Starting phenix.real_space_refine on Fri Jun 5 02:29:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j92_61250/06_2026/9j92_61250_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j92_61250/06_2026/9j92_61250.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j92_61250/06_2026/9j92_61250.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j92_61250/06_2026/9j92_61250.map" model { file = "/net/cci-nas-00/data/ceres_data/9j92_61250/06_2026/9j92_61250_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j92_61250/06_2026/9j92_61250_neut.cif" } resolution = 4.6 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= 0.017 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: 4 Type Number sf(0) Gaussians S 126 5.16 5 C 11110 2.51 5 N 2673 2.21 5 O 2955 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 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: 16864 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3232 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 14, 'TRANS': 395} Chain breaks: 2 Chain: "D" Number of atoms: 3148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3148 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 14, 'TRANS': 387} Chain breaks: 2 Chain: "C" Number of atoms: 3240 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 410, 3232 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 14, 'TRANS': 395} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 410, 3232 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 14, 'TRANS': 395} Chain breaks: 2 bond proxies already assigned to first conformer: 3296 Chain: "B" Number of atoms: 3148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3148 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 14, 'TRANS': 387} Chain breaks: 2 Chain: "E" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1007 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain breaks: 2 Chain: "H" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1007 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain breaks: 2 Chain: "G" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1007 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain breaks: 2 Chain: "F" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1007 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain breaks: 2 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'DQC': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'DQC': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'DQC': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'DQC': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AASP C 586 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP C 586 " occ=0.50 Time building chain proxies: 4.72, per 1000 atoms: 0.28 Number of scatterers: 16864 At special positions: 0 Unit cell: (125.4, 122.1, 141.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 126 16.00 O 2955 8.00 N 2673 7.00 C 11110 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 714 " - pdb=" SG CYS A 769 " distance=2.03 Simple disulfide: pdb=" SG CYS D 714 " - pdb=" SG CYS D 769 " distance=2.03 Simple disulfide: pdb=" SG CYS C 714 " - pdb=" SG CYS C 769 " distance=2.03 Simple disulfide: pdb=" SG CYS B 714 " - pdb=" SG CYS B 769 " 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: 1.70 Conformation dependent library (CDL) restraints added in 869.3 milliseconds 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3918 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 18 sheets defined 59.0% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 412 through 415 Processing helix chain 'A' and resid 419 through 433 removed outlier: 3.568A pdb=" N GLU A 423 " --> pdb=" O GLY A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 466 removed outlier: 3.804A pdb=" N GLU A 462 " --> pdb=" O GLY A 458 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU A 463 " --> pdb=" O MET A 459 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL A 464 " --> pdb=" O VAL A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 483 removed outlier: 4.200A pdb=" N GLU A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 543 removed outlier: 3.808A pdb=" N SER A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 581 Processing helix chain 'A' and resid 591 through 625 Processing helix chain 'A' and resid 631 through 638 Processing helix chain 'A' and resid 649 through 657 removed outlier: 3.881A pdb=" N GLU A 653 " --> pdb=" O GLY A 649 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE A 655 " --> pdb=" O THR A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 672 Processing helix chain 'A' and resid 682 through 692 Processing helix chain 'A' and resid 703 through 708 removed outlier: 3.583A pdb=" N ILE A 708 " --> pdb=" O MET A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 750 removed outlier: 3.756A pdb=" N LEU A 749 " --> pdb=" O ALA A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 764 removed outlier: 4.221A pdb=" N LYS A 759 " --> pdb=" O LEU A 755 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER A 760 " --> pdb=" O ASP A 756 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TRP A 762 " --> pdb=" O LEU A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 818 removed outlier: 3.685A pdb=" N TYR A 793 " --> pdb=" O ALA A 789 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 807 " --> pdb=" O MET A 803 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU A 809 " --> pdb=" O VAL A 805 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE A 810 " --> pdb=" O ALA A 806 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 433 Processing helix chain 'D' and resid 460 through 465 removed outlier: 3.976A pdb=" N VAL D 464 " --> pdb=" O VAL D 460 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N TYR D 465 " --> pdb=" O GLY D 461 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 460 through 465' Processing helix chain 'D' and resid 478 through 482 Processing helix chain 'D' and resid 518 through 543 removed outlier: 3.632A pdb=" N TRP D 522 " --> pdb=" O ALA D 518 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET D 523 " --> pdb=" O TYR D 519 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL D 526 " --> pdb=" O TRP D 522 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 581 Processing helix chain 'D' and resid 591 through 620 removed outlier: 3.823A pdb=" N ARG D 595 " --> pdb=" O SER D 591 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ILE D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL D 597 " --> pdb=" O SER D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 636 removed outlier: 3.702A pdb=" N LEU D 635 " --> pdb=" O SER D 631 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ALA D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 631 through 636' Processing helix chain 'D' and resid 649 through 658 removed outlier: 3.644A pdb=" N GLU D 653 " --> pdb=" O GLY D 649 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N PHE D 655 " --> pdb=" O THR D 651 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG D 657 " --> pdb=" O GLU D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 661 through 671 removed outlier: 3.871A pdb=" N MET D 666 " --> pdb=" O VAL D 662 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TRP D 667 " --> pdb=" O TYR D 663 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 691 removed outlier: 3.556A pdb=" N LYS D 691 " --> pdb=" O ARG D 688 " (cutoff:3.500A) Processing helix chain 'D' and resid 702 through 710 removed outlier: 3.767A pdb=" N GLU D 706 " --> pdb=" O SER D 702 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TYR D 707 " --> pdb=" O THR D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 738 through 753 removed outlier: 3.564A pdb=" N VAL D 742 " --> pdb=" O LEU D 738 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY D 753 " --> pdb=" O LEU D 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 756 through 765 Processing helix