Starting phenix.real_space_refine on Wed May 6 06:30:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ovv_70920/05_2026/9ovv_70920_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ovv_70920/05_2026/9ovv_70920.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ovv_70920/05_2026/9ovv_70920.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ovv_70920/05_2026/9ovv_70920.map" model { file = "/net/cci-nas-00/data/ceres_data/9ovv_70920/05_2026/9ovv_70920_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ovv_70920/05_2026/9ovv_70920_trim.cif" } resolution = 3.76 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= -0.003 sd= 0.947 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 16 5.49 5 S 134 5.16 5 Na 1 4.78 5 C 12122 2.51 5 N 2758 2.21 5 O 3222 1.98 5 H 17444 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35697 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 6383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 6383 Classifications: {'peptide': 404} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 389} Chain breaks: 3 Chain: "B" Number of atoms: 6363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 6363 Classifications: {'peptide': 403} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 389} Chain breaks: 2 Chain: "C" Number of atoms: 6383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 6383 Classifications: {'peptide': 404} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 389} Chain breaks: 3 Chain: "D" Number of atoms: 6363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 6363 Classifications: {'peptide': 403} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 389} Chain breaks: 2 Chain: "E" Number of atoms: 2317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2317 Classifications: {'peptide': 142} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "F" Number of atoms: 2317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2317 Classifications: {'peptide': 142} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "G" Number of atoms: 2317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2317 Classifications: {'peptide': 142} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "H" Number of atoms: 2317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2317 Classifications: {'peptide': 142} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 189 Unusual residues: {' NA': 1, 'FWF': 1, 'POV': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 240 Unusual residues: {'FWF': 1, 'POV': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 208 Unusual residues: {'POV': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 208 Unusual residues: {'POV': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.74, per 1000 atoms: 0.19 Number of scatterers: 35697 At special positions: 0 Unit cell: (133.63, 119.52, 141.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 134 16.00 P 16 15.00 Na 1 11.00 O 3222 8.00 N 2758 7.00 C 12122 6.00 H 17444 1.00 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 B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 714 " - pdb=" SG CYS C 769 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 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: 3.83 Conformation dependent library (CDL) restraints added in 1.1 seconds 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4056 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 20 sheets defined 57.0% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 412 through 415 removed outlier: 3.759A pdb=" N ASP A 415 " --> pdb=" O GLU A 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 412 through 415' Processing helix chain 'A' and resid 419 through 433 removed outlier: 3.651A pdb=" N ALA A 425 " --> pdb=" O CYS A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 464 Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 518 through 542 removed outlier: 3.829A pdb=" N CYS A 524 " --> pdb=" O GLU A 520 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE A 527 " --> pdb=" O MET A 523 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLY A 531 " --> pdb=" O PHE A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 581 removed outlier: 3.844A pdb=" N TRP A 574 " --> pdb=" O PHE A 570 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE A 575 " --> pdb=" O ASN A 571 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N MET A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 620 removed outlier: 3.674A pdb=" N ILE A 607 " --> pdb=" O PHE A 603 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A 608 " --> pdb=" O PHE A 604 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA A 614 " --> pdb=" O SER A 610 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN A 615 " --> pdb=" O SER A 611 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ALA A 617 " --> pdb=" O THR A 613 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A 618 " --> pdb=" O ALA A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 637 removed outlier: 4.101A pdb=" N LYS A 637 " --> pdb=" O GLU A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 658 removed outlier: 3.612A pdb=" N GLU A 653 " --> pdb=" O GLY A 649 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE A 655 " --> pdb=" O THR A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 672 Processing helix chain 'A' and resid 681 through 692 removed outlier: 3.688A pdb=" N GLY A 685 " --> pdb=" O THR A 681 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG A 690 " --> pdb=" O MET A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 705 No H-bonds generated for 'chain 'A' and resid 703 through 705' Processing helix chain 'A' and resid 707 through 711 removed outlier: 3.680A pdb=" N ARG