Starting phenix.real_space_refine on Thu Aug 6 06:46:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uy7_42794/08_2026/8uy7_42794.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uy7_42794/08_2026/8uy7_42794.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uy7_42794/08_2026/8uy7_42794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uy7_42794/08_2026/8uy7_42794.map" model { file = "/net/cci-nas-00/data/ceres_data/8uy7_42794/08_2026/8uy7_42794.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uy7_42794/08_2026/8uy7_42794.cif" } resolution = 2.93 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= 0.009 sd= 0.114 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: 5 Type Number sf(0) Gaussians Mg 6 5.21 5 S 76 5.16 5 C 8865 2.51 5 N 2358 2.21 5 O 2728 1.98 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-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14033 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 898, 6912 Classifications: {'peptide': 898} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 43, 'TRANS': 854} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'GLN:plan1': 4, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 6915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 898, 6915 Classifications: {'peptide': 898} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 43, 'TRANS': 854} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'GLN:plan1': 4, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 100 Classifications: {'water': 100} Link IDs: {None: 99} Chain: "B" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 100 Classifications: {'water': 100} Link IDs: {None: 99} Time building chain proxies: 3.49, per 1000 atoms: 0.25 Number of scatterers: 14033 At special positions: 0 Unit cell: (97.11, 123.67, 130.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 76 16.00 Mg 6 11.99 O 2728 8.00 N 2358 7.00 C 8865 6.00 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=0, symmetry=0 Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 663.6 milliseconds 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3384 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 10 sheets defined 56.1% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 38 through 48 removed outlier: 3.509A pdb=" N VAL A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 57 removed outlier: 4.186A pdb=" N TRP A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N LYS A 55 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR A 56 " --> pdb=" O GLU A 52 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 77 Processing helix chain 'A' and resid 81 through 85 removed outlier: 4.126A pdb=" N GLN A 85 " --> pdb=" O PRO A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 98 Processing helix chain 'A' and resid 99 through 114 removed outlier: 3.554A pdb=" N THR A 106 " --> pdb=" O ASN A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 153 removed outlier: 3.645A pdb=" N VAL A 123 " --> pdb=" O PHE A 119 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 232 through 236 Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 279 through 312 Proline residue: A 301 - end of helix Processing helix chain 'A' and resid 313 through 326 removed outlier: 3.944A pdb=" N LEU A 319 " --> pdb=" O TRP A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 330 Proline residue: A 330 - end of helix No H-bonds generated for 'chain 'A' and resid 327 through 330' Processing helix chain 'A' and resid 331 through 350 removed outlier: 4.102A pdb=" N MET A 335 " --> pdb=" O GLU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 367 removed outlier: 3.686A pdb=" N ASN A 363 " --> pdb=" O ASP A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 410 removed outlier: 3.628A pdb=" N LEU A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 425 Processing helix chain 'A' and resid 426 through 437 Processing helix chain 'A' and resid 471 through 477 removed outlier: 3.766A pdb=" N VAL A 477 " --> pdb=" O GLU A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 507 Processing helix chain 'A' and resid 528 through 532 Processing helix chain 'A' and resid 550 through 561 Processing helix chain 'A' and resid 572 through 584 Processing helix chain 'A' and resid 593 through 597 removed outlier: 3.660A pdb=" N GLU A 597 " --> pdb=" O GLY A 593 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 593 through 597' Processing helix chain 'A' and resid 600 through 610 removed outlier: 3.740A pdb=" N GLN A 609 " --> pdb=" O ALA A 605 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ARG A 610 " --> pdb=" O ASN A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 629 Processing helix chain 'A' and resid 645 through 652 Processing helix chain 'A' and resid 662 through 669 Processing helix chain 'A' and resid 677 through 717 Processing helix chain 'A' and resid 726 through 742 Processing helix chain 'A' and resid 743 through 747 Processing helix chain 'A' and resid 762 through 773 removed outlier: 4.315A pdb=" N GLY A 766 " --> pdb=" O PRO A 762 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG A 767 " --> pdb=" O ALA A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 790 removed outlier: 3.853A pdb=" N PHE A 779 " --> pdb=" O ILE A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 797 No H-bonds generated for 'chain 'A' and resid 795 through 797' Processing helix chain 'A' and resid 798 through 817 removed outlier: 3.774A pdb=" N PHE A 802 " --> pdb=" O THR A 798 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL A 809 " --> pdb=" O GLY A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 820 No H-bonds generated for 'chain 'A' and resid 818 through 820' Processing helix chain 'A' and resid 834 through 851 Processing helix chain 'A' and resid 855 through 860 removed outlier: 4.364A pdb=" N TYR A 859 " --> pdb=" O PRO A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 895 removed outlier: 4.242A pdb=" N TRP A 872 " --> pdb=" O SER A 868 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLY A 889 " --> pdb=" O GLN A 885 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N PHE A 890 " --> pdb=" O LEU A 886 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR A 891 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 48 removed outlier: 3.671A pdb=" N VAL B 47 " --> pdb=" O LEU B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 57 removed outlier: 4.158A pdb=" N TRP B 54 " --> pdb=" O GLU B 50 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N LYS B 55 " --> pdb=" O GLU B 51 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 77 Processing helix chain 'B' and resid 81 through 85 removed outlier: 4.054A pdb=" N GLN B 85 " --> pdb=" O PRO B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 98 Processing helix chain 'B' and resid 99 through 114 removed outlier: 3.995A pdb=" N LEU B 104 " --> pdb=" O PRO B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 153 removed outlier: 3.559A pdb=" N VAL B 123 " --> pdb=" O PHE B 119 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL B 153 " --> pdb=" O LEU