chain 'D' and resid 789 through 817 removed outlier: 3.794A pdb=" N TYR D 793 " --> pdb=" O ALA D 789 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA D 816 " --> pdb=" O TYR D 812 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLU D 817 " --> pdb=" O LYS D 813 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 433 removed outlier: 3.933A pdb=" N ALA C 426 " --> pdb=" O VAL C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 465 Processing helix chain 'C' and resid 478 through 483 removed outlier: 4.013A pdb=" N GLU C 483 " --> pdb=" O LEU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 541 removed outlier: 3.668A pdb=" N SER C 533 " --> pdb=" O TYR C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 581 removed outlier: 3.828A pdb=" N LEU C 573 " --> pdb=" O ILE C 569 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TRP C 574 " --> pdb=" O PHE C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 625 removed outlier: 3.582A pdb=" N ARG C 595 " --> pdb=" O SER C 591 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL C 600 " --> pdb=" O ILE C 596 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TRP C 601 " --> pdb=" O VAL C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 638 Processing helix chain 'C' and resid 649 through 658 removed outlier: 3.552A pdb=" N GLU C 653 " --> pdb=" O GLY C 649 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE C 655 " --> pdb=" O THR C 651 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG C 656 " --> pdb=" O LYS C 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 661 through 672 Processing helix chain 'C' and resid 681 through 692 Processing helix chain 'C' and resid 703 through 708 Processing helix chain 'C' and resid 740 through 745 Processing helix chain 'C' and resid 748 through 753 Processing helix chain 'C' and resid 754 through 764 removed outlier: 4.059A pdb=" N LYS C 759 " --> pdb=" O LEU C 755 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N SER C 760 " --> pdb=" O ASP C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 815 removed outlier: 3.753A pdb=" N TYR C 793 " --> pdb=" O ALA C 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 433 Processing helix chain 'B' and resid 460 through 465 removed outlier: 3.916A pdb=" N VAL B 464 " --> pdb=" O VAL B 460 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N TYR B 465 " --> pdb=" O GLY B 461 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 460 through 465' Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 520 through 543 Processing helix chain 'B' and resid 569 through 581 Processing helix chain 'B' and resid 593 through 620 removed outlier: 4.162A pdb=" N VAL B 597 " --> pdb=" O SER B 593 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA B 618 " --> pdb=" O ALA B 614 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE B 619 " --> pdb=" O ASN B 615 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU B 620 " --> pdb=" O LEU B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 657 Processing helix chain 'B' and resid 660 through 673 removed outlier: 3.911A pdb=" N MET B 666 " --> pdb=" O VAL B 662 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TRP B 667 " --> pdb=" O TYR B 663 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER B 672 " --> pdb=" O THR B 668 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA B 673 " --> pdb=" O TYR B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 692 Processing helix chain 'B' and resid 702 through 710 removed outlier: 3.775A pdb=" N GLN B 710 " --> pdb=" O GLU B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 753 removed outlier: 3.813A pdb=" N VAL B 742 " --> pdb=" O LEU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 765 Processing helix chain 'B' and resid 784 through 787 Processing helix chain 'B' and resid 788 through 815 Processing helix chain 'E' and resid 4 through 34 removed outlier: 3.564A pdb=" N ALA E 19 " --> pdb=" O VAL E 15 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE E 22 " --> pdb=" O ALA E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 67 removed outlier: 3.521A pdb=" N PHE E 62 " --> pdb=" O GLU E 58 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU E 63 " --> pdb=" O ARG E 59 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU E 67 " --> pdb=" O LEU E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 86 removed outlier: 3.861A pdb=" N TYR E 72 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU E 77 " --> pdb=" O SER E 73 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N CYS E 79 " --> pdb=" O HIS E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 108 removed outlier: 3.861A pdb=" N LEU E 91 " --> pdb=" O GLU E 87 " (cutoff:3.500A) Proline residue: E 96 - end of helix Processing helix chain 'E' and resid 128 through 158 Processing helix chain 'H' and resid 4 through 34 removed outlier: 3.564A pdb=" N ALA H 19 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 67 removed outlier: 3.521A pdb=" N PHE H 62 " --> pdb=" O GLU H 58 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU H 63 " --> pdb=" O ARG H 59 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU H 67 " --> pdb=" O LEU H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 86 removed outlier: 3.862A pdb=" N TYR H 72 " --> pdb=" O VAL H 68 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU H 77 " --> pdb=" O SER H 73 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N PHE H 78 " --> pdb=" O ILE H 74 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N CYS H 79 " --> pdb=" O HIS H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 108 removed outlier: 3.861A pdb=" N LEU H 91 " --> pdb=" O GLU H 87 " (cutoff:3.500A) Proline residue: H 96 - end of helix Processing helix chain 'H' and resid 128 through 158 Processing helix chain 'G' and resid 4 through 34 removed outlier: 3.564A pdb=" N ALA G 19 " --> pdb=" O VAL G 15 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE G 22 " --> pdb=" O ALA G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 67 removed outlier: 3.522A pdb=" N PHE G 62 " --> pdb=" O GLU G 58 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU G 63 " --> pdb=" O ARG G 59 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU G 67 " --> pdb=" O LEU G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 86 removed outlier: 3.861A pdb=" N TYR G 72 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU G 77 " --> pdb=" O SER G 73 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N PHE G 78 " --> pdb=" O ILE G 74 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N CYS G 79 " --> pdb=" O HIS G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 108 removed outlier: 3.861A pdb=" N LEU G 91 " --> pdb=" O GLU G 87 " (cutoff:3.500A) Proline residue: G 96 - end of helix Processing helix chain 'G' and resid 128 through 158 Processing helix chain 'F' and resid 4 through 34 removed outlier: 3.563A pdb=" N ALA F 19 " --> pdb=" O VAL F 15 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE F 22 " --> pdb=" O ALA F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 67 removed outlier: 3.522A pdb=" N PHE F 62 " --> pdb=" O GLU F 58 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU F 63 " --> pdb=" O ARG F 59 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU F 67 " --> pdb=" O LEU F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 86 removed outlier: 3.862A pdb=" N TYR F 72 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU F 77 " --> pdb=" O SER F 73 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N PHE F 78 " --> pdb=" O ILE F 74 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N CYS F 79 " --> pdb=" O HIS F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 108 removed outlier: 3.861A pdb=" N LEU F 91 " --> pdb=" O GLU F 87 " (cutoff:3.500A) Proline residue: F 96 - end of helix Processing helix chain 'F' and resid 128 through 158 Processing sheet with id=AA1, first