Starting phenix.real_space_refine on Thu Jun 4 20:49:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zkv_74386/06_2026/9zkv_74386.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zkv_74386/06_2026/9zkv_74386.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zkv_74386/06_2026/9zkv_74386.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zkv_74386/06_2026/9zkv_74386.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zkv_74386/06_2026/9zkv_74386.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zkv_74386/06_2026/9zkv_74386.map" } resolution = 3.45 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= 0.000 sd= 0.018 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 P 3 5.49 5 S 90 5.16 5 C 9786 2.51 5 N 2372 2.21 5 O 2649 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14900 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 2962 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 13, 'TRANS': 389} Chain breaks: 1 Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 11, 'ASN:plan1': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASP:plan': 8, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 118 Chain: "B" Number of atoms: 2950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 2950 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 11, 'TRANS': 391} Chain breaks: 1 Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 13, 'ARG:plan': 3, 'ASP:plan': 6, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 107 Chain: "C" Number of atoms: 2962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 2962 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 13, 'TRANS': 389} Chain breaks: 1 Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 11, 'ASN:plan1': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASP:plan': 8, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 118 Chain: "D" Number of atoms: 2954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 2954 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 391} Chain breaks: 1 Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 167 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 12, 'ARG:plan': 3, 'ASP:plan': 6, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 103 Chain: "G" Number of atoms: 1354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1354 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 1355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1355 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {'OLC': 2, 'PLM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Unusual residues: {'OLC': 2, 'PLM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 104 Unusual residues: {'OLC': 2, 'PLM': 1, 'POV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Unusual residues: {'OLC': 2, 'PLM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Time building chain proxies: 4.20, per 1000 atoms: 0.28 Number of scatterers: 14900 At special positions: 0 Unit cell: (103.95, 116.325, 133.65, 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 90 16.00 P 3 15.00 O 2649 8.00 N 2372 7.00 C 9786 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 714 " - pdb=" SG CYS A 769 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.02 Simple disulfide: pdb=" SG CYS C 714 " - pdb=" SG CYS C 769 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS G 52 " - pdb=" SG CYS G 91 " distance=2.03 Simple disulfide: pdb=" SG CYS G 90 " - pdb=" SG CYS G 100 " distance=2.03 Simple disulfide: pdb=" SG CYS H 52 " - pdb=" SG CYS H 91 " distance=2.03 Simple disulfide: pdb=" SG CYS H 90 " - pdb=" SG CYS H 100 " distance=2.03 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: 1.46 Conformation dependent library (CDL) restraints added in 590.2 milliseconds 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3576 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 19 sheets defined 57.3% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 407 through 411 Processing helix chain 'A' and resid 412 through 417 removed outlier: 3.834A pdb=" N TYR A 417 " --> pdb=" O ASN A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 433 Processing helix chain 'A' and resid 457 through 465 Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 511 through 515 Processing helix chain 'A' and resid 517 through 540 removed outlier: 3.954A pdb=" N ILE A 521 " --> pdb=" O LEU A 517 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TRP A 522 " --> pdb=" O ALA A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 581 Processing helix chain 'A' and resid 591 through 626 Processing helix chain 'A' and resid 631 through 637 Processing helix chain 'A' and resid 649 through 658 Processing helix chain 'A' and resid 660 through 671 Processing helix chain 'A' and resid 681 through 692 Processing helix chain 'A' and resid 702 through 711 Processing helix chain 'A' and resid 739 through 753 Processing helix chain 'A' and resid 753 through 763 removed outlier: 3.628A pdb=" N LYS A 759 " --> pdb=" O LEU A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 813 removed outlier: 3.668A pdb=" N PHE A 792 " --> pdb=" O VAL A 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 436 removed outlier: 3.513A pdb=" N ASP B 427 " --> pdb=" O GLY B 423 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 428 " --> pdb=" O TYR B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 469 removed outlier: 3.760A pdb=" N TYR B 469 " --> pdb=" O GLY B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 489 removed outlier: 3.815A pdb=" N VAL B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 522 through 547 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 626 Processing helix chain 'B' and resid 635 through 643 removed outlier: 3.832A pdb=" N THR B 643 " --> pdb=" O LEU B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 662 Processing helix chain 'B' and resid 666 through 676 Processing helix chain 'B' and resid 685 through 696 Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 742 through 756 removed outlier: 3.706A pdb=" N ASN B 747 " --> pdb=" O ARG B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'B' and resid 775 through 780 removed outlier: 3.766A pdb=" N ASP B 779 " --> pdb=" O SER B 775 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER B 780 " --> pdb=" O GLY B 776 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 775 through 780' Processing helix chain 'B' and resid 792 through 819 removed outlier: 3.542A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 415 Processing helix chain 'C' and resid 419 through 433 Processing helix chain 'C' and resid 459 through 465 Processing helix chain 'C' and resid 478 through 483 Processing helix chain 'C' and resid 511 through 515 removed outlier: 3.833A pdb=" N ASP C 515 " --> pdb=" O SER C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 540 Processing helix chain 'C' and resid 568 through 581 removed outlier: 3.578A pdb=" N MET C 581 " --> pdb=" O LEU C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 626 Processing helix chain 'C' and resid 631 through 638 removed outlier: 3.648A pdb=" N LEU C 635 " --> pdb=" O SER C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 657 removed outlier: 3.636A pdb=" N GLU C 653 " --> pdb=" O GLY C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 660 through 672 Processing helix chain 'C' and resid 681 through 692 Processing helix chain 'C' and resid 702 through 711 Processing helix chain 'C' and resid 739 through 752 removed outlier: 3.700A pdb=" N ASN C 743 " --> pdb=" O ARG C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 754 through 764 removed outlier: 3.886A pdb=" N LYS C 759 " --> pdb=" O LEU C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 775 Processing helix chain 'C' and resid 788 through 813 removed outlier: 3.724A pdb=" N PHE C 792 " --> pdb=" O VAL C 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 421 removed outlier: 3.535A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 462 through 469 Processing helix chain 'D' and resid 482 through 488 removed outlier: 4.160A pdb=" N VAL D 488 " --> pdb=" O VAL D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 519 Processing helix chain 'D' and resid 522 through 547 