A 711 " --> pdb=" O ILE A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 752 removed outlier: 3.635A pdb=" N ASN A 743 " --> pdb=" O ARG A 739 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU A 749 " --> pdb=" O ALA A 745 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN A 752 " --> pdb=" O LYS A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 763 removed outlier: 3.969A pdb=" N LYS A 761 " --> pdb=" O LYS A 757 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TRP A 763 " --> pdb=" O LYS A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 815 removed outlier: 3.504A pdb=" N GLY A 797 " --> pdb=" O TYR A 793 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 804 " --> pdb=" O GLY A 800 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU A 807 " --> pdb=" O MET A 803 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N TYR A 812 " --> pdb=" O ILE A 808 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG A 815 " --> pdb=" O CYS A 811 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 removed outlier: 4.252A pdb=" N GLU B 419 " --> pdb=" O GLU B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 437 removed outlier: 3.592A pdb=" N GLU B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 467 removed outlier: 3.543A pdb=" N LEU B 467 " --> pdb=" O VAL B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 522 through 544 removed outlier: 3.565A pdb=" N TRP B 526 " --> pdb=" O ALA B 522 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET B 527 " --> pdb=" O TYR B 523 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLY B 535 " --> pdb=" O PHE B 531 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL B 539 " --> pdb=" O GLY B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 585 removed outlier: 3.644A pdb=" N MET B 585 " --> pdb=" O LEU B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 617 removed outlier: 4.136A pdb=" N VAL B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY B 602 " --> pdb=" O GLY B 598 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL B 604 " --> pdb=" O ILE B 600 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N PHE B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE B 612 " --> pdb=" O PHE B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 624 Processing helix chain 'B' and resid 637 through 641 Processing helix chain 'B' and resid 653 through 661 removed outlier: 3.737A pdb=" N GLU B 657 " --> pdb=" O GLY B 653 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE B 659 " --> pdb=" O THR B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 675 removed outlier: 3.898A pdb=" N THR B 672 " --> pdb=" O ASP B 668 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR B 673 " --> pdb=" O LYS B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 694 removed outlier: 3.609A pdb=" N ARG B 692 " --> pdb=" O GLU B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 713 removed outlier: 3.846A pdb=" N ASN B 709 " --> pdb=" O GLU B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 750 removed outlier: 3.772A pdb=" N VAL B 746 " --> pdb=" O LEU B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 756 removed outlier: 3.592A pdb=" N GLN B 756 " --> pdb=" O LYS B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 767 removed outlier: 3.693A pdb=" N LYS B 761 " --> pdb=" O GLY B 757 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TRP B 767 " --> pdb=" O LYS B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 817 removed outlier: 3.754A pdb=" N VAL B 792 " --> pdb=" O SER B 788 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N GLY B 794 " --> pdb=" O SER B 790 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL B 795 " --> pdb=" O ASN B 791 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE B 798 " --> pdb=" O GLY B 794 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY B 801 " --> pdb=" O TYR B 797 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU B 805 " --> pdb=" O GLY B 801 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU B 808 " --> pdb=" O GLY B 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 415 removed outlier: 3.760A pdb=" N ASP C 415 " --> pdb=" O GLU C 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 412 through 415' Processing helix chain 'C' and resid 419 through 433 removed outlier: 3.650A pdb=" N ALA C 425 " --> pdb=" O CYS C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 464 Processing helix chain 'C' and resid 478 through 483 Processing helix chain 'C' and resid 518 through 542 removed outlier: 3.829A pdb=" N CYS C 524 " --> pdb=" O GLU C 520 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE C 527 " --> pdb=" O MET C 523 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLY C 531 " --> pdb=" O PHE C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 581 removed outlier: 3.844A pdb=" N TRP C 574 " --> pdb=" O PHE C 570 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE C 575 " --> pdb=" O ASN C 571 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET C 581 " --> pdb=" O LEU C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 620 removed outlier: 3.675A pdb=" N ILE C 607 " --> pdb=" O PHE C 603 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE C 608 " --> pdb=" O PHE C 604 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA C 614 " --> pdb=" O SER C 610 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN C 615 " --> pdb=" O SER C 611 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ALA C 617 " --> pdb=" O THR C 613 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA C 618 " --> pdb=" O ALA C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 637 removed outlier: 4.100A pdb=" N LYS C 