strand: chain 'A' and resid 391 through 393 removed outlier: 6.432A pdb=" N TYR A 391 " --> pdb=" O ARG A 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 404 removed outlier: 3.973A pdb=" N GLU A 418 " --> pdb=" O MET A 403 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 448 through 449 Processing sheet with id=AA4, first strand: chain 'A' and resid 493 through 494 removed outlier: 3.603A pdb=" N LEU A 494 " --> pdb=" O LYS A 726 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 498 through 501 removed outlier: 4.019A pdb=" N ILE A 498 " --> pdb=" O VAL A 719 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 719 " --> pdb=" O ILE A 498 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 642 through 644 Processing sheet with id=AA7, first strand: chain 'D' and resid 391 through 395 removed outlier: 6.936A pdb=" N VAL D 391 " --> pdb=" O LYS D 437 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ALA D 439 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N VAL D 393 " --> pdb=" O ALA D 439 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 403 through 404 Processing sheet with id=AA9, first strand: chain 'D' and resid 492 through 494 removed outlier: 4.243A pdb=" N MET D 492 " --> pdb=" O TYR D 728 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU D 494 " --> pdb=" O LYS D 726 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS D 726 " --> pdb=" O LEU D 494 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 642 through 644 removed outlier: 3.637A pdb=" N LEU D 699 " --> pdb=" O GLY D 644 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N PHE D 696 " --> pdb=" O LYS D 501 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LYS D 501 " --> pdb=" O PHE D 696 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 471 through 472 removed outlier: 3.816A pdb=" N ALA C 471 " --> pdb=" O ALA C 731 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ALA C 731 " --> pdb=" O ALA C 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 498 through 501 removed outlier: 4.069A pdb=" N ILE C 498 " --> pdb=" O VAL C 719 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 642 through 644 removed outlier: 3.623A pdb=" N GLY C 644 " --> pdb=" O ALA C 697 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 391 through 395 removed outlier: 6.668A pdb=" N VAL B 391 " --> pdb=" O LYS B 437 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ALA B 439 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N VAL B 393 " --> pdb=" O ALA B 439 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 403 through 404 Processing sheet with id=AB7, first strand: chain 'B' and resid 485 through 487 removed outlier: 3.790A pdb=" N THR B 732 " --> pdb=" O ASP B 486 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 492 through 494 removed outlier: 4.338A pdb=" N MET B 492 " --> pdb=" O TYR B 728 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU B 494 " --> pdb=" O LYS B 726 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS B 726 " --> pdb=" O LEU B 494 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 642 through 644 removed outlier: 6.880A pdb=" N ALA B 642 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N LEU B 699 " --> pdb=" O ALA B 642 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLY B 644 " --> pdb=" O LEU B 699 " (cutoff:3.500A) removed outlier: 9.287A pdb=" N GLU B 701 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 9.285A pdb=" N PHE B 696 " --> pdb=" O LYS B 501 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N LYS B 501 " --> pdb=" O PHE B 696 " (cutoff:3.500A) 841 hydrogen bonds defined for protein. 2493 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: 2.84 Time building geometry restraints manager: 2.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 2579 1.27 - 1.41: 4677 1.41 - 1.54: 9780 1.54 - 1.68: 73 1.68 - 1.81: 192 Bond restraints: 17301 Sorted by residual: bond pdb=" C8 DQC D 901 " pdb=" N4 DQC D 901 " ideal model delta sigma weight residual 1.452 1.520 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" C ARG B 449 " pdb=" N ASP B 450 " ideal model delta sigma weight residual 1.335 1.290 0.045 1.38e-02 5.25e+03 1.07e+01 bond pdb=" N VAL A 441 " pdb=" CA VAL A 441 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.19e-02 7.06e+03 9.37e+00 bond pdb=" N ILE D 440 " pdb=" CA ILE D 440 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.17e-02 7.31e+03 8.37e+00 bond pdb=" N ILE A 440 " pdb=" CA ILE A 440 " ideal model delta sigma weight residual 1.456 1.493 -0.038 1.30e-02 5.92e+03 8.33e+00 ... (remaining 17296 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 22721 2.01 - 4.01: 584 4.01 - 6.02: 78 6.02 - 8.02: 7 8.02 - 10.03: 2 Bond angle restraints: 23392 Sorted by residual: angle pdb=" N SER B 593 " pdb=" CA SER B 593 " pdb=" C SER B 593 " ideal model delta sigma weight residual 114.75 109.17 5.58 1.26e+00 6.30e-01 1.96e+01 angle pdb=" N THR B 453 " pdb=" CA THR B 453 " pdb=" C THR B 453 " ideal model delta sigma weight residual 112.88 107.27 5.61 1.29e+00 6.01e-01 1.89e+01 angle pdb=" N TYR D 446 " pdb=" CA TYR D 446 " pdb=" C TYR D 446 " ideal model delta sigma weight residual 111.71 106.77 4.94 1.15e+00 7.56e-01 1.84e+01 angle pdb=" N GLU B 664 " pdb=" CA GLU B 664 " pdb=" C GLU B 664 " ideal model delta sigma weight residual 113.28 108.14 5.14 1.22e+00 6.72e-01 1.77e+01 angle pdb=" N TYR B 446 " pdb=" CA TYR B 446 " pdb=" C TYR B 446 " ideal model delta sigma weight residual 113.15 108.16 4.99 1.19e+00 7.06e-01 1.76e+01 ... (remaining 23387 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 8576 17.97 - 35.94: 1151 35.94 - 53.92: 318 53.92 - 71.89: 35 71.89 - 89.86: 26 Dihedral angle restraints: 10106 sinusoidal: 3996 harmonic: 6110 Sorted by residual: 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 93.00 143.70 -50.70 1 1.00e+01 1.00e-02 3.52e+01 dihedral pdb=" CB CYS C 714 " pdb=" SG CYS C 714 " pdb=" SG CYS C 769 " pdb=" CB CYS C 769 " ideal model delta sinusoidal sigma weight residual 93.00 142.24 -49.24 1 1.00e+01 1.00e-02 3.33e+01 dihedral pdb=" CA LYS B 693 " pdb=" C LYS B 693 " pdb=" N GLY B 694 " pdb=" CA GLY B 694 " ideal model delta harmonic sigma weight residual 180.00 163.21 16.79 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 10103 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1858 0.042 - 0.084: 490 0.084 - 0.126: 172 0.126 - 0.168: 31 0.168 - 0.210: 24 Chirality restraints: 2575 Sorted by residual: chirality pdb=" CA VAL C 539 " pdb=" N VAL C 539 " pdb=" C VAL C 539 " pdb=" CB VAL C 539 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CB THR B 681 " pdb=" CA THR B 681 " pdb=" OG1 THR B 681 " pdb=" CG2 THR B 681 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA LEU B 699 " pdb=" N LEU B 699 " pdb=" C LEU B 699 " pdb=" CB LEU B 699 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 2572 not shown) Planarity restraints: 2849 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 DQC D 901 " -0.049 2.00e-02 2.50e+03 8.87e-02 2.16e+02 pdb=" C4 DQC D 901 " 0.029 2.00e-02 2.50e+03 pdb=" C5 DQC D 901 " -0.107 2.00e-02 2.50e+03 pdb=" C6 DQC D 901 " 0.040 2.00e-02 2.50e+03 pdb=" C7 DQC D 901 " -0.092 2.00e-02 2.50e+03 pdb=" C8 DQC D 901 " -0.024 2.00e-02 2.50e+03 pdb=" C9 DQC D 901 " 0.036 2.00e-02 2.50e+03 pdb=" N1 DQC D 901 " -0.034 2.00e-02 2.50e+03 pdb=" N2 DQC D 901 " 0.142 2.00e-02 2.50e+03 pdb=" N4 DQC D 901 " -0.106 2.00e-02 2.50e+03 pdb=" N8 DQC D 901 " 0.165 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 DQC B 901 " 0.055 2.00e-02 2.50e+03 6.47e-02 1.15e+02 pdb=" C4 DQC B 901 " 0.018 2.00e-02 2.50e+03 pdb=" C5 DQC B 901 " 0.085 2.00e-02 2.50e+03 pdb=" C6 DQC B 901 " 0.011 2.00e-02 2.50e+03 pdb=" C7 DQC B 901 " 0.069 2.00e-02 2.50e+03 pdb=" C8 DQC B 901 " 0.036 2.00e-02 2.50e+03 pdb=" C9 DQC B 901 " -0.011 2.00e-02 2.50e+03 pdb=" N1 DQC B 901 " -0.035 2.00e-02 2.50e+03 pdb=" N2 DQC B 901 " -0.118 2.00e-02 2.50e+03 pdb=" N4 DQC B 