B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'B' and resid 232 through 236 removed outlier: 3.689A pdb=" N GLU B 235 " --> pdb=" O ASN B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 279 through 312 Proline residue: B 301 - end of helix Processing helix chain 'B' and resid 313 through 326 removed outlier: 3.925A pdb=" N LEU B 319 " --> pdb=" O TRP B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 330 Proline residue: B 330 - end of helix No H-bonds generated for 'chain 'B' and resid 327 through 330' Processing helix chain 'B' and resid 331 through 350 removed outlier: 3.983A pdb=" N MET B 335 " --> pdb=" O GLU B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 367 removed outlier: 3.698A pdb=" N ASN B 363 " --> pdb=" O ASP B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 410 removed outlier: 3.617A pdb=" N LEU B 400 " --> pdb=" O SER B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 425 Processing helix chain 'B' and resid 426 through 437 Processing helix chain 'B' and resid 471 through 477 removed outlier: 3.738A pdb=" N VAL B 477 " --> pdb=" O GLU B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 507 Processing helix chain 'B' and resid 528 through 532 Processing helix chain 'B' and resid 550 through 561 Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 595 through 599 removed outlier: 3.814A pdb=" N THR B 598 " --> pdb=" O ASP B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 611 removed outlier: 3.852A pdb=" N GLN B 609 " --> pdb=" O ALA B 605 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ARG B 610 " --> pdb=" O ASN B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 629 Processing helix chain 'B' and resid 642 through 644 No H-bonds generated for 'chain 'B' and resid 642 through 644' Processing helix chain 'B' and resid 645 through 652 Processing helix chain 'B' and resid 662 through 669 Processing helix chain 'B' and resid 677 through 717 Processing helix chain 'B' and resid 726 through 742 Processing helix chain 'B' and resid 743 through 747 Processing helix chain 'B' and resid 762 through 790 removed outlier: 4.319A pdb=" N GLY B 766 " --> pdb=" O PRO B 762 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG B 767 " --> pdb=" O ALA B 763 " (cutoff:3.500A) Proline residue: B 774 - end of helix removed outlier: 3.849A pdb=" N PHE B 779 " --> pdb=" O ILE B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 797 No H-bonds generated for 'chain 'B' and resid 795 through 797' Processing helix chain 'B' and resid 798 through 817 removed outlier: 3.826A pdb=" N PHE B 802 " --> pdb=" O THR B 798 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL B 809 " --> pdb=" O GLY B 805 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 822 Processing helix chain 'B' and resid 834 through 851 Processing helix chain 'B' and resid 855 through 860 removed outlier: 4.374A pdb=" N TYR B 859 " --> pdb=" O PRO B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 895 removed outlier: 4.381A pdb=" N TRP B 872 " --> pdb=" O SER B 868 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLY B 889 " --> pdb=" O GLN B 885 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N PHE B 890 " --> pdb=" O LEU B 886 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR B 891 " --> pdb=" O VAL B 887 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 172 through 175 removed outlier: 4.667A pdb=" N THR A 158 " --> pdb=" O LYS A 186 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N VAL A 246 " --> pdb=" O PHE A 206 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N PHE A 206 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N SER A 248 " --> pdb=" O ASP A 204 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ASP A 204 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N THR A 250 " --> pdb=" O ALA A 202 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ALA A 202 " --> pdb=" O THR A 250 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLN A 252 " --> pdb=" O LEU A 200 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 175 removed outlier: 4.667A pdb=" N THR A 158 " --> pdb=" O LYS A 186 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N VAL A 246 " --> pdb=" O PHE A 206 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N PHE A 206 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N SER A 248 " --> pdb=" O ASP A 204 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ASP A 204 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N THR A 250 " --> pdb=" O ALA A 202 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ALA A 202 " --> pdb=" O THR A 250 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLN A 252 " --> pdb=" O LEU A 200 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.605A pdb=" N GLY A 655 " --> pdb=" O ILE A 671 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N LEU A 673 " --> pdb=" O GLY A 655 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N SER A 657 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL A 636 " --> pdb=" O ILE A 654 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ILE A 656 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N PHE A 638 " --> pdb=" O ILE A 656 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N VAL A 658 " --> pdb=" O PHE A 638 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N LEU A 370 " --> pdb=" O LYS A 566 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU A 568 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N THR A 372 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N PHE A 614 " --> pdb=" O VAL A 565 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE A 567 " --> pdb=" O PHE A 614 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL A 591 " --> pdb=" O ALA A 615 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 385 through 389 removed outlier: 3.923A pdb=" N LEU A 385 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL A 515 " --> pdb=" O GLU A 538 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N TYR A 540 " --> pdb=" O VAL A 513 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL A 513 " --> pdb=" O TYR A 540 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA A 542 " --> pdb=" O ARG A 511 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ARG A 511 " --> pdb=" O ALA A 542 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ALA A 457 " --> pdb=" O LYS A 439 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N LYS A 439 " --> pdb=" O ALA A 457 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 385 through 389 removed outlier: 3.923A pdb=" N LEU A 385 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N CYS A 478 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU A 537 " --> pdb=" O CYS A 478 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N GLN A 480 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N GLY A 539 " --> pdb=" O GLN A 480 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N ARG A 482 " --> pdb=" O GLY A 539 " (cutoff:3.500A) removed outlier: 12.413A pdb=" N ILE A 541 " --> pdb=" O ARG A 482 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 