Processing helix chain 'D' and resid 572 through 585 removed outlier: 4.183A pdb=" N TRP D 578 " --> pdb=" O PHE D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 626 Processing helix chain 'D' and resid 635 through 643 Processing helix chain 'D' and resid 653 through 661 removed outlier: 3.629A pdb=" N PHE D 659 " --> pdb=" O THR D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 676 Processing helix chain 'D' and resid 685 through 695 Processing helix chain 'D' and resid 706 through 714 Processing helix chain 'D' and resid 743 through 756 removed outlier: 3.518A pdb=" N ASN D 747 " --> pdb=" O ARG D 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 768 Processing helix chain 'D' and resid 792 through 819 removed outlier: 3.954A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 41 Processing helix chain 'G' and resid 116 through 128 Processing helix chain 'G' and resid 128 through 151 removed outlier: 3.695A pdb=" N ILE G 132 " --> pdb=" O SER G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 184 removed outlier: 3.861A pdb=" N ALA G 184 " --> pdb=" O ILE G 180 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 235 removed outlier: 3.770A pdb=" N TYR G 206 " --> pdb=" O GLY G 202 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 41 Processing helix chain 'H' and resid 116 through 128 Processing helix chain 'H' and resid 128 through 151 removed outlier: 3.628A pdb=" N ILE H 132 " --> pdb=" O SER H 128 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 182 removed outlier: 3.791A pdb=" N LEU H 159 " --> pdb=" O ARG H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 235 removed outlier: 4.021A pdb=" N TYR H 206 " --> pdb=" O GLY H 202 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 391 through 395 removed outlier: 3.831A pdb=" N ARG A 437 " --> pdb=" O TYR A 391 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 471 through 476 removed outlier: 3.534A pdb=" N ALA A 731 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ALA A 473 " --> pdb=" O GLY A 729 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N GLY A 729 " --> pdb=" O ALA A 473 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU A 475 " --> pdb=" O GLY A 727 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLY A 727 " --> pdb=" O LEU A 475 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 471 through 476 removed outlier: 3.534A pdb=" N ALA A 731 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ALA A 473 " --> pdb=" O GLY A 729 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N GLY A 729 " --> pdb=" O ALA A 473 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU A 475 " --> pdb=" O GLY A 727 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLY A 727 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET A 492 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 642 through 644 removed outlier: 8.127A pdb=" N TYR A 696 " --> pdb=" O LYS A 501 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS A 501 " --> pdb=" O TYR A 696 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE A 498 " --> pdb=" O VAL A 719 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA6, first strand: chain 'B' and resid 475 through 480 removed outlier: 7.923A pdb=" N ALA B 477 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ALA B 735 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LEU B 479 " --> pdb=" O GLY B 733 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY B 733 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.990A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.607A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 391 through 395 removed outlier: 6.583A pdb=" N TYR C 391 " --> pdb=" O ARG C 437 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N GLU C 439 " --> pdb=" O TYR C 391 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N VAL C 393 " --> pdb=" O GLU C 439 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 403 through 404 Processing sheet with id=AB1, first strand: chain 'C' and resid 447 through 449 Processing sheet with id=AB2, first strand: chain 'C' and resid 486 through 487 removed outlier: 4.095A pdb=" N ASP C 486 " --> pdb=" O THR C 732 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR C 732 " --> pdb=" O ASP C 486 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 642 through 645 removed outlier: 7.040A pdb=" N ALA C 642 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N LEU C 699 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N GLY C 644 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 9.428A pdb=" N GLU C 701 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N TYR C 696 " --> pdb=" O LYS C 501 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LYS C 501 " --> pdb=" O TYR C 696 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE C 498 " --> pdb=" O VAL C 719 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 397 through 398 removed outlier: 6.311A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AB6, first strand: chain 'D' and resid 475 through 480 removed outlier: 3.792A pdb=" N ALA D 735 " --> pdb=" O ALA D 475 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ALA D 477 " --> pdb=" O GLY D 733 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLY D 733 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU D 479 " --> pdb=" O GLY D 731 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLY D 731 " --> pdb=" O LEU D 479 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 475 through 480 removed outlier: 3.792A pdb=" N ALA D 735 " --> pdb=" O ALA D 475 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ALA D 477 " --> pdb=" O GLY D 733 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLY D 733 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU D 479 " --> pdb=" O GLY D 731 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLY D 731 " --> pdb=" O LEU D 479 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 646 through 648 removed outlier: 8.646A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 100 through 102 Processing sheet with id=AC1, first strand: chain 'H' and resid 100 through 102 884 hydrogen bonds defined for protein. 2556 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: 2.68 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2474 1.33 - 1.45: 4064 1.45 - 1.57: 8515 1.57 - 1.70: 6 1.70 - 1.82: 140 Bond restraints: 15199 Sorted by residual: bond pdb=" O12 POV G 501 " pdb=" P POV G 501 " ideal model delta sigma weight residual 1.657 1.605 0.052 2.00e-02 2.50e+03 6.65e+00 bond pdb=" O12 POV C1003 " pdb=" P POV C1003 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.52e+00 bond pdb=" O12 POV H 501 " pdb=" P POV H 501 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.50e+00 bond pdb=" C11 POV C1003 " pdb=" O12 POV C1003 " ideal model delta sigma weight residual 1.408 1.455 -0.047 2.00e-02 2.50e+03 5.62e+00 bond pdb=" C11 POV G 501 " pdb=" O12 POV G 501 " ideal model delta sigma weight residual 1.408 1.455 -0.047 2.00e-02 2.50e+03 5.45e+00 ... (remaining 15194 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 20099 2.13 - 4.27: 376 4.27 - 6.40: 61 6.40 - 8.53: 15 8.53 - 10.66: 5 Bond angle restraints: 20556 Sorted by residual: angle pdb=" N GLU G 228 " pdb=" CA GLU G 228 " pdb=" CB GLU G 228 " ideal model delta sigma weight residual 110.30 118.71 -8.41 1.54e+00 4.22e-01 2.98e+01 angle pdb=" CA GLU G 228 " pdb=" CB GLU G 228 " pdb=" CG GLU G 228 " ideal model delta sigma weight residual 114.10 122.34 -8.24 2.00e+00 2.50e-01 1.70e+01 angle pdb=" N GLU G 216 " pdb=" CA GLU G 216 " pdb=" CB GLU G 216 " ideal model delta sigma weight residual 110.28 116.62 -6.34 1.55e+00 4.16e-01 1.68e+01 angle pdb=" C ILE G 227 " pdb=" N GLU G 228 " pdb=" CA GLU G 228 " ideal model delta sigma weight residual 120.68 114.12 6.56 1.70e+00 3.46e-01 1.49e+01 angle pdb=" CB MET B 408 " pdb=" CG MET B 408 " pdb=" SD MET B 408 " ideal model delta sigma weight residual 112.70 123.36 -10.66 3.00e+00 1.11e-01 1.26e+01 ... (remaining 20551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.35: 8718 34.35 - 68.69: 143 68.69 - 103.04: 18 103.04 - 137.39: 11 137.39 - 171.73: 3 Dihedral angle restraints: 8893 sinusoidal: 