901 " 0.008 2.00e-02 2.50e+03 pdb=" N8 DQC B 901 " -0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 DQC D 901 " 0.000 2.00e-02 2.50e+03 3.53e-02 1.56e+01 pdb=" C2 DQC D 901 " -0.041 2.00e-02 2.50e+03 pdb=" C4 DQC D 901 " 0.037 2.00e-02 2.50e+03 pdb=" N2 DQC D 901 " -0.038 2.00e-02 2.50e+03 pdb=" O2 DQC D 901 " 0.042 2.00e-02 2.50e+03 ... (remaining 2846 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 3108 2.77 - 3.30: 15938 3.30 - 3.83: 26317 3.83 - 4.37: 28251 4.37 - 4.90: 50407 Nonbonded interactions: 124021 Sorted by model distance: nonbonded pdb=" O SER C 533 " pdb=" CG LEU C 536 " model vdw 2.232 3.470 nonbonded pdb=" OG1 THR B 681 " pdb=" O GLU B 684 " model vdw 2.241 3.040 nonbonded pdb=" NE2 GLN A 582 " pdb=" OE1 GLN B 583 " model vdw 2.261 3.120 nonbonded pdb=" CD1 ILE A 521 " pdb=" CD2 LEU B 785 " model vdw 2.262 3.880 nonbonded pdb=" O PRO B 516 " pdb=" ND2 ASN B 615 " model vdw 2.268 3.120 ... (remaining 124016 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 389 through 390 or resid 393 through 396 or resid 398 or r \ esid 400 through 403 or resid 405 through 407 or resid 411 through 415 or resid \ 417 through 422 or resid 424 through 425 or resid 427 through 431 or resid 433 o \ r resid 436 or resid 440 through 441 or resid 443 through 450 or resid 452 throu \ gh 454 or resid 456 through 466 or resid 468 or resid 471 or resid 473 through 5 \ 44 or resid 566 through 585 or resid 587 through 646 or resid 649 through 662 or \ resid 664 through 670 or resid 672 through 678 or resid 680 through 682 or resi \ d 684 through 685 or resid 688 through 695 or resid 697 or resid 699 through 729 \ or resid 731 through 736 or resid 738 through 739 or resid 741 through 751 or r \ esid 753 through 759 or resid 761 through 770 or resid 779 through 795 or resid \ 797 through 815 or resid 817 or resid 901)) selection = (chain 'B' and (resid 389 through 390 or resid 393 through 396 or resid 398 or r \ esid 400 through 403 or resid 405 through 407 or resid 411 through 415 or resid \ 417 through 422 or resid 424 through 425 or resid 427 through 431 or resid 433 o \ r resid 436 or resid 440 through 441 or resid 443 through 450 or resid 452 throu \ gh 454 or resid 456 through 466 or resid 468 or resid 471 or resid 473 through 5 \ 85 or resid 587 through 646 or resid 649 through 662 or resid 664 through 670 or \ resid 672 through 678 or resid 680 through 682 or resid 684 through 685 or resi \ d 688 through 695 or resid 697 or resid 699 through 729 or resid 731 through 736 \ or resid 738 through 739 or resid 741 through 751 or resid 753 through 759 or r \ esid 761 through 770 or resid 779 through 795 or resid 797 through 815 or resid \ 817 through 901)) selection = (chain 'C' and (resid 389 through 390 or resid 393 through 396 or resid 398 or r \ esid 400 through 403 or resid 405 through 407 or resid 411 through 415 or resid \ 417 through 422 or resid 424 through 425 or resid 427 through 431 or resid 433 o \ r resid 436 or resid 440 through 441 or resid 443 through 450 or resid 452 throu \ gh 454 or resid 456 through 466 or resid 468 or resid 471 or resid 473 through 5 \ 44 or resid 566 through 585 or resid 587 through 646 or resid 649 through 662 or \ resid 664 through 670 or resid 672 through 678 or resid 680 through 682 or resi \ d 684 through 685 or resid 688 through 695 or resid 697 or resid 699 through 729 \ or resid 731 through 736 or resid 738 through 739 or resid 741 through 751 or r \ esid 753 through 759 or resid 761 through 770 or resid 779 through 795 or resid \ 797 through 815 or resid 817 or resid 901)) selection = (chain 'D' and (resid 389 through 390 or resid 393 through 396 or resid 398 or r \ esid 400 through 403 or resid 405 through 407 or resid 411 through 415 or resid \ 417 through 422 or resid 424 through 425 or resid 427 through 431 or resid 433 o \ r resid 436 or resid 440 through 441 or resid 443 through 450 or resid 452 throu \ gh 454 or resid 456 through 466 or resid 468 or resid 471 or resid 473 through 5 \ 85 or resid 587 through 646 or resid 649 through 662 or resid 664 through 670 or \ resid 672 through 678 or resid 680 through 682 or resid 684 through 685 or resi \ d 688 through 695 or resid 697 or resid 699 through 729 or resid 731 through 736 \ or resid 738 through 739 or resid 741 through 751 or resid 753 through 759 or r \ esid 761 through 770 or resid 779 through 795 or resid 797 through 815 or resid \ 817 through 901)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.110 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: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.240 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6572 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 0.068 17305 Z= 0.292 Angle : 0.682 10.028 23400 Z= 0.433 Chirality : 0.047 0.210 2575 Planarity : 0.006 0.125 2849 Dihedral : 17.558 89.861 6176 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 0.00 % Allowed : 30.86 % Favored : 69.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.20), residues: 2051 helix: 1.58 (0.17), residues: 1148 sheet: -2.95 (0.46), residues: 116 loop : -2.45 (0.20), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 449 TYR 0.015 0.001 TYR C 812 PHE 0.023 0.001 PHE E 140 TRP 0.018 0.001 TRP C 456 HIS 0.002 0.001 HIS B 408 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.29 (17301) covalent geometry : angle 0.68193 / 0.43 (23392) SS BOND : bond 0.00185 / 0.09 ( 4) SS BOND : angle 0.51430 / 0.39 ( 8) hydrogen bonds : bond 0.20850 / 13.89 ( 841) hydrogen bonds : angle 5.82388 / 4.21 ( 2493) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 536 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 513 PHE cc_start: 0.7943 (p90) cc_final: 0.7527 (p90) REVERT: A 529 TYR cc_start: 0.7276 (t80) cc_final: 0.6930 (t80) REVERT: A 609 ILE cc_start: 0.9622 (mt) cc_final: 0.9269 (mm) REVERT: C 475 LEU cc_start: 0.8642 (tp) cc_final: 0.8302 (tp) REVERT: C 504 GLN cc_start: 0.7474 (tp-100) cc_final: 0.7041 (pp30) REVERT: C 513 PHE cc_start: 0.7855 (p90) cc_final: 0.7544 (p90) REVERT: C 609 ILE cc_start: 0.9605 (mt) cc_final: 0.9355 (mm) REVERT: C 646 LEU cc_start: 0.8425 (tp) cc_final: 0.8198 (tp) REVERT: B 500 ILE cc_start: 0.9156 (pt) cc_final: 0.8925 (mm) outliers start: 0 outliers final: 0 residues processed: 536 average time/residue: 0.1393 time to fit residues: 110.5845 Evaluate side-chains 246 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 0.9980 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 6.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 583 GLN D 408 HIS C 548 HIS B 582 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.076381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.056195 restraints weight = 174193.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.058426 restraints weight = 101298.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.060140 restraints weight = 60722.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.060212 restraints weight = 48024.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.060253 restraints weight = 43367.840| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17305 Z= 0.162 Angle : 0.671 8.231 23400 Z= 0.348 Chirality : 0.042 0.199 2575 Planarity : 0.005 0.054 2849 Dihedral : 3.906 24.752 2304 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.35 % Favored : 93.60 % Rotamer: Outliers : 0.22 % Allowed : 3.60 % Favored : 96.