds : angle 4.40205 / 3.12 ( 2064) Misc. bond : bond 0.00157 / 0.08 ( 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: 12 poor density : 136 time to evaluate : 0.799 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 406 LYS cc_start: 0.7322 (mmtp) cc_final: 0.6745 (mtmt) REVERT: B 552 MET cc_start: 0.8344 (tpt) cc_final: 0.7699 (tpt) REVERT: B 598 GLU cc_start: 0.8570 (tt0) cc_final: 0.8223 (mt-10) REVERT: C 516 LYS cc_start: 0.8310 (pttt) cc_final: 0.8028 (tttm) REVERT: D 758 GLU cc_start: 0.7864 (tp30) cc_final: 0.7443 (tp30) outliers start: 12 outliers final: 10 residues processed: 143 average time/residue: 0.2736 time to fit residues: 59.0345 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 : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 660 PHE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 458 ILE Chi-restraints excluded: chain D residue 491 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 35 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.147373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.100966 restraints weight = 67937.608| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.32 r_work: 0.3096 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16355 Z= 0.142 Angle : 0.491 6.361 22381 Z= 0.280 Chirality : 0.039 0.198 2503 Planarity : 0.004 0.067 2710 Dihedral : 15.898 133.073 2786 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.90 % Allowed : 7.23 % Favored : 91.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.20), residues: 1824 helix: 2.59 (0.17), residues: 857 sheet: -0.06 (0.40), residues: 176 loop : -1.76 (0.20), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 689 TYR 0.010 0.001 TYR C 266 PHE 0.010 0.001 PHE B 719 TRP 0.006 0.001 TRP D 629 HIS 0.004 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (16353) covalent geometry : angle 0.49068 / 0.28 (22381) hydrogen bonds : bond 0.05265 / 3.50 ( 726) hydrogen bonds : angle 4.38482 / 3.11 ( 2064) Misc. bond : bond 0.00050 / 0.02 ( 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 141 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 0.812 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 406 LYS cc_start: 0.7262 (mmtp) cc_final: 0.6715 (mtmt) REVERT: B 598 GLU cc_start: 0.8520 (tt0) cc_final: 0.8198 (mt-10) REVERT: C 516 LYS cc_start: 0.8311 (pttt) cc_final: 0.8034 (tttm) REVERT: D 758 GLU cc_start: 0.7907 (tp30) cc_final: 0.7472 (tp30) outliers start: 14 outliers final: 11 residues processed: 134 average time/residue: 0.2752 time to fit residues: 55.8654 Evaluate side-chains 134 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 660 PHE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 458 ILE Chi-restraints excluded: chain D residue 491 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 59 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 chunk 84 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 chunk 182 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 160 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.145606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.098613 restraints weight = 67893.028| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.42 r_work: 0.3048 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16355 Z= 0.169 Angle : 0.516 6.243 22381 Z= 0.293 Chirality : 0.040 0.215 2503 Planarity : 0.004 0.082 2710 Dihedral : 16.109 130.989 2786 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.03 % Allowed : 7.48 % 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: 0.66 (0.20), residues: 1824 helix: 2.47 (0.17), residues: 857 sheet: -0.11 (0.40), residues: 176 loop : -1.86 (0.19), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 689 TYR 0.012 0.001 TYR C 266 PHE 0.010 0.001 PHE A 330 TRP 0.006 0.001 TRP D 629 HIS 0.006 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (16353) covalent geometry : angle 0.51557 / 0.29 (22381) hydrogen bonds : bond 0.05731 / 3.82 ( 726) hydrogen bonds : angle 4.42877 / 3.14 ( 2064) Misc. bond : bond 0.00049 / 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 138 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 406 LYS cc_start: 0.7393 (mmtp) cc_final: 0.6767 (mtmt) REVERT: B 598 GLU cc_start: 0.8544 (tt0) cc_final: 0.8266 (tt0) REVERT: B 744 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8170 (mt-10) REVERT: C 209 MET cc_start: 0.8663 (mtp) cc_final: 0.8415 (mtp) REVERT: C 279 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7490 (tt0) REVERT: C 405 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.7727 (mp0) REVERT: C 516 LYS cc_start: 0.8368 (pttt) cc_final: 0.8087 (tttm) REVERT: D 758 GLU cc_start: 0.8080 (tp30) cc_final: 0.7673 (tp30) outliers start: 16 outliers final: 11 residues processed: 131 average time/residue: 0.2611 time to fit residues: 52.5446 Evaluate side-chains 130 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 605 MET Chi-restraints excluded: chain B residue 608 GLU Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 660 PHE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 405 GLU Chi-restraints excluded: chain D residue 491 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 87 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 173 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 176 optimal