3273 harmonic: 5620 Sorted by residual: dihedral pdb=" CB CYS H 52 " pdb=" SG CYS H 52 " pdb=" SG CYS H 91 " pdb=" CB CYS H 91 " ideal model delta sinusoidal sigma weight residual -86.00 -152.39 66.39 1 1.00e+01 1.00e-02 5.76e+01 dihedral pdb=" CB CYS A 714 " pdb=" SG CYS A 714 " pdb=" SG CYS A 769 " pdb=" CB CYS A 769 " ideal model delta sinusoidal sigma weight residual 93.00 145.12 -52.12 1 1.00e+01 1.00e-02 3.71e+01 dihedral pdb=" CB CYS D 718 " pdb=" SG CYS D 718 " pdb=" SG CYS D 773 " pdb=" CB CYS D 773 " ideal model delta sinusoidal sigma weight residual -86.00 -129.47 43.47 1 1.00e+01 1.00e-02 2.63e+01 ... (remaining 8890 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1912 0.056 - 0.112: 385 0.112 - 0.168: 58 0.168 - 0.224: 7 0.224 - 0.280: 1 Chirality restraints: 2363 Sorted by residual: chirality pdb=" CB THR B 443 " pdb=" CA THR B 443 " pdb=" OG1 THR B 443 " pdb=" CG2 THR B 443 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CB ILE C 396 " pdb=" CA ILE C 396 " pdb=" CG1 ILE C 396 " pdb=" CG2 ILE C 396 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CB ILE D 664 " pdb=" CA ILE D 664 " pdb=" CG1 ILE D 664 " pdb=" CG2 ILE D 664 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.79e-01 ... (remaining 2360 not shown) Planarity restraints: 2519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 716 " 0.048 5.00e-02 4.00e+02 7.25e-02 8.40e+00 pdb=" N PRO B 717 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO B 717 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 717 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 626 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.62e+00 pdb=" C VAL D 626 " -0.044 2.00e-02 2.50e+03 pdb=" O VAL D 626 " 0.017 2.00e-02 2.50e+03 pdb=" N GLU D 627 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE H 177 " -0.013 2.00e-02 2.50e+03 2.56e-02 6.53e+00 pdb=" C ILE H 177 " 0.044 2.00e-02 2.50e+03 pdb=" O ILE H 177 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL H 178 " -0.015 2.00e-02 2.50e+03 ... (remaining 2516 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1242 2.74 - 3.28: 15294 3.28 - 3.82: 24901 3.82 - 4.36: 27489 4.36 - 4.90: 48559 Nonbonded interactions: 117485 Sorted by model distance: nonbonded pdb=" OG1 THR G 82 " pdb=" O CYS G 90 " model vdw 2.205 3.040 nonbonded pdb=" OG1 THR C 394 " pdb=" OE2 GLU C 439 " model vdw 2.283 3.040 nonbonded pdb=" O PHE A 580 " pdb=" OG1 THR A 605 " model vdw 2.311 3.040 nonbonded pdb=" OE1 GLU C 423 " pdb=" NE1 TRP C 762 " model vdw 2.351 3.120 nonbonded pdb=" O23 OLC A1002 " pdb=" O20 OLC A1003 " model vdw 2.352 3.040 ... (remaining 117480 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 393 through 398 or resid 400 through 403 or resid 405 thro \ ugh 407 or resid 412 through 414 or resid 416 through 422 or resid 424 through 4 \ 29 or (resid 430 and (name N or name CA or name C or name O or name CB )) or res \ id 431 or resid 433 or resid 436 or resid 438 or resid 440 through 441 or resid \ 443 through 450 or resid 452 through 454 or resid 456 through 461 or (resid 462 \ and (name N or name CA or name C or name O or name CB )) or resid 463 through 46 \ 6 or (resid 468 through 469 and (name N or name CA or name C or name O or name C \ B )) or resid 471 or resid 473 through 481 or (resid 482 through 483 and (name N \ or name CA or name C or name O or name CB )) or resid 484 through 543 or (resid \ 565 and (name N or name CA or name C or name O or name CB )) or resid 566 throu \ gh 581 or resid 583 through 629 or (resid 630 and (name N or name CA or name C o \ r name O or name CB )) or resid 631 through 635 or (resid 637 through 640 and (n \ ame N or name CA or name C or name O or name CB )) or resid 641 through 646 or r \ esid 649 or (resid 650 and (name N or name CA or name C or name O or name CB )) \ or resid 651 or (resid 652 through 653 and (name N or name CA or name C or name \ O or name CB )) or resid 654 through 663 or resid 665 through 669 or (resid 670 \ and (name N or name CA or name C or name O or name CB )) or resid 672 through 67 \ 5 or (resid 676 and (name N or name CA or name C or name O or name CB )) or resi \ d 677 through 682 or resid 684 through 685 or resid 688 through 733 or (resid 73 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 735 through \ 736 or resid 738 through 739 or resid 742 through 749 or resid 751 through 753 o \ r resid 755 through 759 or resid 761 through 771 or resid 776 through 777 or res \ id 779 through 795 or resid 797 through 811 or (resid 812 through 813 and (name \ N or name CA or name C or name O or name CB )) or resid 1001 through 1002)) selection = (chain 'B' and (resid 397 through 401 or (resid 402 and (name N or name CA or na \ me C or name O or name CB )) or resid 404 through 407 or resid 409 through 411 o \ r resid 416 through 418 or resid 420 through 426 or resid 428 through 435 or res \ id 437 or resid 440 or resid 442 or resid 444 through 445 or resid 447 through 4 \ 54 or (resid 456 through 458 and (name N or name CA or name C or name O or name \ CB )) or resid 460 through 470 or resid 472 through 473 or resid 475 or resid 47 \ 7 through 486 or (resid 487 and (name N or name CA or name C or name O or name C \ B )) or resid 488 through 507 or (resid 508 through 509 and (name N or name CA o \ r name C or name O or name CB )) or resid 510 or (resid 511 and (name N or name \ CA or name C or name O or name CB )) or resid 512 through 585 or resid 587 throu \ gh 639 or resid 641 through 650 or resid 653 through 659 or (resid 660 through 6 \ 61 and (name N or name CA or name C or name O or name CB )) or resid 662 or (res \ id 663 and (name N or name CA or name C or name O or name CB )) or resid 664 thr \ ough 667 or resid 669 through 674 or resid 676 through 684 or (resid 685 and (na \ me N or name CA or name C or name O or name CB )) or resid 686 or (resid 688 and \ (name N or name CA or name C or name O or name CB )) or resid 689 or (resid 692 \ and (name N or name CA or name C or name O or name CB )) or resid 693 through 6 \ 95 or (resid 696 through 697 and (name N or name CA or name C or name O or name \ CB )) or resid 698 through 714 or (resid 715 through 716 and (name N or name CA \ or name C or name O or name CB )) or resid 717 through 740 or resid 742 through \ 743 or resid 746 through 753 or resid 755 through 757 or resid 759 through 763 o \ r resid 765 through 768 or (resid 769 and (name N or name CA or name C or name O \ or name CB )) or resid 770 through 775 or resid 780 through 781 or (resid 783 t \ hrough 784 and (name N or name CA or name C or name O or name CB )) or resid 785 \ through 799 or resid 801 through 817 or resid 1001 through 1002)) selection = (chain 'C' and (resid 393 through 398 or resid 400 through 403 or resid 405 thro \ ugh 407 or resid 412 through 414 or resid 416 through 422 or resid 424 through 4 \ 29 or (resid 430 and (name N or name CA or name C or name O or name CB )) or res \ id 431 or resid 433 or resid 436 or resid 438 or resid 440 through 441 or resid \ 443 through 450 or resid 452 through 454 or resid 456 through 461 or (resid 462 \ and (name N or name CA or name C or name O or name CB )) or resid 463 through 46 \ 6 or (resid 468 through 469 and (name N or name CA or name C or name O or name C \ B )) or resid 471 or resid 473 through 481 or (resid 482 through 483 and (name N \ or name CA or name C or name O or name CB )) or resid 484 through 543 or (resid \ 565 and (name N or name CA or name C or name O or name CB )) or resid 566 throu \ gh 581 or resid 583 through 629 or (resid 630 and (name N or name CA or name C o \ r name O or name CB )) or resid 631 through 635 or (resid 637 through 640 and (n \ ame N or name CA or name C or name O or name CB )) or resid 641 through 646 or r \ esid 649 or (resid 650 and (name N or name CA or name C or name O or name CB )) \ or resid 651 or (resid 652 through 653 and (name N or name CA or name C or name \ O or name CB )) or resid 654 through 663 or resid 665 through 669 or (resid 670 \ and (name N or name CA or name C or name O or name CB )) or resid 672 through 67 \ 5 or (resid 676 and (name N or name CA or name C or name O or name CB )) or resi \ d 677 through 682 