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.19), residues: 2051 helix: 1.59 (0.16), residues: 1138 sheet: -1.60 (0.42), residues: 142 loop : -2.58 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 739 TYR 0.030 0.002 TYR A 434 PHE 0.022 0.002 PHE A 527 TRP 0.016 0.002 TRP A 456 HIS 0.006 0.001 HIS A 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 (17301) covalent geometry : angle 0.66864 / 0.35 (23392) SS BOND : bond 0.00365 / 0.19 ( 4) SS BOND : angle 3.10839 / 2.29 ( 8) hydrogen bonds : bond 0.05941 / 4.00 ( 841) hydrogen bonds : angle 4.46204 / 3.26 ( 2493) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 301 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 MET cc_start: 0.8952 (mtp) cc_final: 0.8605 (mmm) REVERT: A 666 MET cc_start: 0.9487 (mtm) cc_final: 0.9212 (ptp) REVERT: D 390 THR cc_start: 0.9160 (m) cc_final: 0.8650 (t) REVERT: D 499 MET cc_start: 0.8353 (tpp) cc_final: 0.8098 (tpp) REVERT: D 536 LEU cc_start: 0.9681 (tp) cc_final: 0.9478 (tp) REVERT: D 704 MET cc_start: 0.8735 (tpt) cc_final: 0.8345 (tpp) REVERT: D 717 MET cc_start: 0.8713 (tmm) cc_final: 0.8382 (tmm) REVERT: C 504 GLN cc_start: 0.8302 (tp-100) cc_final: 0.7513 (pp30) REVERT: C 513 PHE cc_start: 0.8884 (p90) cc_final: 0.8624 (p90) REVERT: C 581 MET cc_start: 0.9462 (mmt) cc_final: 0.9218 (mmm) REVERT: C 633 GLU cc_start: 0.9432 (tp30) cc_final: 0.9078 (pm20) REVERT: C 666 MET cc_start: 0.9485 (mtm) cc_final: 0.9185 (ptp) REVERT: B 704 MET cc_start: 0.8888 (tpp) cc_final: 0.8619 (tpp) REVERT: E 16 LEU cc_start: 0.9504 (mp) cc_final: 0.9256 (tt) REVERT: E 27 HIS cc_start: 0.9038 (t-90) cc_final: 0.8815 (t-170) REVERT: E 82 PHE cc_start: 0.8951 (m-80) cc_final: 0.8495 (m-80) REVERT: H 75 HIS cc_start: 0.9047 (t-170) cc_final: 0.8708 (t-170) REVERT: H 77 LEU cc_start: 0.9384 (tp) cc_final: 0.8992 (tp) REVERT: H 80 ILE cc_start: 0.8042 (tp) cc_final: 0.7638 (tp) REVERT: H 81 MET cc_start: 0.9105 (mmp) cc_final: 0.8473 (ppp) REVERT: G 16 LEU cc_start: 0.9463 (mp) cc_final: 0.9178 (tt) REVERT: G 27 HIS cc_start: 0.9053 (t-90) cc_final: 0.8835 (t-170) REVERT: G 82 PHE cc_start: 0.8906 (m-80) cc_final: 0.8502 (m-80) REVERT: F 75 HIS cc_start: 0.9036 (t-170) cc_final: 0.8715 (t-170) REVERT: F 77 LEU cc_start: 0.9385 (tp) cc_final: 0.9040 (tp) REVERT: F 80 ILE cc_start: 0.8000 (tp) cc_final: 0.7622 (tp) REVERT: F 81 MET cc_start: 0.9129 (mmp) cc_final: 0.8519 (ppp) outliers start: 4 outliers final: 1 residues processed: 304 average time/residue: 0.1344 time to fit residues: 61.5841 Evaluate side-chains 212 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 211 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 165 optimal weight: 20.0000 chunk 137 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 186 optimal weight: 8.9990 chunk 196 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 177 optimal weight: 20.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 ASN A 583 GLN ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 407 ASN ** C 582 GLN ** 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 = 0.3453 r_free = 0.3453 target = 0.068227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.047121 restraints weight = 249379.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.049164 restraints weight = 119822.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.050473 restraints weight = 77266.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.051297 restraints weight = 58079.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.051847 restraints weight = 48580.821| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.6097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 17305 Z= 0.275 Angle : 0.780 9.206 23400 Z= 0.410 Chirality : 0.045 0.194 2575 Planarity : 0.006 0.087 2849 Dihedral : 4.707 22.906 2304 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.03 % Favored : 92.92 % Rotamer: Outliers : 0.17 % Allowed : 5.15 % Favored : 94.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.18), residues: 2051 helix: 1.09 (0.15), residues: 1176 sheet: -1.82 (0.46), residues: 126 loop : -2.55 (0.21), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 416 TYR 0.027 0.002 TYR H 141 PHE 0.035 0.003 PHE G 145 TRP 0.043 0.002 TRP D 574 HIS 0.007 0.001 HIS G 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.28 (17301) covalent geometry : angle 0.77899 / 0.41 (23392) SS BOND : bond 0.00499 / 0.24 ( 4) SS BOND : angle 1.78894 / 1.40 ( 8) hydrogen bonds : bond 0.05793 / 3.88 ( 841) hydrogen bonds : angle 4.69018 / 3.35 ( 2493) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 229 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 MET cc_start: 0.9163 (mtp) cc_final: 0.8934 (mtp) REVERT: A 666 MET cc_start: 0.9547 (mtm) cc_final: 0.8747 (mtt) REVERT: A 670 MET cc_start: 0.9428 (mmp) cc_final: 0.9200 (mmm) REVERT: D 403 MET cc_start: 0.8957 (mpp) cc_final: 0.8720 (mpp) REVERT: D 499 MET cc_start: 0.9061 (tpp) cc_final: 0.8684 (tpp) REVERT: D 536 LEU cc_start: 0.9740 (tp) cc_final: 0.9535 (tp) REVERT: D 666 MET cc_start: 0.8841 (tpp) cc_final: 0.8449 (tpp) REVERT: D 704 MET cc_start: 0.8907 (tpt) cc_final: 0.8561 (tpp) REVERT: D 717 MET cc_start: 0.8964 (tmm) cc_final: 0.8495 (tmm) REVERT: C 504 GLN cc_start: 0.8008 (tp-100) cc_final: 0.7362 (pm20) REVERT: C 513 PHE cc_start: 0.9207 (p90) cc_final: 0.8802 (p90) REVERT: C 581 MET cc_start: 0.9582 (mmt) cc_final: 0.9202 (mmm) REVERT: C 619 PHE cc_start: 0.8606 (t80) cc_final: 0.8324 (t80) REVERT: C 664 GLU cc_start: 0.8791 (mp0) cc_final: 0.8009 (mp0) REVERT: C 666 MET cc_start: 0.9502 (mtm) cc_final: 0.9168 (ptp) REVERT: C 786 SER cc_start: 0.9681 (m) cc_final: 0.9476 (p) REVERT: B 704 MET cc_start: 0.8854 (tpp) cc_final: 0.8627 (tpp) REVERT: B 758 LEU cc_start: 0.9633 (mp) cc_final: 0.9355 (tp) REVERT: H 75 HIS cc_start: 0.9202 (t-170) cc_final: 0.8788 (t-170) REVERT: H 77 LEU cc_start: 0.9404 (tp) cc_final: 0.9007 (tp) REVERT: H 81 MET cc_start: 0.9117 (mmp) cc_final: 0.8462 (ppp) REVERT: H 151 CYS cc_start: 0.7273 (m) cc_final: 0.6907 (m) REVERT: G 27 HIS cc_start: 0.9204 (t-90) cc_final: 0.9002 (t-90) REVERT: G 105 TYR cc_start: 0.9057 (t80) cc_final: 0.8849 (t80) REVERT: F 75 HIS cc_start: 0.9221 (t-170) cc_final: 0.8829 (t-170) REVERT: F 77 LEU cc_start: 0.9419 (tp) cc_final: 0.9045 (tp) REVERT: F 80 ILE cc_start: 0.8226 (tp) cc_final: 0.7853 (tp) REVERT: F 81 MET cc_start: 0.8986 (mmp) cc_final: 0.8445 (ppp) REVERT: F 151 CYS cc_start: 0.7263 (m) cc_final: 0.6961 (p) outliers start: 3 outliers final: 2 residues processed: 232 average time/residue: 0.1265 time to fit residues: 45.8101 Evaluate side-chains 183 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 181 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 108 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 191 optimal weight: 5.9990 chunk 152 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 HIS ** C 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 HIS B 760 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.068187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.047620 restraints weight = 204874.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.049518 restraints weight = 104363.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.050727 restraints weight = 69293.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.051477 restraints weight = 53315.