weight: 0.6980 chunk 156 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.144778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.097656 restraints weight = 68482.092| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.48 r_work: 0.3045 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 16355 Z= 0.174 Angle : 0.518 6.194 22381 Z= 0.295 Chirality : 0.040 0.217 2503 Planarity : 0.004 0.049 2710 Dihedral : 16.209 131.202 2786 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.97 % Allowed : 7.68 % Favored : 91.35 % 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: 0.58 (0.20), residues: 1824 helix: 2.41 (0.18), residues: 857 sheet: -0.16 (0.40), residues: 176 loop : -1.91 (0.19), residues: 791 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 0.009 0.001 PHE A 330 TRP 0.006 0.001 TRP D 629 HIS 0.006 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.17 (16353) covalent geometry : angle 0.51835 / 0.29 (22381) hydrogen bonds : bond 0.05857 / 3.92 ( 726) hydrogen bonds : angle 4.43219 / 3.14 ( 2064) 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 136 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 406 LYS cc_start: 0.7401 (mmtp) cc_final: 0.6767 (mtmt) REVERT: B 598 GLU cc_start: 0.8570 (tt0) cc_final: 0.8296 (tt0) REVERT: B 744 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8162 (mt-10) REVERT: C 279 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7520 (tt0) REVERT: C 405 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.7589 (mp0) REVERT: C 516 LYS cc_start: 0.8355 (pttt) cc_final: 0.8073 (tttm) REVERT: D 758 GLU cc_start: 0.8135 (tp30) cc_final: 0.7742 (tp30) outliers start: 15 outliers final: 11 residues processed: 130 average time/residue: 0.2654 time to fit residues: 53.1263 Evaluate side-chains 130 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 605 MET Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 660 PHE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 405 GLU Chi-restraints excluded: chain D residue 491 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 78 optimal weight: 6.9990 chunk 27 optimal weight: 0.4980 chunk 154 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 184 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.145625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.098934 restraints weight = 68125.693| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.44 r_work: 0.3051 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 16355 Z= 0.129 Angle : 0.487 6.161 22381 Z= 0.277 Chirality : 0.039 0.230 2503 Planarity : 0.004 0.047 2710 Dihedral : 16.241 132.363 2786 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.97 % Allowed : 7.68 % Favored : 91.35 % 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: 0.71 (0.20), residues: 1824 helix: 2.51 (0.18), residues: 856 sheet: -0.15 (0.40), residues: 176 loop : -1.82 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 46 TYR 0.010 0.001 TYR C 266 PHE 0.011 0.001 PHE D 719 TRP 0.006 0.001 TRP D 629 HIS 0.004 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (16353) covalent geometry : angle 0.48730 / 0.28 (22381) hydrogen bonds : bond 0.05341 / 3.57 ( 726) hydrogen bonds : angle 4.29323 / 3.05 ( 2064) Misc. bond : bond 0.00019 / 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 135 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 406 LYS cc_start: 0.7442 (mmtp) cc_final: 0.6734 (mtmt) REVERT: B 598 GLU cc_start: 0.8603 (tt0) cc_final: 0.8274 (mt-10) REVERT: B 744 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8229 (mt-10) REVERT: C 209 MET cc_start: 0.8637 (mtp) cc_final: 0.8392 (mtp) REVERT: C 279 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7543 (tt0) REVERT: C 504 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.8025 (mp0) REVERT: C 516 LYS cc_start: 0.8357 (pttt) cc_final: 0.8078 (tttm) outliers start: 15 outliers final: 12 residues processed: 130 average time/residue: 0.2542 time to fit residues: 50.9294 Evaluate side-chains 131 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain B residue 605 MET Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 660 PHE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain D residue 491 HIS Chi-restraints excluded: chain D residue 663 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 95 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 26 optimal weight: 0.4980 chunk 62 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 176 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.147001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.100538 restraints weight = 68013.703| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.40 r_work: 0.3074 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 16355 Z= 0.107 Angle : 0.468 6.181 22381 Z= 0.267 Chirality : 0.039 0.219 2503 Planarity : 0.004 0.048 2710 Dihedral : 16.221 133.066 2786 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.84 % Allowed : 7.87 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.20), residues: 1824 helix: 2.59 (0.18), residues: 859 sheet: -0.12 (0.40), residues: 176 loop : -1.77 (0.20), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 689 TYR 0.008 0.001 TYR C 266 PHE 0.012 0.001 PHE D 719 TRP 0.006 0.001 TRP D 629 HIS 0.004 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.11 (16353) covalent geometry : angle 0.46826 / 0.27 (22381) hydrogen bonds : bond 0.04931 / 3.29 ( 726) hydrogen bonds : angle 4.19327 / 2.98 ( 2064) Misc. bond : bond 0.00017 / 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 137 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 406 LYS cc_start: 0.7356 (mmtp) cc_final: 0.6666 (mtmt) REVERT: B 598 GLU cc_start: 0.8610 (tt0) cc_final: 0.8289 (mt-10) REVERT: B 744 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8243 (mt-10) REVERT: C 209 MET cc_start: 0.8562 (mtp) cc_final: 0.8325 (mtp) REVERT: C 279 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7554 (tt0) REVERT: C 504 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7994 (mp0) REVERT: C 516 LYS cc_start: 0.8323 (pttt) cc_final: 0.8040 (tttm) REVERT: D 597 MET cc_start: 0.6333 (ptp) cc_final: 0.6048 (ptp) outliers start: 13 outliers final: 10 residues processed: 132 average time/residue: 0.2757 time to fit residues: 55.0456 Evaluate side-chains 131 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain B residue 605 MET Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 660 PHE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain D residue 491 HIS Chi-restraints excluded: chain D residue 663 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 29 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 172 optimal weight: 10.0000 chunk 31 optimal weight: 0.7980 chunk 142 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 164 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 319 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.146008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.099716 restraints weight = 68006.745| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.38 r_work: 0.3071 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 16355 Z= 0.133 Angle : 0.482 6.196 22381 Z= 0.273 Chirality : 0.039 0.198 2503 Planarity : 0.004 0.045 2710 Dihedral : 16.253 131.971 2786 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.90 % Allowed : 7.87 % 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: 0.75 (0.20), residues: 1824 helix: 2.53 (0.18), residues: 860 sheet: -0.14 (0.40), residues: 176 loop : -1.81 (0.20), residues: 788 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 0.012 0.001 PHE D 719 TRP 0.006 0.001 TRP D 629 HIS 0.004 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (16353) covalent geometry : angle 0.48157 / 0.27 (22381) hydrogen bonds : bond 0.05174 / 3.46 ( 726) hydrogen bonds : angle 4.19978 / 2.99 ( 2064) Misc. bond : bond 0.00027 / 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 136 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 406 LYS cc_start: 0.7330 (mmtp) cc_final: 0.6612 (mtmt) REVERT: B 598 GLU cc_start: 0.8600 (tt0) cc_final: 0.8277 (mt-10) REVERT: B 744 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8227 (mt-10) REVERT: C 209 MET cc_start: 0.8566 (mtp) cc_final: 0.8334 (mtp) REVERT: C 279 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7547 (tt0) REVERT: C 405 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.7597 (mp0) REVERT: C 504 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7954 (mp0) REVERT: C 516 LYS cc_start: 0.8336 (pttt) cc_final: 0.8049 (tttm) outliers start: 14 outliers final: 11 residues processed: 129 average time/residue: 0.2728 time to fit residues: 53.5319 Evaluate side-chains 134 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain B residue 605 MET Chi-restraints excluded: chain B residue 608 GLU Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 660 PHE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 405 GLU Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain D residue 491 HIS Chi-restraints excluded: chain D residue 663 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 140 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 126 optimal weight: 0.7980 chunk 160 optimal weight: 9.9990 chunk 134 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 89 optimal weight: 0.5980 chunk 177 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 163 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.146736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.101028 restraints weight = 67896.354| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.29 r_work: 0.3081 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 16355 Z= 0.113 Angle : 0.470 6.174 22381 Z= 0.267 Chirality : 0.039 0.215 2503 Planarity : 0.004 0.048 2710 Dihedral : 16.271 131.917 2786 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.90 % Allowed : 7.74 % Favored : 91.35 % 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: 0.80 (0.20), residues: 1824 helix: 2.58 (0.18), residues: 860 sheet: -0.13 (0.40), residues: 176 loop : -1.78 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 46 TYR 0.008 0.001 TYR C 266 PHE 0.013 0.001 PHE D 719 TRP 0.005 0.001 TRP D 629 HIS 0.004 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (16353) covalent geometry : angle 0.46965 / 0.27 (22381) hydrogen bonds : bond 0.04926 / 3.29 ( 726) hydrogen bonds : angle 4.14339 / 2.95 ( 2064) Misc. bond : bond 0.00017 / 0.01 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7512.73 seconds wall clock time: 127 minutes 48.02 seconds (7668.02 seconds total)