or resid 684 through 685 or resid 688 through 733 or (resid 73 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 735 through \ 736 or resid 738 through 739 or resid 742 through 749 or resid 751 through 753 o \ r resid 755 through 759 or resid 761 through 771 or resid 776 through 777 or res \ id 779 through 795 or resid 797 through 811 or (resid 812 through 813 and (name \ N or name CA or name C or name O or name CB )) or resid 1001 through 1002)) selection = (chain 'D' and (resid 397 through 401 or (resid 402 and (name N or name CA or na \ me C or name O or name CB )) or resid 404 through 407 or resid 409 through 411 o \ r resid 416 through 418 or resid 420 through 426 or resid 428 through 435 or res \ id 437 or resid 440 or resid 442 or resid 444 through 445 or resid 447 through 4 \ 54 or (resid 456 through 458 and (name N or name CA or name C or name O or name \ CB )) or resid 460 through 470 or resid 472 through 473 or resid 475 or resid 47 \ 7 through 486 or (resid 487 and (name N or name CA or name C or name O or name C \ B )) or resid 488 through 507 or (resid 508 through 509 and (name N or name CA o \ r name C or name O or name CB )) or resid 510 or (resid 511 and (name N or name \ CA or name C or name O or name CB )) or resid 512 through 585 or resid 587 throu \ gh 639 or resid 641 through 650 or resid 653 through 659 or (resid 660 through 6 \ 61 and (name N or name CA or name C or name O or name CB )) or resid 662 or (res \ id 663 and (name N or name CA or name C or name O or name CB )) or resid 664 thr \ ough 667 or resid 669 through 674 or resid 676 through 684 or (resid 685 and (na \ me N or name CA or name C or name O or name CB )) or resid 686 or (resid 688 and \ (name N or name CA or name C or name O or name CB )) or resid 689 or (resid 692 \ and (name N or name CA or name C or name O or name CB )) or resid 693 through 6 \ 95 or (resid 696 through 697 and (name N or name CA or name C or name O or name \ CB )) or resid 698 through 714 or (resid 715 through 716 and (name N or name CA \ or name C or name O or name CB )) or resid 717 through 740 or resid 742 through \ 743 or resid 746 through 753 or resid 755 through 757 or resid 759 through 763 o \ r resid 765 through 768 or (resid 769 and (name N or name CA or name C or name O \ or name CB )) or resid 770 through 775 or resid 780 through 781 or (resid 783 t \ hrough 784 and (name N or name CA or name C or name O or name CB )) or resid 785 \ through 799 or resid 801 through 817 or resid 1001 through 1002)) } ncs_group { reference = (chain 'G' and (resid 15 through 230 or (resid 231 and (name N or name CA or nam \ e C or name O or name CB )) or resid 232 through 501)) selection = (chain 'H' and (resid 15 through 185 or (resid 196 through 197 and (name N or na \ me CA or name C or name O or name CB )) or resid 198 through 235 or (resid 501 a \ nd (name N or name C1 or name C11 or name C12 or name C13 or name C14 or name C1 \ 5 or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name \ C26 or name C27 or name C28 or name C3 or name C31 or name C32 or name C33 or n \ ame C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name O11 \ or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name \ O32 or name P or name C310 or name C311 or name C312 or name C313 or name C314)) \ )) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.900 Find NCS groups from input model: 0.390 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: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 15207 Z= 0.201 Angle : 0.725 10.664 20572 Z= 0.369 Chirality : 0.045 0.280 2363 Planarity : 0.005 0.072 2519 Dihedral : 14.961 171.732 5293 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.07 % Allowed : 0.14 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: -0.18 (0.19), residues: 1936 helix: 1.06 (0.15), residues: 1082 sheet: -2.15 (0.39), residues: 150 loop : -1.48 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 449 TYR 0.038 0.002 TYR H 226 PHE 0.040 0.002 PHE A 619 TRP 0.028 0.001 TRP H 44 HIS 0.007 0.001 HIS G 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.20 (15199) covalent geometry : angle 0.72443 / 0.37 (20556) SS BOND : bond 0.00341 / 0.18 ( 8) SS BOND : angle 1.19415 / 0.70 ( 16) hydrogen bonds : bond 0.12366 / 8.29 ( 882) hydrogen bonds : angle 5.46907 / 3.73 ( 2556) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 370 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 443 ASP cc_start: 0.7301 (p0) cc_final: 0.6924 (p0) REVERT: A 523 MET cc_start: 0.6665 (tpt) cc_final: 0.5816 (tmm) REVERT: A 542 PHE cc_start: 0.5970 (p90) cc_final: 0.5707 (p90) REVERT: A 638 GLN cc_start: 0.5745 (pp30) cc_final: 0.5544 (pp30) REVERT: B 402 GLU cc_start: 0.7378 (mt-10) cc_final: 0.6263 (mm-30) REVERT: B 431 GLU cc_start: 0.8147 (tp30) cc_final: 0.7783 (tp30) REVERT: B 594 ARG cc_start: 0.8250 (mmm-85) cc_final: 0.7898 (mmm160) REVERT: B 627 GLU cc_start: 0.8463 (pp20) cc_final: 0.8171 (pp20) REVERT: B 756 GLN cc_start: 0.8048 (mt0) cc_final: 0.7785 (mt0) REVERT: B 807 MET cc_start: 0.6433 (tmm) cc_final: 0.6233 (ttm) REVERT: C 443 ASP cc_start: 0.8069 (p0) cc_final: 0.7308 (t0) REVERT: C 465 TYR cc_start: 0.6305 (m-10) cc_final: 0.5613 (m-10) REVERT: C 541 ARG cc_start: 0.7826 (mmp-170) cc_final: 0.7607 (mmp-170) REVERT: C 717 MET cc_start: 0.7560 (pmm) cc_final: 0.7318 (pmm) REVERT: C 769 CYS cc_start: 0.5509 (t) cc_final: 0.5284 (m) REVERT: D 407 MET cc_start: 0.7386 (ptm) cc_final: 0.7174 (ptm) REVERT: D 586 ARG cc_start: 0.7997 (mmm-85) cc_final: 0.7735 (mmt90) REVERT: D 688 GLU cc_start: 0.7909 (pt0) cc_final: 0.7227 (mm-30) REVERT: D 711 TYR cc_start: 0.7462 (t80) cc_final: 0.7163 (t80) REVERT: D 753 LEU cc_start: 0.9042 (mm) cc_final: 0.8820 (mp) REVERT: D 756 GLN cc_start: 0.8556 (mt0) cc_final: 0.8350 (mt0) REVERT: D 764 ASN cc_start: 0.8503 (t0) cc_final: 0.8227 (t0) REVERT: G 171 SER cc_start: 0.8300 (m) cc_final: 0.7790 (p) REVERT: G 224 ASN cc_start: 0.8119 (m110) cc_final: 0.7857 (m110) REVERT: H 32 PHE cc_start: 0.8909 (t80) cc_final: 0.8647 (t80) REVERT: H 97 ARG cc_start: 0.7115 (mmm-85) cc_final: 0.6855 (mmm-85) REVERT: H 152 LYS cc_start: 0.7622 (mmtm) cc_final: 0.7374 (mmmt) REVERT: H 174 ILE cc_start: 0.7349 (mm) cc_final: 0.7083 (mm) outliers start: 1 outliers final: 0 residues processed: 371 average time/residue: 0.1300 time to fit residues: 70.1948 Evaluate side-chains 275 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 HIS ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 ASN D 726 ASN G 105 HIS G 183 ASN H 183 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.171946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.137387 restraints weight = 26509.812| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 3.47 r_work: 0.3626 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15207 Z= 0.121 Angle : 0.536 11.624 20572 Z= 0.278 Chirality : 0.040 0.137 2363 Planarity : 0.004 0.064 2519 Dihedral : 9.582 146.053 2398 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.31 % Allowed : 9.72 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.65 (0.19), residues: 1936 helix: 1.86 (0.16), residues: 1086 sheet: -2.10 (0.42), residues: 134 loop : -1.33 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 449 TYR 0.022 0.001 TYR G 226 PHE 0.032 0.001 PHE G 165 TRP 0.014 0.001 TRP H 44 HIS 0.002 0.001 HIS G 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (15199) covalent geometry : angle 0.53532 / 0.28 (20556) SS BOND : bond 0.00329 / 0.20 ( 8) SS BOND : angle 1.03105 / 0.60 ( 16) hydrogen bonds : bond 0.03641 / 2.50 ( 882) hydrogen bonds : angle 4.11383 / 2.86 ( 2556) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 304 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 443 ASP cc_start: 0.7227 (p0) cc_final: 0.6969 (p0) REVERT: A 523 MET cc_start: 0.7560 (tpt) cc_final: 0.7260 (tmm) REVERT: A 542 PHE cc_start: 0.6598 (p90) cc_final: 0.6326 (p90) REVERT: A 638 GLN cc_start: 0.7332 (pp30) cc_final: 0.6865 (pp30) REVERT: B 402 GLU cc_start: 0.6608 (mt-10) cc_final: 0.6130 (mm-30) REVERT: B 537 SER cc_start: 0.8081 (m) cc_final: 0.7767 (p) REVERT: C 486 ASP cc_start: 0.7747 (p0) cc_final: 0.7465 (p0) REVERT: C 541 ARG cc_start: 