172 through 175 removed outlier: 4.691A pdb=" N THR B 158 " --> pdb=" O LYS B 186 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR B 245 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N PHE B 206 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ASP B 204 " --> pdb=" O GLY B 249 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA B 251 " --> pdb=" O ALA B 202 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ALA B 202 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA B 253 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N LEU B 200 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N VAL B 255 " --> pdb=" O ARG B 198 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ARG B 198 " --> pdb=" O VAL B 255 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 172 through 175 removed outlier: 4.691A pdb=" N THR B 158 " --> pdb=" O LYS B 186 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR B 245 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N PHE B 206 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ASP B 204 " --> pdb=" O GLY B 249 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA B 251 " --> pdb=" O ALA B 202 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ALA B 202 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA B 253 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N LEU B 200 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N VAL B 255 " --> pdb=" O ARG B 198 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ARG B 198 " --> pdb=" O VAL B 255 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 353 through 355 removed outlier: 6.645A pdb=" N GLY B 655 " --> pdb=" O ILE B 671 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N LEU B 673 " --> pdb=" O GLY B 655 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N SER B 657 " --> pdb=" O LEU B 673 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL B 636 " --> pdb=" O ILE B 654 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ILE B 656 " --> pdb=" O VAL B 636 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N PHE B 638 " --> pdb=" O ILE B 656 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N VAL B 658 " --> pdb=" O PHE B 638 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N LEU B 370 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU B 568 " --> pdb=" O LEU B 370 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N THR B 372 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N PHE B 614 " --> pdb=" O VAL B 565 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE B 567 " --> pdb=" O PHE B 614 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL B 591 " --> pdb=" O ALA B 615 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 385 through 389 removed outlier: 3.916A pdb=" N LEU B 385 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL B 515 " --> pdb=" O GLU B 538 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N TYR B 540 " --> pdb=" O VAL B 513 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL B 513 " --> pdb=" O TYR B 540 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA B 542 " --> pdb=" O ARG B 511 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ARG B 511 " --> pdb=" O ALA B 542 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N SER B 453 " --> pdb=" O GLU B 442 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N GLU B 442 " --> pdb=" O SER B 453 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL B 455 " --> pdb=" O ILE B 440 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 385 through 389 removed outlier: 3.916A pdb=" N LEU B 385 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N CYS B 478 " --> pdb=" O LEU B 535 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LEU B 537 " --> pdb=" O CYS B 478 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N GLN B 480 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N GLY B 539 " --> pdb=" O GLN B 480 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N ARG B 482 " --> pdb=" O GLY B 539 " (cutoff:3.500A) removed outlier: 12.464A pdb=" N ILE B 541 " --> pdb=" O ARG B 482 " (cutoff:3.500A) 781 hydrogen bonds defined for protein. 2256 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.26 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2297 1.30 - 1.43: 3401 1.43 - 1.56: 8287 1.56 - 1.68: 0 1.68 - 1.81: 132 Bond restraints: 14117 Sorted by residual: bond pdb=" C ASN A 506 " pdb=" O ASN A 506 " ideal model delta sigma weight residual 1.236 1.179 0.057 1.29e-02 6.01e+03 1.96e+01 bond pdb=" C ASN A 387 " pdb=" O ASN A 387 " ideal model delta sigma weight residual 1.235 1.187 0.049 1.12e-02 7.97e+03 1.89e+01 bond pdb=" C HIS B 388 " pdb=" O HIS B 388 " ideal model delta sigma weight residual 1.235 1.187 0.048 1.23e-02 6.61e+03 1.55e+01 bond pdb=" C HIS A 388 " pdb=" O HIS A 388 " ideal model delta sigma weight residual 1.235 1.190 0.046 1.19e-02 7.06e+03 1.47e+01 bond pdb=" CA THR B 823 " pdb=" C THR B 823 " ideal model delta sigma weight residual 1.522 1.476 0.046 1.24e-02 6.50e+03 1.36e+01 ... (remaining 14112 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 18533 1.79 - 3.57: 581 3.57 - 5.36: 89 5.36 - 7.15: 16 7.15 - 8.93: 7 Bond angle restraints: 19226 Sorted by residual: angle pdb=" N ARG A 825 " pdb=" CA ARG A 825 " pdb=" CB ARG A 825 " ideal model delta sigma weight residual 110.39 101.77 8.62 1.59e+00 3.96e-01 2.94e+01 angle pdb=" N LEU B 23 " pdb=" CA LEU B 23 " pdb=" C LEU B 23 " ideal model delta sigma weight residual 110.31 103.10 7.21 1.38e+00 5.25e-01 2.73e+01 angle pdb=" C ASN A 387 " pdb=" CA ASN A 387 " pdb=" CB ASN A 387 " ideal model delta sigma weight residual 110.14 102.16 7.98 1.60e+00 3.91e-01 2.49e+01 angle pdb=" C GLN B 85 " pdb=" N PRO B 86 " pdb=" CA PRO B 86 " ideal model delta sigma weight residual 119.76 124.70 -4.94 1.00e+00 1.00e+00 2.44e+01 angle pdb=" CA ASN A 506 " pdb=" CB ASN A 506 " pdb=" CG ASN A 506 " ideal model delta sigma weight residual 112.60 117.47 -4.87 1.00e+00 1.00e+00 2.37e+01 ... (remaining 19221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.98: 7759 16.98 - 33.95: 587 33.95 - 50.93: 117 50.93 - 67.91: 16 67.91 - 84.89: 7 Dihedral angle restraints: 8486 sinusoidal: 3280 harmonic: 5206 Sorted by residual: dihedral pdb=" N ASN A 164 " pdb=" C ASN A 164 " pdb=" CA ASN A 164 " pdb=" CB ASN A 164 " ideal model delta harmonic sigma weight residual 122.80 134.15 -11.35 0 2.50e+00 1.60e-01 2.06e+01 dihedral pdb=" C ASN A 387 " pdb=" N ASN A 387 " pdb=" CA ASN A 387 " pdb=" CB ASN A 387 " ideal model delta harmonic sigma weight residual -122.60 -111.49 -11.11 0 2.50e+00 1.60e-01 1.97e+01 dihedral pdb=" C ASN A 164 " pdb=" N ASN A 164 " pdb=" CA ASN A 164 " pdb=" CB ASN A 164 " ideal model delta harmonic sigma weight residual -122.60 -132.94 10.34 0 2.50e+00 1.60e-01 1.71e+01 ... (remaining 8483 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2064 0.083 - 0.167: 195 0.167 - 0.250: 12 0.250 - 0.334: 2 0.334 - 0.417: 1 Chirality restraints: 2274 Sorted by residual: chirality pdb=" CA ASN A 164 " pdb=" N ASN A 164 " pdb=" C ASN A 164 " pdb=" CB