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.051986 restraints weight = 45283.571| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3018 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3018 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.6597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17305 Z= 0.201 Angle : 0.657 7.594 23400 Z= 0.344 Chirality : 0.042 0.185 2575 Planarity : 0.005 0.061 2849 Dihedral : 4.374 21.494 2304 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.64 % Favored : 93.31 % Rotamer: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.19), residues: 2051 helix: 1.32 (0.15), residues: 1170 sheet: -1.35 (0.46), residues: 124 loop : -2.50 (0.21), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 624 TYR 0.029 0.002 TYR F 141 PHE 0.025 0.002 PHE G 145 TRP 0.022 0.001 TRP D 574 HIS 0.006 0.001 HIS D 408 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.20 (17301) covalent geometry : angle 0.65677 / 0.34 (23392) SS BOND : bond 0.01078 / 0.56 ( 4) SS BOND : angle 1.24622 / 0.73 ( 8) hydrogen bonds : bond 0.05030 / 3.35 ( 841) hydrogen bonds : angle 4.47585 / 3.20 ( 2493) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 666 MET cc_start: 0.9613 (mtm) cc_final: 0.9140 (mtp) REVERT: A 670 MET cc_start: 0.9487 (mmp) cc_final: 0.9159 (mmm) REVERT: D 397 MET cc_start: 0.8499 (pmm) cc_final: 0.8279 (pmm) REVERT: D 499 MET cc_start: 0.9051 (tpp) cc_final: 0.8669 (tpp) REVERT: D 666 MET cc_start: 0.8921 (tpp) cc_final: 0.8469 (tpp) REVERT: D 704 MET cc_start: 0.8916 (tpt) cc_final: 0.8543 (tpp) REVERT: D 717 MET cc_start: 0.8883 (tmm) cc_final: 0.8411 (tmm) REVERT: C 498 ILE cc_start: 0.9816 (mt) cc_final: 0.9504 (pt) REVERT: C 504 GLN cc_start: 0.8027 (tp-100) cc_final: 0.7436 (pm20) REVERT: C 581 MET cc_start: 0.9577 (mmt) cc_final: 0.9306 (mmm) REVERT: C 664 GLU cc_start: 0.8839 (mp0) cc_final: 0.8263 (mp0) REVERT: C 666 MET cc_start: 0.9576 (mtm) cc_final: 0.8944 (ptp) REVERT: C 786 SER cc_start: 0.9642 (m) cc_final: 0.9428 (p) REVERT: B 536 LEU cc_start: 0.9729 (tp) cc_final: 0.9527 (tp) REVERT: B 655 PHE cc_start: 0.9278 (m-80) cc_final: 0.9038 (m-80) REVERT: B 666 MET cc_start: 0.8899 (mmm) cc_final: 0.8547 (tpp) REVERT: B 670 MET cc_start: 0.8925 (mmp) cc_final: 0.8650 (mmp) REVERT: B 758 LEU cc_start: 0.9572 (mp) cc_final: 0.9325 (tp) REVERT: E 82 PHE cc_start: 0.8774 (m-80) cc_final: 0.8396 (m-80) REVERT: H 81 MET cc_start: 0.9086 (mmp) cc_final: 0.8646 (mmt) REVERT: H 151 CYS cc_start: 0.7385 (m) cc_final: 0.7066 (m) REVERT: G 105 TYR cc_start: 0.9091 (t80) cc_final: 0.8878 (t80) REVERT: F 151 CYS cc_start: 0.7373 (m) cc_final: 0.7159 (p) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.1199 time to fit residues: 40.0695 Evaluate side-chains 175 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 25 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 chunk 109 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 186 optimal weight: 0.9990 chunk 199 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 149 optimal weight: 10.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 75 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.068637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.048843 restraints weight = 168229.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.050504 restraints weight = 95792.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.051567 restraints weight = 66912.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.052178 restraints weight = 53186.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.052653 restraints weight = 46549.057| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3027 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3027 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.6968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17305 Z= 0.164 Angle : 0.620 7.518 23400 Z= 0.323 Chirality : 0.041 0.203 2575 Planarity : 0.004 0.053 2849 Dihedral : 4.257 21.316 2304 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.59 % Favored : 93.36 % Rotamer: Outliers : 0.06 % Allowed : 3.10 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.19), residues: 2051 helix: 1.45 (0.15), residues: 1180 sheet: -1.37 (0.45), residues: 128 loop : -2.47 (0.21), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 739 TYR 0.037 0.002 TYR F 148 PHE 0.024 0.002 PHE G 145 TRP 0.017 0.001 TRP D 574 HIS 0.005 0.001 HIS H 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (17301) covalent geometry : angle 0.61943 / 0.32 (23392) SS BOND : bond 0.00429 / 0.21 ( 4) SS BOND : angle 1.40850 / 1.04 ( 8) hydrogen bonds : bond 0.04661 / 3.12 ( 841) hydrogen bonds : angle 4.28153 / 3.07 ( 2493) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 219 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 MET cc_start: 0.9100 (mtp) cc_final: 0.8595 (mmt) REVERT: A 666 MET cc_start: 0.9491 (mtm) cc_final: 0.9048 (mtm) REVERT: A 670 MET cc_start: 0.9483 (mmp) cc_final: 0.9149 (mmm) REVERT: D 397 MET cc_start: 0.8706 (pmm) cc_final: 0.8469 (pmm) REVERT: D 499 MET cc_start: 0.9013 (tpp) cc_final: 0.8659 (tpp) REVERT: D 666 MET cc_start: 0.8892 (tpp) cc_final: 0.8469 (tpp) REVERT: D 704 MET cc_start: 0.8886 (tpt) cc_final: 0.8463 (tpp) REVERT: D 717 MET cc_start: 0.8813 (tmm) cc_final: 0.8343 (tmm) REVERT: C 498 ILE cc_start: 0.9808 (mt) cc_final: 0.9492 (pt) REVERT: C 581 MET cc_start: 0.9501 (mmt) cc_final: 0.9205 (mmm) REVERT: C 664 GLU cc_start: 0.8909 (mp0) cc_final: 0.8315 (mp0) REVERT: C 666 MET cc_start: 0.9602 (mtm) cc_final: 0.9026 (ptp) REVERT: C 786 SER cc_start: 0.9623 (m) cc_final: 0.9414 (p) REVERT: B 403 MET cc_start: 0.7347 (mmm) cc_final: 0.7046 (mmt) REVERT: B 499 MET cc_start: 0.9173 (tpp) cc_final: 0.8885 (tpp) REVERT: B 536 LEU cc_start: 0.9718 (tp) cc_final: 0.9514 (tp) REVERT: B 655 PHE cc_start: 0.9316 (m-80) cc_final: 0.9088 (m-80) REVERT: B 704 MET cc_start: 0.8626 (tpp) cc_final: 0.8302 (tpp) REVERT: B 758 LEU cc_start: 0.9579 (mp) cc_final: 0.9378 (tp) REVERT: E 82 PHE cc_start: 0.8836 (m-80) cc_final: 0.8527 (m-80) REVERT: E 105 TYR cc_start: 0.9090 (t80) cc_final: 0.8882 (t80) REVERT: H 81 MET cc_start: 0.9047 (mmp) cc_final: 0.8223 (ptt) REVERT: H 151 CYS cc_start: 0.7570 (m) cc_final: 0.7363 (m) REVERT: G 105 TYR cc_start: 0.9097 (t80) cc_final: 0.8874 (t80) outliers start: 1 outliers final: 1 residues processed: 220 average time/residue: 0.1198 time to fit residues: 41.8205 Evaluate side-chains 179 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 178 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 75 optimal weight: 7.9990 chunk 166 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 67 optimal weight: 0.7980 chunk 170 optimal weight: 20.0000 chunk 158 optimal weight: 0.9980 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.067354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.048555 restraints weight = 241547.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.050492 restraints weight = 127156.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.050649 restraints weight = 83629.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.050787 restraints weight = 83437.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.050858 restraints weight = 71522.085| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2970 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.7435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17305 Z= 0.211 Angle : 0.675 8.261 23400 Z= 0.352 Chirality : 0.043 0.204 2575 Planarity : 0.005 0.077 2849 Dihedral : 4.442 22.138 2304 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.18), residues: 2051 helix: 1.24 (0.15), residues: 1190 sheet: -1.51 (0.42), residues: 134 loop : -2.39 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 595 TYR 0.029 0.002 TYR H 141 PHE 0.028 0.002 PHE G 145 TRP 0.019 0.002 TRP D 574 HIS 0.010 0.001 HIS E 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.21 (17301) covalent geometry : angle 0.67499 / 0.35 (23392) SS BOND : bond 0.00296 / 0.15 ( 4) SS BOND : angle 1.20089 / 0.78 ( 8) hydrogen bonds : bond 0.04910 / 3.26 ( 841) hydrogen bonds : angle 4.42991 / 3.17 ( 2493) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 MET cc_start: 0.9236 (mtp) cc_final: 0.8940 (mtp) REVERT: A 666 MET cc_start: 0.9557 (mtm) cc_final: 0.9135 (mtp) REVERT: A 670 MET cc_start: 0.9556 (mmp) cc_final: 0.9214 (mmm) REVERT: D 397 MET cc_start: 0.8988 (pmm) cc_final: 0.8661 (pmm) REVERT: D 499 MET cc_start: 0.9011 (tpp) cc_final: 0.8708 (tpp) REVERT: D 666 MET cc_start: 0.9014 (tpp) cc_final: 0.8669 (tpp) REVERT: D 704 MET cc_start: 0.8866 (tpt) cc_final: 0.8450 (tpp) REVERT: D 717 MET cc_start: 0.8894 (tmm) cc_final: 0.8450 (tmm) REVERT: D 748 LYS cc_start: 0.9765 (tmtt) cc_final: 0.9543 (tptp) REVERT: C 498 ILE cc_start: 0.9773 (mt) cc_final: 0.9561 (tp) REVERT: C 581 MET cc_start: 0.9538 (mmt) cc_final: 0.9304 (mmm) REVERT: C 664 GLU cc_start: 0.8964 (mp0) cc_final: 0.8372 (mp0) REVERT: C 666 MET cc_start: 0.9679 (mtm) cc_final: 0.9089 (ptp) REVERT: C 670 MET cc_start: 