0.8278 (mmp-170) cc_final: 0.7980 (mmp-170) REVERT: C 717 MET cc_start: 0.8181 (pmm) cc_final: 0.7431 (ptt) REVERT: C 739 ARG cc_start: 0.7705 (ttp80) cc_final: 0.7225 (ttt90) REVERT: D 508 GLN cc_start: 0.8191 (pp30) cc_final: 0.7984 (pp30) REVERT: D 586 ARG cc_start: 0.8588 (mmm-85) cc_final: 0.8355 (mmt90) REVERT: D 711 TYR cc_start: 0.8009 (t80) cc_final: 0.7768 (t80) REVERT: G 122 ARG cc_start: 0.8659 (tpp80) cc_final: 0.8318 (tpp-160) REVERT: G 171 SER cc_start: 0.8120 (m) cc_final: 0.7852 (p) REVERT: G 224 ASN cc_start: 0.8331 (m110) cc_final: 0.8067 (m-40) REVERT: H 45 LEU cc_start: 0.6633 (OUTLIER) cc_final: 0.6354 (pp) REVERT: H 206 TYR cc_start: 0.7750 (m-10) cc_final: 0.7538 (m-10) REVERT: H 226 TYR cc_start: 0.8351 (t80) cc_final: 0.8113 (t80) outliers start: 33 outliers final: 20 residues processed: 322 average time/residue: 0.1306 time to fit residues: 61.2321 Evaluate side-chains 286 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 265 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain B residue 469 TYR Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 523 TYR Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 668 ASP Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain H residue 100 CYS Chi-restraints excluded: chain H residue 129 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 193 optimal weight: 6.9990 chunk 93 optimal weight: 0.6980 chunk 162 optimal weight: 8.9990 chunk 179 optimal weight: 10.0000 chunk 94 optimal weight: 0.5980 chunk 85 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 0.0170 chunk 10 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 148 optimal weight: 0.7980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 HIS A 710 GLN B 714 GLN G 105 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.172173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.136848 restraints weight = 26875.178| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 3.16 r_work: 0.3642 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15207 Z= 0.108 Angle : 0.514 7.906 20572 Z= 0.267 Chirality : 0.039 0.142 2363 Planarity : 0.003 0.059 2519 Dihedral : 8.561 134.838 2398 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.03 % Allowed : 13.36 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.94 (0.20), residues: 1936 helix: 2.16 (0.16), residues: 1086 sheet: -2.01 (0.39), residues: 156 loop : -1.29 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 449 TYR 0.017 0.001 TYR D 424 PHE 0.028 0.001 PHE C 542 TRP 0.007 0.001 TRP D 766 HIS 0.003 0.001 HIS H 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (15199) covalent geometry : angle 0.51234 / 0.27 (20556) SS BOND : bond 0.00545 / 0.23 ( 8) SS BOND : angle 1.35165 / 0.77 ( 16) hydrogen bonds : bond 0.03401 / 2.32 ( 882) hydrogen bonds : angle 3.91243 / 2.75 ( 2556) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 297 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 443 ASP cc_start: 0.7251 (p0) cc_final: 0.6966 (p0) REVERT: A 523 MET cc_start: 0.7401 (tpt) cc_final: 0.7164 (tmm) REVERT: A 542 PHE cc_start: 0.6654 (p90) cc_final: 0.6386 (p90) REVERT: A 638 GLN cc_start: 0.7320 (pp30) cc_final: 0.6830 (pp30) REVERT: B 537 SER cc_start: 0.8154 (m) cc_final: 0.7823 (p) REVERT: B 670 MET cc_start: 0.8073 (mtt) cc_final: 0.7867 (mtt) REVERT: C 465 TYR cc_start: 0.6759 (m-10) cc_final: 0.6410 (m-10) REVERT: C 467 ARG cc_start: 0.7455 (mtm110) cc_final: 0.7066 (ptt180) REVERT: C 486 ASP cc_start: 0.7794 (p0) cc_final: 0.7462 (p0) REVERT: C 541 ARG cc_start: 0.8250 (mmp-170) cc_final: 0.7880 (mmp-170) REVERT: C 704 MET cc_start: 0.8536 (tpp) cc_final: 0.8293 (tpt) REVERT: C 717 MET cc_start: 0.8173 (pmm) cc_final: 0.7502 (ptt) REVERT: C 728 TYR cc_start: 0.8831 (m-10) cc_final: 0.8437 (m-10) REVERT: C 739 ARG cc_start: 0.7737 (ttp80) cc_final: 0.7458 (ttt90) REVERT: D 711 TYR cc_start: 0.8067 (t80) cc_final: 0.7766 (t80) REVERT: D 753 LEU cc_start: 0.9346 (mp) cc_final: 0.9093 (mp) REVERT: G 171 SER cc_start: 0.8134 (m) cc_final: 0.7882 (p) REVERT: G 224 ASN cc_start: 0.8278 (m110) cc_final: 0.8011 (m-40) REVERT: H 32 PHE cc_start: 0.8747 (t80) cc_final: 0.8391 (t80) REVERT: H 206 TYR cc_start: 0.7689 (m-10) cc_final: 0.7365 (m-10) outliers start: 29 outliers final: 21 residues processed: 312 average time/residue: 0.1349 time to fit residues: 60.9838 Evaluate side-chains 290 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 269 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 HIS Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain B residue 469 TYR Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 696 TYR Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 758 LEU Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain G residue 198 HIS Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 228 GLU Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain H residue 100 CYS Chi-restraints excluded: chain H residue 234 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 184 optimal weight: 9.9990 chunk 180 optimal weight: 7.9990 chunk 74 optimal weight: 0.1980 chunk 185 optimal weight: 6.9990 chunk 120 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 187 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 106 optimal weight: 0.0770 overall best weight: 2.8544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 HIS A 582 GLN ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 HIS G 172 ASN G 183 ASN H 104 ASN ** H 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.163045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.128128 restraints weight = 26868.801| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 3.48 r_work: 0.3495 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 15207 Z= 0.285 Angle : 0.668 6.576 20572 Z= 0.354 Chirality : 0.045 0.185 2363 Planarity : 0.004 0.058 2519 Dihedral : 10.018 134.637 2398 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.36 % Allowed : 13.92 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.53 (0.20), residues: 1936 helix: 1.80 (0.16), residues: 1086 sheet: -2.20 (0.42), residues: 132 loop : -1.46 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 229 TYR 0.024 0.002 TYR C 764 PHE 0.031 0.002 PHE C 542 TRP 0.021 0.002 TRP B 767 HIS 0.021 0.002 HIS A 431 Details of bonding type rmsd/Z covalent geometry : bond 0.00684 / 0.28 (15199) covalent geometry : angle 0.66748 / 0.35 (20556) SS BOND : bond 0.00556 / 0.27 ( 8) SS BOND : angle 1.30752 / 0.79 ( 16) hydrogen bonds : bond 0.04466 / 3.02 ( 882) hydrogen bonds : angle 4.38307 / 3.08 ( 2556) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 274 time to evaluate : 0.607 Fit side-chains REVERT: A 443 ASP cc_start: 0.7259 (p0) cc_final: 0.6996 (p0) REVERT: A 541 ARG cc_start: 0.8703 (tpp80) cc_final: 0.8502 (tpp-160) REVERT: B 402 GLU cc_start: 0.7193 (mt-10) cc_final: 0.6756 (mm-30) REVERT: B 596 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8487 (tt) REVERT: C 397 LEU cc_start: 0.7561 (tt) cc_final: 0.7353 (tt) REVERT: C 443 ASP cc_start: 0.8164 (p0) cc_final: 0.7631 (t0) REVERT: C 486 ASP cc_start: 0.7778 (p0) cc_final: 0.7447 (p0) REVERT: C 717 MET cc_start: 0.8511 (pmm) cc_final: 0.7955 (ptt) REVERT: C 739 ARG cc_start: 0.7806 (ttp80) cc_final: 0.7381 (ttt90) REVERT: D 463 MET cc_start: 0.7315 (OUTLIER) cc_final: 0.6871 (mtt) REVERT: D 508 GLN cc_start: 0.8382 (pp30) cc_final: 0.8159 (pp30) REVERT: D 688 GLU cc_start: 0.7968 (pt0) cc_final: 0.7598 (mm-30) REVERT: D 753 LEU cc_start: 0.9290 (mp) cc_final: 0.8960 (mp) REVERT: H 32 PHE cc_start: 0.8794 (t80) cc_final: 0.8515 (t80) REVERT: H 97 ARG cc_start: 0.7381 (mmm-85) cc_final: 0.7167 (mmm-85) REVERT: H 174 ILE cc_start: 0.8151 (mm) cc_final: 0.7916 (mt) outliers start: 48 outliers final: 37 residues processed: 304 average time/residue: 0.1388 time to fit residues: 60.5828 Evaluate side-chains 293 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 254 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 469 TYR Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 545 ARG Chi-restraints excluded: chain D residue 595 SER Chi-restraints excluded: chain D residue 668 ASP Chi-restraints excluded: chain D residue 758 