ASN A 164 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.35e+00 chirality pdb=" CA PRO A 100 " pdb=" N PRO A 100 " pdb=" C PRO A 100 " pdb=" CB PRO A 100 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA GLN B 528 " pdb=" N GLN B 528 " pdb=" C GLN B 528 " pdb=" CB GLN B 528 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 2271 not shown) Planarity restraints: 2449 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 528 " -0.011 2.00e-02 2.50e+03 2.30e-02 5.28e+00 pdb=" C GLN B 528 " 0.040 2.00e-02 2.50e+03 pdb=" O GLN B 528 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG B 529 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 488 " -0.037 5.00e-02 4.00e+02 5.60e-02 5.02e+00 pdb=" N PRO B 489 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 489 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 489 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 449 " 0.198 9.50e-02 1.11e+02 8.89e-02 4.91e+00 pdb=" NE ARG A 449 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 449 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 449 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 449 " 0.006 2.00e-02 2.50e+03 ... (remaining 2446 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 195 2.63 - 3.19: 12574 3.19 - 3.76: 22162 3.76 - 4.33: 30808 4.33 - 4.90: 51704 Nonbonded interactions: 117443 Sorted by model distance: nonbonded pdb=" OD1 ASN A 709 " pdb="MG MG A1001 " model vdw 2.057 2.170 nonbonded pdb=" OD1 ASN B 709 " pdb="MG MG B1001 " model vdw 2.069 2.170 nonbonded pdb=" OD1 ASP A 441 " pdb="MG MG A1003 " model vdw 2.108 2.170 nonbonded pdb=" OD1 ASP B 191 " pdb="MG MG B1002 " model vdw 2.196 2.170 nonbonded pdb=" OD1 ASP B 426 " pdb=" OG SER B 429 " model vdw 2.198 3.040 ... (remaining 117438 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 'B' and (resid 1 through 164 or (resid 165 through 166 and (name N or nam \ e CA or name C or name O or name CB )) or resid 167 through 1003)) } 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: 5.310 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: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.180 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 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 0.057 14117 Z= 0.295 Angle : 0.738 8.934 19226 Z= 0.457 Chirality : 0.048 0.417 2274 Planarity : 0.006 0.089 2449 Dihedral : 12.806 84.887 5102 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.34 % Allowed : 1.15 % Favored : 98.51 % Cbeta Deviations : 0.18 % 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: 0.34 (0.20), residues: 1792 helix: 1.10 (0.18), residues: 884 sheet: -0.33 (0.33), residues: 194 loop : -0.65 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 650 TYR 0.017 0.001 TYR B 698 PHE 0.017 0.001 PHE B 364 TRP 0.009 0.001 TRP A 89 HIS 0.004 0.001 HIS B 388 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.30 (14117) covalent geometry : angle 0.73765 / 0.46 (19226) hydrogen bonds : bond 0.15213 / 10.71 ( 747) hydrogen bonds : angle 6.63030 / 4.66 ( 2256) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 283 time to evaluate : 0.525 Fit side-chains REVERT: A 203 ARG cc_start: 0.7692 (tpt90) cc_final: 0.7310 (tmt170) REVERT: A 247 VAL cc_start: 0.8975 (t) cc_final: 0.8752 (m) REVERT: A 487 ILE cc_start: 0.8965 (mm) cc_final: 0.8706 (mt) REVERT: A 632 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7382 (mt-10) REVERT: A 823 THR cc_start: 0.8978 (p) cc_final: 0.8573 (t) REVERT: A 895 TYR cc_start: 0.7048 (m-80) cc_final: 0.6729 (m-80) REVERT: B 49 PRO cc_start: 0.8820 (Cg_exo) cc_final: 0.8551 (Cg_endo) REVERT: B 62 GLU cc_start: 0.6610 (pt0) cc_final: 0.6239 (pp20) REVERT: B 290 MET cc_start: 0.8660 (mmm) cc_final: 0.8459 (tpt) REVERT: B 823 THR cc_start: 0.8976 (p) cc_final: 0.8742 (t) REVERT: B 895 TYR cc_start: 0.7133 (m-80) cc_final: 0.6799 (m-80) outliers start: 5 outliers final: 1 residues processed: 288 average time/residue: 0.6308 time to fit residues: 198.6458 Evaluate side-chains 176 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 0.9990 chunk 91 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 54.8452 > 50:) chunk 149 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 169 ASN A 209 GLN A 227 GLN A 506 ASN A 528 GLN ** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 GLN A 830 GLN B 84 GLN B 169 ASN B 209 GLN B 362 GLN B 464 GLN B 753 GLN B 830 GLN B 863 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.124520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.094528 restraints weight = 18039.115| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.07 r_work: 0.2975 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14117 Z= 0.146 Angle : 0.564 8.579 19226 Z= 0.291 Chirality : 0.042 0.155 2274 Planarity : 0.005 0.052 2449 Dihedral : 4.309 28.175 1908 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.96 % Allowed : 10.83 % Favored : 87.20 % 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: 1792 helix: 1.56 (0.18), residues: 908 sheet: 0.15 (0.34), residues: 172 loop : -0.61 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 496 TYR 0.027 0.001 TYR A 698 PHE 0.015 0.001 PHE B 364 TRP 0.013 0.001 TRP A 806 HIS 0.003 0.001 HIS B 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (14117) covalent geometry : angle 0.56410 / 0.29 (19226) hydrogen bonds : bond 0.04356 / 2.94 ( 747) hydrogen bonds : angle 4.74671 / 3.34 ( 2256) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 0.370 Fit side-chains REVERT: A 203 ARG cc_start: 0.8157 (tpt90) cc_final: 0.7810 (tmt170) REVERT: A 487 ILE cc_start: 0.8954 (mm) cc_final: 0.8720 (mt) REVERT: A 632 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7566 (mt-10) REVERT: A 823 THR cc_start: 0.8948 (p) cc_final: 0.8590 (t) REVERT: A 838 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7428 (mmt) REVERT: A 895 TYR cc_start: 0.7219 (m-80) cc_final: 0.6886 (m-80) REVERT: B 85 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.8257 (mt0) REVERT: B 220 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.7427 (tp30) REVERT: B 487 ILE cc_start: 0.8927 (mm) cc_final: 0.8695 (mt) REVERT: B 895 TYR cc_start: 0.7228 (m-80) cc_final: 0.6880 (m-80) outliers start: 29 outliers final: 13 residues processed: 183 average time/residue: 0.6159 time to fit residues: 123.4029 Evaluate side-chains 164 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 717 SER Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 820 MET Chi-restraints excluded: chain A residue 838 MET Chi-restraints excluded: chain A residue 854 SER Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 85 GLN Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 717 SER Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 854 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 23 optimal weight: 3.9990 chunk 58 optimal weight: 0.0570 chunk 37 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 97 optimal weight: 0.0470 chunk 162 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 159 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN ** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 