0.9275 (mmp) cc_final: 0.9006 (mmm) REVERT: C 786 SER cc_start: 0.9606 (m) cc_final: 0.9401 (p) REVERT: B 398 GLU cc_start: 0.8911 (tm-30) cc_final: 0.8352 (pm20) REVERT: B 403 MET cc_start: 0.7728 (mmm) cc_final: 0.7273 (mmt) REVERT: B 499 MET cc_start: 0.8979 (tpp) cc_final: 0.8751 (tpp) REVERT: B 655 PHE cc_start: 0.9351 (m-80) cc_final: 0.9077 (m-80) REVERT: B 704 MET cc_start: 0.8611 (tpp) cc_final: 0.8336 (tpt) REVERT: B 717 MET cc_start: 0.9007 (ptm) cc_final: 0.8216 (ppp) REVERT: B 758 LEU cc_start: 0.9625 (mp) cc_final: 0.9362 (tp) REVERT: E 82 PHE cc_start: 0.8864 (m-80) cc_final: 0.8516 (m-80) REVERT: E 105 TYR cc_start: 0.9129 (t80) cc_final: 0.8919 (t80) REVERT: H 77 LEU cc_start: 0.9537 (tp) cc_final: 0.9185 (tp) REVERT: H 81 MET cc_start: 0.9188 (mmp) cc_final: 0.8442 (ppp) REVERT: G 105 TYR cc_start: 0.9112 (t80) cc_final: 0.8892 (t80) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.1154 time to fit residues: 38.3881 Evaluate side-chains 167 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 14 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 196 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 111 optimal weight: 7.9990 chunk 170 optimal weight: 10.0000 chunk 117 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 HIS E 101 HIS ** G 101 HIS ** 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 = 0.3469 r_free = 0.3469 target = 0.068988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.048232 restraints weight = 229903.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.050775 restraints weight = 116541.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.052222 restraints weight = 66830.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.052833 restraints weight = 46690.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.052875 restraints weight = 42858.443| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.7509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17305 Z= 0.119 Angle : 0.599 8.295 23400 Z= 0.305 Chirality : 0.040 0.186 2575 Planarity : 0.004 0.049 2849 Dihedral : 4.139 20.166 2304 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.19), residues: 2051 helix: 1.57 (0.15), residues: 1168 sheet: -1.27 (0.44), residues: 124 loop : -2.22 (0.22), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 595 TYR 0.034 0.001 TYR H 141 PHE 0.022 0.001 PHE F 23 TRP 0.018 0.001 TRP D 574 HIS 0.009 0.001 HIS E 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (17301) covalent geometry : angle 0.59899 / 0.31 (23392) SS BOND : bond 0.00152 / 0.08 ( 4) SS BOND : angle 0.78685 / 0.61 ( 8) hydrogen bonds : bond 0.04303 / 2.85 ( 841) hydrogen bonds : angle 4.12379 / 2.97 ( 2493) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 MET cc_start: 0.9176 (mtp) cc_final: 0.8905 (mtp) REVERT: A 581 MET cc_start: 0.9313 (mmp) cc_final: 0.8943 (mmp) REVERT: A 666 MET cc_start: 0.9547 (mtm) cc_final: 0.9040 (mtp) REVERT: A 670 MET cc_start: 0.9458 (mmp) cc_final: 0.9104 (mmm) REVERT: D 397 MET cc_start: 0.8959 (pmm) cc_final: 0.8725 (pmm) REVERT: D 459 MET cc_start: 0.9339 (mmt) cc_final: 0.8977 (mmt) REVERT: D 499 MET cc_start: 0.8888 (tpp) cc_final: 0.8608 (tpp) REVERT: D 666 MET cc_start: 0.8960 (tpp) cc_final: 0.8574 (tpp) REVERT: D 704 MET cc_start: 0.8872 (tpt) cc_final: 0.8359 (tpp) REVERT: D 717 MET cc_start: 0.8683 (tmm) cc_final: 0.8220 (tmm) REVERT: D 748 LYS cc_start: 0.9729 (tmtt) cc_final: 0.9487 (tptp) REVERT: C 581 MET cc_start: 0.9416 (mmt) cc_final: 0.9187 (mmp) REVERT: C 666 MET cc_start: 0.9612 (mtm) cc_final: 0.9071 (ptp) REVERT: C 670 MET cc_start: 0.9143 (mmp) cc_final: 0.8941 (mmm) REVERT: C 786 SER cc_start: 0.9519 (m) cc_final: 0.9290 (p) REVERT: B 499 MET cc_start: 0.8909 (tpp) cc_final: 0.8697 (tpp) REVERT: B 704 MET cc_start: 0.8554 (tpp) cc_final: 0.8194 (tpp) REVERT: B 717 MET cc_start: 0.8809 (ptm) cc_final: 0.7887 (ppp) REVERT: B 758 LEU cc_start: 0.9626 (mp) cc_final: 0.9401 (tp) REVERT: E 82 PHE cc_start: 0.8775 (m-80) cc_final: 0.8530 (m-80) REVERT: E 105 TYR cc_start: 0.9110 (t80) cc_final: 0.8896 (t80) REVERT: H 77 LEU cc_start: 0.9493 (tp) cc_final: 0.9218 (tp) REVERT: H 81 MET cc_start: 0.9213 (mmp) cc_final: 0.8436 (ppp) REVERT: G 105 TYR cc_start: 0.9114 (t80) cc_final: 0.8892 (t80) REVERT: F 16 LEU cc_start: 0.9586 (mp) cc_final: 0.9361 (tp) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.1121 time to fit residues: 39.5258 Evaluate side-chains 171 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 191 optimal weight: 0.7980 chunk 179 optimal weight: 9.9990 chunk 204 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 154 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 162 optimal weight: 0.8980 chunk 186 optimal weight: 10.0000 chunk 187 optimal weight: 9.9990 chunk 171 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 HIS E 101 HIS ** G 101 HIS ** 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 = 0.3420 r_free = 0.3420 target = 0.066757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.048192 restraints weight = 219990.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.049402 restraints weight = 118796.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.049808 restraints weight = 81827.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.050129 restraints weight = 74542.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.050887 restraints weight = 65310.525| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.7885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17305 Z= 0.197 Angle : 0.668 8.066 23400 Z= 0.346 Chirality : 0.042 0.189 2575 Planarity : 0.005 0.075 2849 Dihedral : 4.390 22.982 2304 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.19), residues: 2051 helix: 1.35 (0.15), residues: 1190 sheet: -1.50 (0.41), residues: 136 loop : -2.26 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 624 TYR 0.031 0.002 TYR H 141 PHE 0.023 0.002 PHE E 145 TRP 0.014 0.002 TRP D 574 HIS 0.006 0.001 HIS E 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.20 (17301) covalent geometry : angle 0.66810 / 0.35 (23392) SS BOND : bond 0.00384 / 0.20 ( 4) SS BOND : angle 0.89860 / 0.58 ( 8) hydrogen bonds : bond 0.04572 / 3.03 ( 841) hydrogen bonds : angle 4.36513 / 3.14 ( 2493) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 MET cc_start: 0.9193 (mtp) cc_final: 0.8851 (mtp) REVERT: A 666 MET cc_start: 0.9596 (mtm) cc_final: 0.9153 (mtp) REVERT: A 670 MET cc_start: 0.9515 (mmp) cc_final: 0.9277 (mmm) REVERT: D 397 MET cc_start: 0.9009 (pmm) cc_final: 0.8761 (pmm) REVERT: D 666 MET cc_start: 0.8969 (tpp) cc_final: 0.8535 (tpp) REVERT: D 704 MET cc_start: 0.8875 (tpt) cc_final: 0.8557 (tpp) REVERT: D 717 MET cc_start: 0.8793 (tmm) cc_final: 0.8318 (tmm) REVERT: C 619 PHE cc_start: 0.8770 (t80) cc_final: 0.8435 (t80) REVERT: C 666 MET cc_start: 0.9653 (mtm) cc_final: 0.9057 (ptp) REVERT: C 670 MET cc_start: 0.9218 (mmp) cc_final: 0.8988 (mmm) REVERT: C 786 SER cc_start: 0.9562 (m) cc_final: 0.9339 (p) REVERT: B 403 MET cc_start: 0.5924 (mmt) cc_final: 0.5488 (mmt) REVERT: B 704 MET cc_start: 0.8604 (tpp) cc_final: 0.8371 (tpt) REVERT: B 717 MET cc_start: 0.8918 (ptm) cc_final: 0.8019 (ppp) REVERT: B 758 LEU cc_start: 0.9650 (mp) cc_final: 0.9377 (tp) REVERT: E 82 PHE cc_start: 0.8837 (m-80) cc_final: 0.8572 (m-80) REVERT: H 77 LEU cc_start: 0.9500 (tp) cc_final: 0.9121 (pp) REVERT: H 151 CYS cc_start: 0.7773 (m) cc_final: 0.7425 (t) REVERT: G 105 TYR cc_start: 0.9110 (t80) cc_final: 0.8875 (t80) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.1113 time to fit residues: 36.7679 Evaluate side-chains 171 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 75 optimal weight: 10.0000 chunk 160 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 3 optimal weight: 8.9990 chunk 169 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 chunk 2 optimal weight: 0.0030 chunk 185 optimal weight: 10.0000 overall best weight: 1.