LEU Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain G residue 198 HIS Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain G residue 230 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain H residue 100 CYS Chi-restraints excluded: chain H residue 104 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 77 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 97 optimal weight: 0.0020 chunk 91 optimal weight: 0.0980 chunk 53 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 GLN D 756 GLN G 105 HIS G 183 ASN ** H 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.164145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.134093 restraints weight = 26331.788| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.89 r_work: 0.3595 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15207 Z= 0.113 Angle : 0.538 8.112 20572 Z= 0.284 Chirality : 0.040 0.186 2363 Planarity : 0.003 0.053 2519 Dihedral : 8.886 124.647 2398 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.17 % Allowed : 17.20 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.96 (0.20), residues: 1936 helix: 2.17 (0.16), residues: 1090 sheet: -2.05 (0.41), residues: 146 loop : -1.27 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 449 TYR 0.031 0.001 TYR H 226 PHE 0.023 0.001 PHE C 542 TRP 0.012 0.001 TRP D 766 HIS 0.004 0.001 HIS H 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (15199) covalent geometry : angle 0.53696 / 0.28 (20556) SS BOND : bond 0.00270 / 0.15 ( 8) SS BOND : angle 1.05962 / 0.64 ( 16) hydrogen bonds : bond 0.03519 / 2.39 ( 882) hydrogen bonds : angle 4.01306 / 2.83 ( 2556) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 294 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 443 ASP cc_start: 0.7182 (p0) cc_final: 0.6944 (p0) REVERT: A 523 MET cc_start: 0.7579 (tpt) cc_final: 0.7248 (tmm) REVERT: A 542 PHE cc_start: 0.6769 (p90) cc_final: 0.6490 (p90) REVERT: A 638 GLN cc_start: 0.7554 (pp30) cc_final: 0.7020 (pp30) REVERT: B 537 SER cc_start: 0.8026 (m) cc_final: 0.7777 (p) REVERT: C 439 GLU cc_start: 0.8133 (pp20) cc_final: 0.7892 (pp20) REVERT: C 717 MET cc_start: 0.8409 (pmm) cc_final: 0.7781 (ptt) REVERT: C 728 TYR cc_start: 0.8897 (m-10) cc_final: 0.8502 (m-10) REVERT: D 463 MET cc_start: 0.7084 (OUTLIER) cc_final: 0.6528 (mtt) REVERT: D 688 GLU cc_start: 0.7728 (pt0) cc_final: 0.7325 (tp30) REVERT: D 753 LEU cc_start: 0.9308 (mp) cc_final: 0.8950 (mp) REVERT: G 171 SER cc_start: 0.8045 (m) cc_final: 0.7800 (p) REVERT: G 199 TYR cc_start: 0.6360 (m-10) cc_final: 0.6113 (m-80) REVERT: G 224 ASN cc_start: 0.8287 (m110) cc_final: 0.7865 (m-40) REVERT: H 32 PHE cc_start: 0.8737 (t80) cc_final: 0.8325 (t80) REVERT: H 97 ARG cc_start: 0.7435 (mmm-85) cc_final: 0.7231 (mmm-85) REVERT: H 139 LEU cc_start: 0.8976 (tp) cc_final: 0.8759 (tp) REVERT: H 165 PHE cc_start: 0.7466 (m-80) cc_final: 0.7264 (m-80) REVERT: H 228 GLU cc_start: 0.7851 (tp30) cc_final: 0.7133 (pt0) outliers start: 31 outliers final: 23 residues processed: 315 average time/residue: 0.1323 time to fit residues: 60.4363 Evaluate side-chains 294 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 270 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 469 TYR Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 668 THR Chi-restraints excluded: chain C residue 696 TYR Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 595 SER Chi-restraints excluded: chain D residue 668 ASP Chi-restraints excluded: chain D residue 758 LEU Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain G residue 198 HIS Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 216 GLU Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain H residue 100 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 45 optimal weight: 0.0000 chunk 78 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 106 optimal weight: 0.2980 chunk 127 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 overall best weight: 0.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 HIS ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 HIS H 172 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.168222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.133286 restraints weight = 26596.386| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 3.32 r_work: 0.3584 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15207 Z= 0.125 Angle : 0.550 8.149 20572 Z= 0.288 Chirality : 0.040 0.233 2363 Planarity : 0.004 0.051 2519 Dihedral : 8.445 110.411 2398 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.73 % Allowed : 18.88 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 1.07 (0.20), residues: 1936 helix: 2.25 (0.16), residues: 1090 sheet: -2.07 (0.41), residues: 146 loop : -1.20 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 229 TYR 0.038 0.001 TYR H 226 PHE 0.018 0.001 PHE G 165 TRP 0.008 0.001 TRP D 766 HIS 0.003 0.001 HIS G 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (15199) covalent geometry : angle 0.54916 / 0.29 (20556) SS BOND : bond 0.00269 / 0.15 ( 8) SS BOND : angle 1.05476 / 0.65 ( 16) hydrogen bonds : bond 0.03452 / 2.35 ( 882) hydrogen bonds : angle 3.97384 / 2.82 ( 2556) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 284 time to evaluate : 0.587 Fit side-chains revert: symmetry clash REVERT: A 443 ASP cc_start: 0.7209 (p0) cc_final: 0.6947 (p0) REVERT: A 523 MET cc_start: 0.7628 (tpt) cc_final: 0.7224 (tmm) REVERT: A 542 PHE cc_start: 0.6781 (p90) cc_final: 0.6443 (p90) REVERT: A 638 GLN cc_start: 0.7447 (pp30) cc_final: 0.6901 (pp30) REVERT: A 734 LYS cc_start: 0.7387 (mmmt) cc_final: 0.6788 (mmmt) REVERT: B 402 GLU cc_start: 0.6723 (mt-10) cc_final: 0.6230 (mm-30) REVERT: B 537 SER cc_start: 0.8118 (m) cc_final: 0.7821 (p) REVERT: C 439 GLU cc_start: 0.8241 (pp20) cc_final: 0.7953 (pp20) REVERT: C 443 ASP cc_start: 0.8221 (p0) cc_final: 0.7487 (t0) REVERT: C 467 ARG cc_start: 0.7333 (ttp-110) cc_final: 0.7101 (ttp-110) REVERT: C 486 ASP cc_start: 0.7581 (p0) cc_final: 0.7298 (p0) REVERT: C 717 MET cc_start: 0.8424 (pmm) cc_final: 0.7968 (ptt) REVERT: C 739 ARG cc_start: 0.7619 (ttp80) cc_final: 0.7172 (ttt90) REVERT: D 463 MET cc_start: 0.7170 (OUTLIER) cc_final: 0.6638 (mtt) REVERT: D 508 GLN cc_start: 0.8310 (pp30) cc_final: 0.8046 (pp30) REVERT: D 688 GLU cc_start: 0.7782 (pt0) cc_final: 0.7290 (tp30) REVERT: D 753 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9018 (mp) REVERT: G 171 SER cc_start: 0.8128 (m) cc_final: 0.7828 (p) REVERT: G 183 ASN cc_start: 0.8875 (t160) cc_final: 0.8615 (t0) REVERT: G 199 TYR cc_start: 0.6436 (m-10) cc_final: 0.6150 (m-80) REVERT: G 224 ASN cc_start: 0.8155 (m110) cc_final: 0.7860 (m110) REVERT: H 32 PHE cc_start: 0.8800 (t80) cc_final: 0.8316 (t80) REVERT: H 97 ARG cc_start: 0.7427 (mmm-85) cc_final: 0.7225 (mmm-85) REVERT: H 139 LEU cc_start: 0.8958 (tp) cc_final: 0.8703 (tp) REVERT: H 228 GLU cc_start: 0.7911 (tp30) cc_final: 0.7121 (pt0) outliers start: 39 outliers final: 30 residues processed: 307 average time/residue: 0.1296 time to fit residues: 57.4495 Evaluate side-chains 302 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 270 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 714 CYS Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 469 TYR Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 696 TYR Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 575 ASN Chi-restraints excluded: chain D residue 595 SER Chi-restraints excluded: chain D residue 753 LEU Chi-restraints excluded: chain D residue 758 LEU Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain G residue 198 HIS Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 216 GLU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain H residue 100 CYS Chi-restraints excluded: chain H residue 172 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 84 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 153 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 144 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 HIS G 105 HIS ** H 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.166574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.134572 restraints weight = 26440.118| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 