GLN B 102 ASN B 232 ASN B 863 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.125712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.096361 restraints weight = 18216.117| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.05 r_work: 0.3004 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14117 Z= 0.106 Angle : 0.506 8.192 19226 Z= 0.259 Chirality : 0.040 0.141 2274 Planarity : 0.005 0.049 2449 Dihedral : 4.082 27.939 1908 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.11 % Allowed : 11.65 % Favored : 85.24 % 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: 1.21 (0.20), residues: 1792 helix: 1.99 (0.18), residues: 896 sheet: 0.11 (0.35), residues: 172 loop : -0.52 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 529 TYR 0.019 0.001 TYR A 698 PHE 0.011 0.001 PHE A 779 TRP 0.008 0.001 TRP A 806 HIS 0.003 0.000 HIS B 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (14117) covalent geometry : angle 0.50554 / 0.26 (19226) hydrogen bonds : bond 0.03658 / 2.47 ( 747) hydrogen bonds : angle 4.38463 / 3.08 ( 2256) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 165 time to evaluate : 0.567 Fit side-chains REVERT: A 70 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7592 (mp0) REVERT: A 203 ARG cc_start: 0.8136 (tpt90) cc_final: 0.7727 (tpt90) REVERT: A 215 GLU cc_start: 0.7740 (pt0) cc_final: 0.7464 (pt0) REVERT: A 427 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7973 (mp0) REVERT: A 448 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8096 (tm-30) REVERT: A 487 ILE cc_start: 0.8905 (mm) cc_final: 0.8661 (mt) REVERT: A 526 ASP cc_start: 0.7775 (OUTLIER) cc_final: 0.7415 (t0) REVERT: A 632 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7494 (mt-10) REVERT: A 838 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7293 (mtt) REVERT: A 895 TYR cc_start: 0.7094 (m-80) cc_final: 0.6760 (m-80) REVERT: B 70 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7828 (mt-10) REVERT: B 220 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.7093 (tp30) REVERT: B 235 GLU cc_start: 0.9051 (mt-10) cc_final: 0.8851 (mt-10) REVERT: B 359 ASP cc_start: 0.9054 (OUTLIER) cc_final: 0.8846 (p0) REVERT: B 838 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.6971 (mpp) REVERT: B 895 TYR cc_start: 0.7167 (m-80) cc_final: 0.6824 (m-80) outliers start: 46 outliers final: 16 residues processed: 195 average time/residue: 0.6054 time to fit residues: 130.1275 Evaluate side-chains 180 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 717 SER Chi-restraints excluded: chain A residue 820 MET Chi-restraints excluded: chain A residue 838 MET Chi-restraints excluded: chain A residue 854 SER Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain B residue 717 SER Chi-restraints excluded: chain B residue 752 GLU Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 838 MET Chi-restraints excluded: chain B residue 854 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 175 optimal weight: 0.1980 chunk 70 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 114 optimal weight: 0.0370 chunk 163 optimal weight: 0.6980 chunk 158 optimal weight: 0.5980 chunk 171 optimal weight: 0.7980 chunk 39 optimal weight: 0.0980 chunk 87 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 overall best weight: 0.3258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN ** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 GLN B 863 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.126533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.097339 restraints weight = 18094.936| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.05 r_work: 0.3003 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14117 Z= 0.100 Angle : 0.492 8.051 19226 Z= 0.252 Chirality : 0.040 0.138 2274 Planarity : 0.005 0.049 2449 Dihedral : 3.922 27.079 1908 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.71 % Allowed : 13.54 % Favored : 83.75 % 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: 1.32 (0.20), residues: 1792 helix: 2.00 (0.18), residues: 908 sheet: 0.07 (0.33), residues: 196 loop : -0.37 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 496 TYR 0.015 0.001 TYR A 698 PHE 0.010 0.001 PHE A 779 TRP 0.007 0.001 TRP B 806 HIS 0.003 0.000 HIS B 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (14117) covalent geometry : angle 0.49218 / 0.25 (19226) hydrogen bonds : bond 0.03420 / 2.33 ( 747) hydrogen bonds : angle 4.27477 / 3.02 ( 2256) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 159 time to evaluate : 0.570 Fit side-chains REVERT: A 70 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7522 (mp0) REVERT: A 203 ARG cc_start: 0.8127 (tpt90) cc_final: 0.7702 (tpt90) REVERT: A 215 GLU cc_start: 0.7684 (pt0) cc_final: 0.7370 (pt0) REVERT: A 448 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8021 (tm-30) REVERT: A 526 ASP cc_start: 0.7810 (OUTLIER) cc_final: 0.7445 (t0) REVERT: A 632 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7497 (mt-10) REVERT: A 838 MET cc_start: 0.7903 (mmt) cc_final: 0.7248 (mtt) REVERT: A 895 TYR cc_start: 0.6963 (m-80) cc_final: 0.6634 (m-80) REVERT: B 70 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7816 (mp0) REVERT: B 85 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8226 (mt0) REVERT: B 220 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.7121 (tp30) REVERT: B 235 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8798 (mt-10) REVERT: B 250 THR cc_start: 0.9094 (OUTLIER) cc_final: 0.8766 (p) REVERT: B 838 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7112 (mpp) REVERT: B 895 TYR cc_start: 0.7141 (m-80) cc_final: 0.6769 (m-80) outliers start: 40 outliers final: 20 residues processed: 182 average time/residue: 0.6047 time to fit residues: 121.3275 Evaluate side-chains 184 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 717 SER Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 820 MET Chi-restraints excluded: chain A residue 854 SER Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 85 GLN Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 717 SER Chi-restraints excluded: chain B residue 752 GLU Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 838 MET Chi-restraints excluded: chain B residue 851 LEU Chi-restraints excluded: chain B residue 854 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 157 optimal weight: 1.9990 chunk 146 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 113 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 741 GLN B 84 GLN B 863 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.122661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.092139 restraints weight = 18332.805| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.21 r_work: 0.2891 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14117 Z= 0.132 Angle : 0.522 9.265 19226 Z= 0.266 Chirality : 0.041 0.145 2274 Planarity : 0.005 0.047 2449 Dihedral : 3.970 19.761 1908 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.91 % Allowed : 14.29 % Favored : 82.80 % 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: 1.29 (0.20), residues: 1792 helix: 1.98 (0.18), residues: 908 sheet: 0.22 (0.35), residues: 184 loop : -0.43 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 431 TYR 0.017 0.001 TYR B 698 PHE 0.013 0.001 PHE A 779 TRP 0.010 0.001 TRP A 263 HIS 0.003 0.001 HIS B 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.13 (14117) covalent geometry : angle 0.52151 / 0.27 (19226) hydrogen bonds : bond 0.03756 / 2.55 ( 747) hydrogen bonds : angle 4.30314 / 3.04 ( 2256) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 153 time to evaluate : 0.548 Fit side-chains REVERT: A 48 MET cc_start: 0.8586 (tmt) cc_final: 0.8383 (tmt) REVERT: A 70 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7383 (mp0) REVERT: A 144 LYS cc_start: 0.8411 (tttm) cc_final: 0.8143 (tttp) REVERT: A 203 ARG cc_start: 0.8130 (tpt90) cc_final: 0.7666 (tpt90) REVERT: A 215 GLU cc_start: 0.7656 (pt0) cc_final: 0.7336 (pt0) REVERT: A 448 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8060 (tm-30) REVERT: A 487 ILE cc_start: 0.8918 (mm) cc_final: 0.8705 (mt) REVERT: A 632 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7504 (mt-10) REVERT: A 838 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7191 (mtt) REVERT: A 895 TYR cc_start: 0.7039 (m-80) cc_final: 0.6641 (m-80) REVERT: B 70 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7808 (mp0) REVERT: B 85 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.8206 (mt0) REVERT: B 220 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.7126 (tp30) REVERT: B 235 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8640 (mt-10) REVERT: B 250 THR cc_start: 0.8986 (m) cc_final: 0.8707 (p) REVERT: B 632 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7527 (mt-10) REVERT: B 838 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.6975 (mpp) REVERT: B 895 TYR cc_start: 0.7184 (m-80) cc_final: 0.6797 (m-80) outliers start: 43 outliers final: 19 residues processed: 182 average time/residue: 0.6025 time to fit residues: 120.8461 Evaluate side-chains 177 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 717 SER Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 820 MET Chi-restraints excluded: chain A residue 838 MET Chi-restraints excluded: chain A residue 854 SER Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 85 GLN Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 679 MET Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 717 SER Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 838 MET Chi-restraints excluded: chain B residue 854 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 142 optimal weight: 2.9990 chunk 172 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 101 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 150 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 84 GLN B 863 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.122453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.092078 restraints weight = 18296.580| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.20 r_work: 0.2887 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14117 Z= 0.128 Angle : 0.513 8.183 19226 Z= 0.262 Chirality : 0.041 0.144 2274 Planarity : 0.005 0.046 2449 Dihedral : 3.933 14.950 1906 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.84 % Allowed : 14.96 % Favored : 82.19 % 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: 1.33 (0.20), residues: 1792 helix: 2.02 (0.18), residues: 908 sheet: 0.20 (0.35), residues: 184 loop : -0.41 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 431 TYR 0.014 0.001 TYR A 698 PHE 0.013 0.001 PHE A 779 TRP 0.008 0.001 TRP A 263 HIS 0.004 0.001 HIS B 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (14117) covalent geometry : angle 0.51284 / 0.26 (19226) hydrogen bonds : bond 0.03706 / 2.51 ( 747) hydrogen bonds : angle 4.26440 / 3.01 ( 2256) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 150 time to evaluate : 0.634 Fit side-chains REVERT: A 48 MET cc_start: 0.8689 (tmt) cc_final: 0.8481 (tmt) REVERT: A 70 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7748 (mp0) REVERT: A 144 LYS cc_start: 0.8434 (tttm) cc_final: 0.8173 (tttp) REVERT: A 203 ARG cc_start: 0.8153 (tpt90) cc_final: 0.7689 (tpt90) REVERT: A 215 GLU cc_start: 0.7670 (pt0) cc_final: 0.7365 (pt0) REVERT: A 448 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8067 (tm-30) REVERT: A 632 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7542 (mt-10) REVERT: A 838 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.7233 (mtt) REVERT: A 895 TYR cc_start: 0.7032 (m-80) cc_final: 0.6595 (m-80) REVERT: B 70 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7829 (mp0) REVERT: B 85 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.8294 (mt0) REVERT: B 220 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.7130 (tp30) REVERT: B 235 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8620 (mt-10) REVERT: B 250 THR cc_start: 0.8957 (m) cc_final: 0.8693 (p) REVERT: B 632 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7554 (mt-10) REVERT: B 838 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7600 (mtt) REVERT: B 895 TYR cc_start: 0.7183 (m-80) cc_final: 0.6796 (m-80) outliers start: 42 outliers final: 21 residues processed: 179 average time/residue: 0.6068 time to fit residues: 119.8732 Evaluate side-chains 180 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 717 SER Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 820 MET Chi-restraints excluded: chain A residue 838 MET Chi-restraints excluded: chain A residue 854 SER Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 85 GLN Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 752 GLU Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 838 MET Chi-restraints excluded: chain B residue 851 LEU Chi-restraints excluded: chain B residue 854 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 22 optimal weight: 0.6980 chunk 109 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 133 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 150 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 84 GLN B 863 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.122204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.091591 restraints weight = 18165.496| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.20 r_work: 0.2882 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14117 Z= 0.138 Angle : 0.525 7.652 19226 Z= 0.268 Chirality : 0.041 0.144 2274 Planarity : 0.005 0.046 2449 Dihedral : 3.974 15.025 1906 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.18 % Allowed : 15.03 % Favored : 81.79 % 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: 1.30 (0.20), residues: 1792 helix: 1.98 (0.18), residues: 908 sheet: 0.18 (0.35), residues: 184 loop : -0.41 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 431 TYR 0.014 0.001 TYR A 698 PHE 0.013 0.001 PHE A 779 TRP 0.009 0.001 TRP A 263 HIS 0.003 0.001 HIS B 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 (14117) covalent geometry : angle 0.52465 / 0.27 (19226) hydrogen bonds : bond 0.03825 / 2.59 ( 747) hydrogen bonds : angle 4.30050 / 