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 HIS ** G 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.067628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.047869 restraints weight = 201524.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.049919 restraints weight = 109329.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.051199 restraints weight = 65304.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.051335 restraints weight = 49603.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.051379 restraints weight = 47858.172| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.8008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17305 Z= 0.154 Angle : 0.643 8.047 23400 Z= 0.329 Chirality : 0.041 0.188 2575 Planarity : 0.004 0.068 2849 Dihedral : 4.286 21.295 2304 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.19), residues: 2051 helix: 1.51 (0.15), residues: 1166 sheet: -1.45 (0.40), residues: 134 loop : -2.11 (0.22), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 595 TYR 0.033 0.001 TYR F 141 PHE 0.020 0.002 PHE G 145 TRP 0.015 0.001 TRP C 456 HIS 0.005 0.001 HIS E 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (17301) covalent geometry : angle 0.64237 / 0.33 (23392) SS BOND : bond 0.00136 / 0.07 ( 4) SS BOND : angle 1.13689 / 0.71 ( 8) hydrogen bonds : bond 0.04351 / 2.87 ( 841) hydrogen bonds : angle 4.31898 / 3.11 ( 2493) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 MET cc_start: 0.9153 (mtp) cc_final: 0.8842 (mtp) REVERT: A 581 MET cc_start: 0.9365 (mmp) cc_final: 0.8975 (mmp) REVERT: A 666 MET cc_start: 0.9613 (mtm) cc_final: 0.9067 (mtp) REVERT: A 670 MET cc_start: 0.9484 (mmp) cc_final: 0.9251 (mmm) REVERT: D 666 MET cc_start: 0.8970 (tpp) cc_final: 0.8566 (tpp) REVERT: D 704 MET cc_start: 0.8891 (tpt) cc_final: 0.8558 (tpp) REVERT: D 717 MET cc_start: 0.8809 (tmm) cc_final: 0.8224 (tmm) REVERT: D 748 LYS cc_start: 0.9746 (tmtt) cc_final: 0.9494 (tptp) REVERT: C 459 MET cc_start: 0.9295 (mtm) cc_final: 0.8478 (mpp) REVERT: C 547 TRP cc_start: 0.5408 (t-100) cc_final: 0.4650 (m-10) REVERT: C 581 MET cc_start: 0.9514 (mmm) cc_final: 0.9220 (mmp) REVERT: C 666 MET cc_start: 0.9618 (mtm) cc_final: 0.9035 (ptp) REVERT: C 670 MET cc_start: 0.9188 (mmp) cc_final: 0.8986 (mmm) REVERT: C 786 SER cc_start: 0.9534 (m) cc_final: 0.9300 (p) REVERT: B 704 MET cc_start: 0.8519 (tpp) cc_final: 0.8310 (tpt) REVERT: B 717 MET cc_start: 0.8991 (ptm) cc_final: 0.8183 (ppp) REVERT: B 758 LEU cc_start: 0.9678 (mp) cc_final: 0.9434 (tp) REVERT: E 149 LEU cc_start: 0.9136 (tp) cc_final: 0.8827 (pp) REVERT: H 151 CYS cc_start: 0.7725 (m) cc_final: 0.7343 (t) REVERT: G 105 TYR cc_start: 0.9116 (t80) cc_final: 0.8879 (t80) REVERT: G 149 LEU cc_start: 0.9135 (tp) cc_final: 0.8819 (pp) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.1179 time to fit residues: 40.6935 Evaluate side-chains 177 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 54 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 chunk 163 optimal weight: 8.9990 chunk 193 optimal weight: 8.9990 chunk 86 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 136 optimal weight: 7.9990 chunk 176 optimal weight: 10.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.065396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.047900 restraints weight = 211918.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.048813 restraints weight = 111581.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.048647 restraints weight = 95313.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.049243 restraints weight = 80445.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.049564 restraints weight = 69596.162| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.8417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 17305 Z= 0.268 Angle : 0.768 8.605 23400 Z= 0.401 Chirality : 0.044 0.213 2575 Planarity : 0.005 0.069 2849 Dihedral : 4.859 23.492 2304 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.18), residues: 2051 helix: 1.00 (0.15), residues: 1176 sheet: -1.76 (0.38), residues: 150 loop : -2.32 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 711 TYR 0.032 0.002 TYR F 141 PHE 0.026 0.002 PHE E 22 TRP 0.016 0.002 TRP F 88 HIS 0.011 0.002 HIS E 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.27 (17301) covalent geometry : angle 0.76816 / 0.40 (23392) SS BOND : bond 0.00407 / 0.20 ( 4) SS BOND : angle 1.03516 / 0.58 ( 8) hydrogen bonds : bond 0.05151 / 3.41 ( 841) hydrogen bonds : angle 4.80252 / 3.45 ( 2493) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4102 Ramachandran restraints generated. 2051 Oldfield, 0 Emsley, 2051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 666 MET cc_start: 0.9598 (mtm) cc_final: 0.8983 (mpp) REVERT: A 670 MET cc_start: 0.9524 (mmp) cc_final: 0.9273 (mmm) REVERT: D 459 MET cc_start: 0.9304 (mmt) cc_final: 0.8874 (mmt) REVERT: D 666 MET cc_start: 0.9008 (tpp) cc_final: 0.8592 (tpp) REVERT: D 704 MET cc_start: 0.8840 (tpt) cc_final: 0.8547 (tpp) REVERT: D 717 MET cc_start: 0.8880 (tmm) cc_final: 0.8298 (tmm) REVERT: C 459 MET cc_start: 0.9407 (mtm) cc_final: 0.8479 (mpp) REVERT: C 547 TRP cc_start: 0.5818 (t-100) cc_final: 0.4733 (m-10) REVERT: C 581 MET cc_start: 0.9616 (mmm) cc_final: 0.9181 (mmp) REVERT: C 619 PHE cc_start: 0.8659 (t80) cc_final: 0.8364 (t80) REVERT: C 666 MET cc_start: 0.9649 (mtm) cc_final: 0.9037 (ptp) REVERT: C 670 MET cc_start: 0.9250 (mmp) cc_final: 0.9045 (mmm) REVERT: C 786 SER cc_start: 0.9576 (m) cc_final: 0.9364 (p) REVERT: B 717 MET cc_start: 0.8954 (ptm) cc_final: 0.8066 (ppp) REVERT: B 758 LEU cc_start: 0.9699 (mp) cc_final: 0.9424 (tp) REVERT: E 82 PHE cc_start: 0.8610 (m-80) cc_final: 0.8186 (m-80) REVERT: E 105 TYR cc_start: 0.9116 (t80) cc_final: 0.8910 (t80) REVERT: E 149 LEU cc_start: 0.9091 (tp) cc_final: 0.8750 (pp) REVERT: H 151 CYS cc_start: 0.7736 (m) cc_final: 0.7519 (p) REVERT: H 152 MET cc_start: 0.7299 (tmm) cc_final: 0.7091 (tmm) REVERT: G 105 TYR cc_start: 0.9137 (t80) cc_final: 0.8748 (t80) REVERT: G 149 LEU cc_start: 0.9077 (tp) cc_final: 0.8734 (pp) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.1093 time to fit residues: 36.9185 Evaluate side-chains 170 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 98 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 134 optimal weight: 0.8980 chunk 150 optimal weight: 0.0870 chunk 77 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.068680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.049170 restraints weight = 198486.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.051129 restraints weight = 108161.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.052453 restraints weight = 65438.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.052455 restraints weight = 55930.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.052521 restraints weight = 50291.353| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3027 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3027 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.8303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17305 Z= 0.121 Angle : 0.651 10.160 23400 Z= 0.328 Chirality : 0.042 0.187 2575 Planarity : 0.004 0.065 2849 Dihedral : 4.373 24.531 2304 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.19), residues: 2051 helix: 1.50 (0.15), residues: 1164 sheet: -1.50 (0.47), residues: 92 loop : -2.14 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 595 TYR 0.027 0.001 TYR H 141 PHE 0.024 0.001 PHE F 23 TRP 0.019 0.001 TRP C 456 HIS 0.005 0.001 HIS B 408 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (17301) covalent geometry : angle 0.65077 / 0.33 (23392) SS BOND : bond 0.00147 / 0.07 ( 4) SS BOND : angle 1.07411 / 0.73 ( 8) hydrogen bonds : bond 0.04265 / 2.81 ( 841) hydrogen bonds : angle 4.30674 / 3.10 ( 2493) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3238.40 seconds wall clock time: 56 minutes 46.64 seconds (3406.64 seconds total)