3.07 r_work: 0.3581 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15207 Z= 0.162 Angle : 0.579 9.228 20572 Z= 0.302 Chirality : 0.041 0.222 2363 Planarity : 0.004 0.052 2519 Dihedral : 8.498 105.813 2398 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.15 % Allowed : 19.65 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.97 (0.20), residues: 1936 helix: 2.18 (0.16), residues: 1088 sheet: -2.08 (0.41), residues: 144 loop : -1.26 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 229 TYR 0.046 0.002 TYR H 226 PHE 0.034 0.002 PHE C 542 TRP 0.009 0.001 TRP B 766 HIS 0.002 0.001 HIS G 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (15199) covalent geometry : angle 0.57873 / 0.30 (20556) SS BOND : bond 0.00327 / 0.18 ( 8) SS BOND : angle 1.07711 / 0.67 ( 16) hydrogen bonds : bond 0.03638 / 2.47 ( 882) hydrogen bonds : angle 4.06558 / 2.89 ( 2556) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 272 time to evaluate : 0.547 Fit side-chains revert: symmetry clash REVERT: A 443 ASP cc_start: 0.7224 (p0) cc_final: 0.6962 (p0) REVERT: A 523 MET cc_start: 0.7686 (tpt) cc_final: 0.7300 (tmm) REVERT: A 638 GLN cc_start: 0.7475 (pp30) cc_final: 0.6893 (pp30) REVERT: B 402 GLU cc_start: 0.6676 (mt-10) cc_final: 0.6271 (mm-30) REVERT: B 537 SER cc_start: 0.8112 (m) cc_final: 0.7831 (p) REVERT: C 443 ASP cc_start: 0.8159 (p0) cc_final: 0.7587 (t0) REVERT: C 467 ARG cc_start: 0.7271 (ttp-110) cc_final: 0.7046 (ttp-110) REVERT: C 486 ASP cc_start: 0.7732 (p0) cc_final: 0.7431 (p0) REVERT: C 717 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.8163 (ptt) REVERT: C 739 ARG cc_start: 0.7661 (ttp80) cc_final: 0.7203 (ttt90) REVERT: D 463 MET cc_start: 0.7263 (OUTLIER) cc_final: 0.6752 (mtt) REVERT: D 508 GLN cc_start: 0.8379 (pp30) cc_final: 0.8113 (pp30) REVERT: D 688 GLU cc_start: 0.7828 (pt0) cc_final: 0.7399 (tp30) REVERT: D 711 TYR cc_start: 0.8067 (t80) cc_final: 0.7471 (t80) REVERT: D 753 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9018 (mp) REVERT: G 171 SER cc_start: 0.8087 (m) cc_final: 0.7804 (p) REVERT: G 224 ASN cc_start: 0.8124 (m110) cc_final: 0.7874 (m110) REVERT: H 16 GLU cc_start: 0.6397 (tm-30) cc_final: 0.3906 (tp30) REVERT: H 32 PHE cc_start: 0.8829 (t80) cc_final: 0.8325 (t80) REVERT: H 139 LEU cc_start: 0.8944 (tp) cc_final: 0.8680 (tp) REVERT: H 228 GLU cc_start: 0.7942 (tp30) cc_final: 0.7148 (pt0) outliers start: 45 outliers final: 36 residues processed: 301 average time/residue: 0.1319 time to fit residues: 57.4583 Evaluate side-chains 305 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 266 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 HIS Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 714 CYS Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 469 TYR Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 668 THR Chi-restraints excluded: chain C residue 696 TYR Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 545 ARG Chi-restraints excluded: chain D residue 575 ASN Chi-restraints excluded: chain D residue 595 SER Chi-restraints excluded: chain D residue 668 ASP Chi-restraints excluded: chain D residue 753 LEU Chi-restraints excluded: chain D residue 758 LEU Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain G residue 198 HIS Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 216 GLU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain H residue 100 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 143 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 139 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 145 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 HIS G 105 HIS ** H 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.167990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.135166 restraints weight = 26722.178| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 3.00 r_work: 0.3611 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15207 Z= 0.128 Angle : 0.571 11.106 20572 Z= 0.294 Chirality : 0.041 0.360 2363 Planarity : 0.004 0.051 2519 Dihedral : 8.188 99.654 2398 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.15 % Allowed : 20.14 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 1.07 (0.20), residues: 1936 helix: 2.25 (0.16), residues: 1088 sheet: -2.00 (0.42), residues: 144 loop : -1.21 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 229 TYR 0.045 0.001 TYR H 226 PHE 0.031 0.001 PHE C 542 TRP 0.009 0.001 TRP D 605 HIS 0.003 0.001 HIS G 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (15199) covalent geometry : angle 0.57014 / 0.29 (20556) SS BOND : bond 0.00276 / 0.16 ( 8) SS BOND : angle 1.05200 / 0.65 ( 16) hydrogen bonds : bond 0.03463 / 2.35 ( 882) hydrogen bonds : angle 4.01017 / 2.85 ( 2556) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 277 time to evaluate : 0.560 Fit side-chains revert: symmetry clash REVERT: A 443 ASP cc_start: 0.7209 (p0) cc_final: 0.6935 (p0) REVERT: A 523 MET cc_start: 0.7625 (tpt) cc_final: 0.7268 (tmm) REVERT: A 638 GLN cc_start: 0.7562 (pp30) cc_final: 0.6948 (pp30) REVERT: A 734 LYS cc_start: 0.7702 (mmmt) cc_final: 0.7497 (mmmt) REVERT: B 402 GLU cc_start: 0.6679 (mt-10) cc_final: 0.6244 (mm-30) REVERT: B 537 SER cc_start: 0.8070 (m) cc_final: 0.7783 (p) REVERT: C 443 ASP cc_start: 0.8150 (p0) cc_final: 0.7550 (t0) REVERT: C 467 ARG cc_start: 0.7322 (ttp-110) cc_final: 0.6917 (ttp-110) REVERT: C 486 ASP cc_start: 0.7731 (p0) cc_final: 0.7526 (p0) REVERT: C 717 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8113 (ptt) REVERT: C 739 ARG cc_start: 0.7611 (ttp80) cc_final: 0.7163 (ttt90) REVERT: D 463 MET cc_start: 0.7197 (OUTLIER) cc_final: 0.6687 (mtt) REVERT: D 688 GLU cc_start: 0.7742 (pt0) cc_final: 0.7308 (tp30) REVERT: D 711 TYR cc_start: 0.7979 (t80) cc_final: 0.7351 (t80) REVERT: D 753 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.8984 (mp) REVERT: G 171 SER cc_start: 0.8088 (m) cc_final: 0.7793 (p) REVERT: H 16 GLU cc_start: 0.6437 (tm-30) cc_final: 0.4060 (tp30) REVERT: H 32 PHE cc_start: 0.8809 (t80) cc_final: 0.8291 (t80) REVERT: H 139 LEU cc_start: 0.8926 (tp) cc_final: 0.8663 (tp) REVERT: H 228 GLU cc_start: 0.7845 (tp30) cc_final: 0.7128 (pt0) outliers start: 45 outliers final: 37 residues processed: 304 average time/residue: 0.1240 time to fit residues: 55.1599 Evaluate side-chains 308 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 268 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 714 CYS Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 469 TYR Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 668 THR Chi-restraints excluded: chain C residue 696 TYR Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 545 ARG Chi-restraints excluded: chain D residue 575 ASN Chi-restraints excluded: chain D residue 595 SER Chi-restraints excluded: chain D residue 668 ASP Chi-restraints excluded: chain D residue 753 LEU Chi-restraints excluded: chain D residue 758 LEU Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain G residue 198 HIS Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain G residue 216 GLU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain H residue 100 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 17 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 63 optimal weight: 6.9990 chunk 61 optimal weight: 0.0270 chunk 164 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 163 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 overall best weight: 1.1444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 HIS ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 HIS ** G 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 224 ASN ** H 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.167185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.133540 restraints weight = 26684.543| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 3.17 r_work: 0.3560 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15207 Z= 0.146 Angle : 0.591 9.969 20572 Z= 0.305 Chirality : 0.042 0.367 2363 Planarity : 0.004 0.054 2519 Dihedral : 8.184 95.011 2398 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.01 % Allowed : 19.79 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 1.04 (0.20), residues: 1936 helix: 2.23 (0.16), residues: 1086 sheet: -2.03 (0.42), residues: 144 loop : -1.21 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 229 TYR 0.042 0.001 TYR H 226 PHE 0.030 0.001 PHE H 165 TRP 0.008 0.001 TRP B 766 HIS 0.003 0.001 HIS G 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (15199) covalent geometry : angle 0.59002 / 0.30 (20556) SS BOND : bond 0.00307 / 0.17 ( 8) SS BOND : angle 1.04806 / 0.65 ( 16) hydrogen bonds : bond 0.03530 / 2.39 ( 882) hydrogen bonds : angle 4.02257 / 2.85 ( 2556) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 269 time to evaluate : 0.620 Fit side-chains revert: symmetry clash REVERT: A 443 ASP cc_start: 0.7158 (p0) cc_final: 0.6921 (p0) REVERT: A 523 MET cc_start: 0.7677 (tpt) cc_final: 0.7328 (tmm) REVERT: A 638 GLN cc_start: 0.7543 (pp30) cc_final: 0.6928 (pp30) REVERT: A 739 ARG cc_start: 0.7750 (ttt180) cc_final: 0.7516 (ttt-90) REVERT: B 402 GLU cc_start: 0.6690 (mt-10) cc_final: 0.6266 (mm-30) REVERT: B 537 SER cc_start: 0.8065 (m) cc_final: 0.7784 (p) REVERT: C 443 ASP cc_start: 0.8101 (p0) cc_final: 0.7564 (t0) REVERT: C 467 ARG cc_start: 0.7312 (ttp-110) cc_final: 0.6840 (ttp-110) REVERT: C 486 ASP cc_start: 0.7667 (p0) cc_final: 0.7432 (p0) REVERT: C 717 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.8130 (ptt) REVERT: C 739 ARG cc_start: 0.7537 (ttp80) cc_final: 0.7102 (ttt90) REVERT: D 463 MET cc_start: 0.7286 (OUTLIER) cc_final: 0.6788 (mtt) REVERT: D 688 GLU cc_start: 0.7785 (pt0) cc_final: 0.7345 (tp30) REVERT: D 711 TYR cc_start: 0.8055 (t80) cc_final: 0.7455 (t80) REVERT: D 753 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.8993 (mp) REVERT: G 171 SER cc_start: 0.8099 (m) cc_final: 0.7814 (p) REVERT: H 32 PHE cc_start: 0.8764 (t80) cc_final: 0.8251 (t80) REVERT: H 139 LEU cc_start: 0.8890 (tp) cc_final: 0.8614 (tp) REVERT: H 228 GLU cc_start: 0.7836 (tp30) cc_final: 0.7161 (pt0) outliers start: 43 outliers final: 38 residues processed: 295 average time/residue: 0.1361 time to fit residues: 58.3990 Evaluate side-chains 305 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 264 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 HIS Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 714 CYS Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 469 TYR Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 668 THR Chi-restraints excluded: chain C residue 696 TYR Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 545 ARG Chi-restraints excluded: chain D residue 575 ASN Chi-restraints excluded: chain D residue 595 SER Chi-restraints excluded: chain D residue 668 ASP Chi-restraints excluded: chain D residue 753 LEU Chi-restraints excluded: chain D residue 758 LEU Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain G residue 198 HIS Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain G residue 216 GLU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain H residue 100 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 127 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 192 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 193 optimal weight: 7.9990 chunk 54 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 HIS ** G 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 183 ASN ** H 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.165338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.132287 restraints weight = 26604.751| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.98 r_work: 0.3531 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 15207 Z= 0.193 Angle : 0.637 10.327 20572 Z= 0.330 Chirality : 0.044 0.366 2363 Planarity : 0.004 0.063 2519 Dihedral : 8.560 97.702 2398 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.08 % Allowed : 20.28 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.20), residues: 1936 helix: 2.11 (0.16), residues: 1086 sheet: -2.09 (0.42), residues: 144 loop : -1.32 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 229 TYR 0.035 0.002 TYR H 226 PHE 0.030 0.002 PHE C 542 TRP 0.013 0.001 TRP B 767 HIS 0.009 0.001 HIS A 431 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.19 (15199) covalent geometry : angle 0.63685 / 0.33 (20556) SS BOND : bond 0.00379 / 0.20 ( 8) SS BOND : angle 1.20313 / 0.75 ( 16) hydrogen bonds : bond 0.03843 / 2.60 ( 882) hydrogen bonds : angle 4.18547 / 2.96 ( 2556) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 263 time to evaluate : 0.604 Fit side-chains revert: symmetry clash REVERT: A 443 ASP cc_start: 0.7173 (p0) cc_final: 0.6921 (p0) REVERT: A 523 MET cc_start: 0.7780 (tpt) cc_final: 0.7406 (tmm) REVERT: A 638 GLN cc_start: 0.7625 (pp30) cc_final: 0.6908 (pp30) REVERT: B 402 GLU cc_start: 0.6805 (mt-10) cc_final: 0.6489 (mm-30) REVERT: B 537 SER cc_start: 0.8098 (m) cc_final: 0.7830 (p) REVERT: C 443 ASP cc_start: 0.8020 (p0) cc_final: 0.7574 (t0) REVERT: C 467 ARG cc_start: 0.7338 (ttp-110) cc_final: 0.6845 (ttp-110) REVERT: C 486 ASP cc_start: 0.7770 (p0) cc_final: 0.7519 (p0) REVERT: C 717 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.8218 (ptt) REVERT: C 739 ARG cc_start: 0.7538 (ttp80) cc_final: 0.7113 (ttt90) REVERT: D 463 MET cc_start: 0.7313 (OUTLIER) cc_final: 0.6837 (mtt) REVERT: D 508 GLN cc_start: 0.8631 (pm20) cc_final: 0.7910 (pm20) REVERT: D 688 GLU cc_start: 0.7879 (pt0) cc_final: 0.7484 (tp30) REVERT: D 711 TYR cc_start: 0.8121 (t80) cc_final: 0.7539 (t80) REVERT: D 753 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8967 (mp) REVERT: G 171 SER cc_start: 0.8128 (m) cc_final: 0.7851 (p) REVERT: H 16 GLU cc_start: 0.6401 (tm-30) cc_final: 0.4121 (tp30) REVERT: H 159 LEU cc_start: 0.8008 (mt) cc_final: 0.7489 (pp) REVERT: H 228 GLU cc_start: 0.7824 (tp30) cc_final: 0.7087 (pt0) outliers start: 44 outliers final: 36 residues processed: 288 average time/residue: 0.1390 time to fit residues: 57.7701 Evaluate side-chains 293 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 254 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 714 CYS Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 469 TYR Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 668 THR Chi-restraints excluded: chain C residue 696 TYR Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 545 ARG Chi-restraints excluded: chain D residue 575 ASN Chi-restraints excluded: chain D residue 595 SER Chi-restraints excluded: chain D residue 668 ASP Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain D residue 753 LEU Chi-restraints excluded: chain D residue 758 LEU Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain G residue 198 HIS Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain G residue 216 GLU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 90 CYS Chi-restraints excluded: chain H residue 100 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 120 optimal weight: 7.9990 chunk 182 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 185 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 HIS D 756 GLN ** G 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.167666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.133441 restraints weight = 26511.167| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 3.50 r_work: 0.3596 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15207 Z= 0.134 Angle : 0.595 10.720 20572 Z= 0.307 Chirality : 0.042 0.353 2363 Planarity : 0.004 0.060 2519 Dihedral : 8.213 92.681 2398 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.94 % Allowed : 20.63 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 1.02 (0.20), residues: 1936 helix: 2.22 (0.16), residues: 1086 sheet: -2.01 (0.43), residues: 144 loop : -1.25 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 229 TYR 0.026 0.001 TYR H 226 PHE 0.041 0.002 PHE H 165 TRP 0.009 0.001 TRP D 578 HIS 0.002 0.001 HIS H 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (15199) covalent geometry : angle 0.59413 / 0.31 (20556) SS BOND : bond 0.00307 / 0.17 ( 8) SS BOND : angle 1.07678 / 0.67 ( 16) hydrogen bonds : bond 0.03517 / 2.39 ( 882) hydrogen bonds : angle 4.07561 / 2.88 ( 2556) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3667.00 seconds wall clock time: 63 minutes 38.52 seconds (3818.52 seconds total)