3.03 ( 2256) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 151 time to evaluate : 0.443 Fit side-chains REVERT: A 48 MET cc_start: 0.8778 (tmt) cc_final: 0.8514 (tmt) REVERT: A 70 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7384 (mp0) REVERT: A 144 LYS cc_start: 0.8425 (tttm) cc_final: 0.8160 (tttp) REVERT: A 203 ARG cc_start: 0.8128 (tpt90) cc_final: 0.7653 (tpt90) REVERT: A 262 THR cc_start: 0.8487 (m) cc_final: 0.7914 (p) REVERT: A 448 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8099 (tm-30) REVERT: A 486 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7742 (pm20) REVERT: A 632 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7581 (mt-10) REVERT: A 838 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.7273 (mtt) REVERT: A 895 TYR cc_start: 0.7018 (m-80) cc_final: 0.6594 (m-80) REVERT: B 70 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7817 (mp0) REVERT: B 85 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8265 (mt0) REVERT: B 220 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.7091 (tp30) REVERT: B 250 THR cc_start: 0.8945 (m) cc_final: 0.8683 (p) REVERT: B 262 THR cc_start: 0.8518 (m) cc_final: 0.7955 (p) REVERT: B 448 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6988 (tm-30) REVERT: B 632 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7541 (mt-10) REVERT: B 838 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7615 (mtt) REVERT: B 895 TYR cc_start: 0.7169 (m-80) cc_final: 0.6767 (m-80) outliers start: 47 outliers final: 25 residues processed: 183 average time/residue: 0.5949 time to fit residues: 119.4398 Evaluate side-chains 178 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 717 SER Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 820 MET Chi-restraints excluded: chain A residue 838 MET Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 854 SER Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 85 GLN Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 448 GLU Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 752 GLU Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 838 MET Chi-restraints excluded: chain B residue 851 LEU Chi-restraints excluded: chain B residue 854 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 7 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 97 optimal weight: 0.0270 chunk 131 optimal weight: 0.4980 chunk 121 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 119 optimal weight: 0.0970 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 84 GLN B 863 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.123340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.093106 restraints weight = 18183.752| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.19 r_work: 0.2904 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14117 Z= 0.109 Angle : 0.503 7.681 19226 Z= 0.257 Chirality : 0.040 0.141 2274 Planarity : 0.005 0.047 2449 Dihedral : 3.864 14.447 1906 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.71 % Allowed : 15.64 % Favored : 81.65 % 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: 1.42 (0.20), residues: 1792 helix: 2.12 (0.18), residues: 908 sheet: 0.16 (0.35), residues: 184 loop : -0.38 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 431 TYR 0.012 0.001 TYR A 698 PHE 0.012 0.001 PHE B 779 TRP 0.008 0.001 TRP A 806 HIS 0.003 0.000 HIS B 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (14117) covalent geometry : angle 0.50251 / 0.26 (19226) hydrogen bonds : bond 0.03515 / 2.38 ( 747) hydrogen bonds : angle 4.20889 / 2.98 ( 2256) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 162 time to evaluate : 0.532 Fit side-chains REVERT: A 48 MET cc_start: 0.8751 (tmt) cc_final: 0.8415 (tmt) REVERT: A 70 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7765 (mt-10) REVERT: A 144 LYS cc_start: 0.8410 (tttm) cc_final: 0.8139 (tttp) REVERT: A 203 ARG cc_start: 0.8124 (tpt90) cc_final: 0.7647 (tpt90) REVERT: A 215 GLU cc_start: 0.7654 (pt0) cc_final: 0.7248 (pt0) REVERT: A 351 GLN cc_start: 0.8743 (mt0) cc_final: 0.8493 (mt0) REVERT: A 448 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8074 (tm-30) REVERT: A 632 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7501 (mt-10) REVERT: A 838 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.7290 (mtt) REVERT: A 895 TYR cc_start: 0.7017 (m-80) cc_final: 0.6584 (m-80) REVERT: B 70 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7774 (mp0) REVERT: B 85 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8262 (mt0) REVERT: B 89 TRP cc_start: 0.7883 (p-90) cc_final: 0.7617 (p-90) REVERT: B 220 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.7095 (tp30) REVERT: B 250 THR cc_start: 0.8866 (m) cc_final: 0.8614 (p) REVERT: B 262 THR cc_start: 0.8494 (m) cc_final: 0.7917 (p) REVERT: B 351 GLN cc_start: 0.8743 (mt0) cc_final: 0.8521 (mt0) REVERT: B 487 ILE cc_start: 0.8877 (mm) cc_final: 0.8650 (mm) REVERT: B 632 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7495 (mt-10) REVERT: B 838 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7574 (mtt) REVERT: B 895 TYR cc_start: 0.7081 (m-80) cc_final: 0.6672 (m-80) outliers start: 40 outliers final: 21 residues processed: 190 average time/residue: 0.6359 time to fit residues: 132.7248 Evaluate side-chains 187 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 159 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 717 SER Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 838 MET Chi-restraints excluded: chain A residue 854 SER Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 85 GLN Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 752 GLU Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 838 MET Chi-restraints excluded: chain B residue 851 LEU Chi-restraints excluded: chain B residue 854 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 134 optimal weight: 0.9980 chunk 114 optimal weight: 0.0670 chunk 150 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 174 optimal weight: 0.6980 chunk 101 optimal weight: 0.5980 chunk 152 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 282 GLN B 84 GLN B 863 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.122593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.092356 restraints weight = 18293.688| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.20 r_work: 0.2902 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14117 Z= 0.121 Angle : 0.516 7.864 19226 Z= 0.264 Chirality : 0.041 0.156 2274 Planarity : 0.005 0.047 2449 Dihedral : 3.870 14.687 1906 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.71 % Allowed : 16.18 % Favored : 81.11 % 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: 1.41 (0.20), residues: 1792 helix: 2.11 (0.18), residues: 908 sheet: 0.14 (0.35), residues: 184 loop : -0.39 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 431 TYR 0.013 0.001 TYR B 698 PHE 0.013 0.001 PHE B 779 TRP 0.008 0.001 TRP A 263 HIS 0.003 0.001 HIS B 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.12 (14117) covalent geometry : angle 0.51570 / 0.26 (19226) hydrogen bonds : bond 0.03639 / 2.47 ( 747) hydrogen bonds : angle 4.22331 / 2.99 ( 2256) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 159 time to evaluate : 0.574 Fit side-chains REVERT: A 48 MET cc_start: 0.8905 (tmt) cc_final: 0.8655 (tmt) REVERT: A 144 LYS cc_start: 0.8475 (tttm) cc_final: 0.8210 (tttp) REVERT: A 203 ARG cc_start: 0.8183 (tpt90) cc_final: 0.7711 (tpt90) REVERT: A 262 THR cc_start: 0.8527 (m) cc_final: 0.7970 (p) REVERT: A 351 GLN cc_start: 0.8787 (mt0) cc_final: 0.8566 (mt0) REVERT: A 448 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8099 (tm-30) REVERT: A 632 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7560 (mt-10) REVERT: A 838 MET cc_start: 0.7774 (OUTLIER) cc_final: 0.7381 (mtt) REVERT: A 895 TYR cc_start: 0.7022 (m-80) cc_final: 0.6586 (m-80) REVERT: B 70 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7822 (mp0) REVERT: B 85 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8303 (mt0) REVERT: B 89 TRP cc_start: 0.7919 (p-90) cc_final: 0.7662 (p-90) REVERT: B 220 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.7092 (tp30) REVERT: B 250 THR cc_start: 0.8814 (m) cc_final: 0.8595 (p) REVERT: B 262 THR cc_start: 0.8527 (m) cc_final: 0.7955 (p) REVERT: B 448 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6939 (tm-30) REVERT: B 487 ILE cc_start: 0.8897 (mm) cc_final: 0.8686 (mm) REVERT: B 632 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7551 (mt-10) REVERT: B 838 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7657 (mtt) REVERT: B 895 TYR cc_start: 0.7113 (m-80) cc_final: 0.6693 (m-80) outliers start: 40 outliers final: 23 residues processed: 186 average time/residue: 0.6159 time to fit residues: 126.0644 Evaluate side-chains 184 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 717 SER Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 820 MET Chi-restraints excluded: chain A residue 838 MET Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 854 SER Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 85 GLN Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 448 GLU Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 838 MET Chi-restraints excluded: chain B residue 851 LEU Chi-restraints excluded: chain B residue 854 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 91 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 148 optimal weight: 1.9990 chunk 97 optimal weight: 0.0870 chunk 37 optimal weight: 1.9990 chunk 132 optimal weight: 0.4980 chunk 1 optimal weight: 0.7980 chunk 112 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 = 0.3456 r_free = 0.3456 target = 0.122814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.092463 restraints weight = 18411.698| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.22 r_work: 0.2894 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14117 Z= 0.118 Angle : 0.514 8.206 19226 Z= 0.263 Chirality : 0.041 0.153 2274 Planarity : 0.005 0.050 2449 Dihedral : 3.860 15.007 1906 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.37 % Allowed : 16.18 % Favored : 81.45 % 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: 1.43 (0.20), residues: 1792 helix: 2.11 (0.18), residues: 912 sheet: 0.12 (0.35), residues: 184 loop : -0.37 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 431 TYR 0.012 0.001 TYR A 698 PHE 0.013 0.001 PHE B 779 TRP 0.008 0.001 TRP A 806 HIS 0.003 0.000 HIS B 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (14117) covalent geometry : angle 0.51359 / 0.26 (19226) hydrogen bonds : bond 0.03578 / 2.43 ( 747) hydrogen bonds : angle 4.21035 / 2.98 ( 2256) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 156 time to evaluate : 0.533 Fit side-chains REVERT: A 48 MET cc_start: 0.8936 (tmt) cc_final: 0.8686 (tmt) REVERT: A 144 LYS cc_start: 0.8409 (tttm) cc_final: 0.8141 (tttp) REVERT: A 203 ARG cc_start: 0.8146 (tpt90) cc_final: 0.7663 (tpt90) REVERT: A 262 THR cc_start: 0.8498 (m) cc_final: 0.7943 (p) REVERT: A 351 GLN cc_start: 0.8738 (mt0) cc_final: 0.8489 (mt0) REVERT: A 448 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.7989 (tm-30) REVERT: A 632 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7507 (mt-10) REVERT: A 838 MET cc_start: 0.7691 (OUTLIER) cc_final: 0.7299 (mtt) REVERT: A 895 TYR cc_start: 0.6995 (m-80) cc_final: 0.6547 (m-80) REVERT: B 70 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7797 (mp0) REVERT: B 220 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.7101 (tp30) REVERT: B 250 THR cc_start: 0.8758 (m) cc_final: 0.8522 (p) REVERT: B 262 THR cc_start: 0.8493 (m) cc_final: 0.7925 (p) REVERT: B 448 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6894 (tm-30) REVERT: B 487 ILE cc_start: 0.8875 (mm) cc_final: 0.8659 (mm) REVERT: B 632 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7513 (mt-10) REVERT: B 838 MET cc_start: 0.7951 (OUTLIER) cc_final: 0.7605 (mtt) REVERT: B 895 TYR cc_start: 0.7109 (m-80) cc_final: 0.6686 (m-80) outliers start: 35 outliers final: 25 residues processed: 181 average time/residue: 0.5680 time to fit residues: 113.7259 Evaluate side-chains 184 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 153 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 717 SER Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 820 MET Chi-restraints excluded: chain A residue 838 MET Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 854 SER Chi-restraints excluded: chain B residue 60 HIS Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 448 GLU Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 717 SER Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 838 MET Chi-restraints excluded: chain B residue 851 LEU Chi-restraints excluded: chain B residue 854 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 100 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 165 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 102 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 753 GLN B 60 HIS B 84 GLN B 232 ASN B 753 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.120733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.090098 restraints weight = 18196.406| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.21 r_work: 0.2866 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14117 Z= 0.165 Angle : 0.557 8.826 19226 Z= 0.285 Chirality : 0.042 0.150 2274 Planarity : 0.005 0.047 2449 Dihedral : 4.038 15.257 1906 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.64 % Allowed : 16.32 % Favored : 81.04 % 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: 1.25 (0.20), residues: 1792 helix: 1.98 (0.18), residues: 908 sheet: 0.25 (0.37), residues: 160 loop : -0.50 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 431 TYR 0.014 0.001 TYR A 698 PHE 0.016 0.001 PHE B 779 TRP 0.011 0.001 TRP A 263 HIS 0.004 0.001 HIS A 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.16 (14117) covalent geometry : angle 0.55666 / 0.29 (19226) hydrogen bonds : bond 0.04060 / 2.75 ( 747) hydrogen bonds : angle 4.33729 / 3.06 ( 2256) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4923.77 seconds wall clock time: 84 minutes 49.10 seconds (5089.10 seconds total)