637 " --> pdb=" O GLU C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 658 removed outlier: 3.613A pdb=" N GLU C 653 " --> pdb=" O GLY C 649 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE C 655 " --> pdb=" O THR C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 660 through 672 Processing helix chain 'C' and resid 681 through 692 removed outlier: 3.688A pdb=" N GLY C 685 " --> pdb=" O THR C 681 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG C 690 " --> pdb=" O MET C 686 " (cutoff:3.500A) Processing helix chain 'C' and resid 703 through 705 No H-bonds generated for 'chain 'C' and resid 703 through 705' Processing helix chain 'C' and resid 707 through 711 removed outlier: 3.679A pdb=" N ARG C 711 " --> pdb=" O ILE C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 752 removed outlier: 3.636A pdb=" N ASN C 743 " --> pdb=" O ARG C 739 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU C 749 " --> pdb=" O ALA C 745 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN C 752 " --> pdb=" O LYS C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 763 removed outlier: 3.969A pdb=" N LYS C 761 " --> pdb=" O LYS C 757 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP C 763 " --> pdb=" O LYS C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 815 removed outlier: 3.504A pdb=" N GLY C 797 " --> pdb=" O TYR C 793 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU C 804 " --> pdb=" O GLY C 800 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU C 807 " --> pdb=" O MET C 803 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE C 808 " --> pdb=" O LEU C 804 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N TYR C 812 " --> pdb=" O ILE C 808 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG C 815 " --> pdb=" O CYS C 811 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 421 removed outlier: 4.252A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 437 removed outlier: 3.593A pdb=" N GLU D 431 " --> pdb=" O ASP D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 467 removed outlier: 3.543A pdb=" N LEU D 467 " --> pdb=" O VAL D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 515 through 519 Processing helix chain 'D' and resid 522 through 544 removed outlier: 3.566A pdb=" N TRP D 526 " --> pdb=" O ALA D 522 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET D 527 " --> pdb=" O TYR D 523 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N CYS D 528 " --> pdb=" O GLU D 524 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY D 535 " --> pdb=" O PHE D 531 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL D 539 " --> pdb=" O GLY D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 585 removed outlier: 3.645A pdb=" N MET D 585 " --> pdb=" O LEU D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 617 removed outlier: 4.135A pdb=" N VAL D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY D 602 " --> pdb=" O GLY D 598 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL D 604 " --> pdb=" O ILE D 600 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N PHE D 607 " --> pdb=" O GLY D 603 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE D 611 " --> pdb=" O PHE D 607 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE D 612 " --> pdb=" O PHE D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 624 Processing helix chain 'D' and resid 637 through 641 Processing helix chain 'D' and resid 653 through 661 removed outlier: 3.736A pdb=" N GLU D 657 " --> pdb=" O GLY D 653 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE D 659 " --> pdb=" O THR D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 675 removed outlier: 3.897A pdb=" N THR D 672 " --> pdb=" O ASP D 668 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR D 673 " --> pdb=" O LYS D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 694 removed outlier: 3.608A pdb=" N ARG D 692 " --> pdb=" O GLU D 688 " (cutoff:3.500A) Processing helix chain 'D' and resid 705 through 713 removed outlier: 3.846A pdb=" N ASN D 709 " --> pdb=" O GLU D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 750 removed outlier: 3.772A pdb=" N VAL D 746 " --> pdb=" O LEU D 742 " (cutoff:3.500A) Processing helix chain 'D' and resid 750 through 756 removed outlier: 3.592A pdb=" N GLN D 756 " --> pdb=" O LYS D 752 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 767 removed outlier: 3.694A pdb=" N LYS D 761 " --> pdb=" O GLY D 757 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TRP D 767 " --> pdb=" O LYS D 763 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 817 removed outlier: 3.754A pdb=" N VAL D 792 " --> pdb=" O SER D 788 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N GLY D 794 " --> pdb=" O SER D 790 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL D 795 " --> pdb=" O ASN D 791 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE D 798 " --> pdb=" O GLY D 794 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY D 801 " --> pdb=" O TYR D 797 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU D 805 " --> pdb=" O GLY D 801 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU D 808 " --> pdb=" O GLY D 804 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 32 removed outlier: 4.386A pdb=" N TYR E 10 " --> pdb=" O ALA E 6 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU E 12 " --> pdb=" O PHE E 8 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA E 13 " --> pdb=" O CYS E 9 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU E 15 " --> pdb=" O MET E 11 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA E 18 " --> pdb=" O LEU E 14 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE E 23 " --> pdb=" O ALA E 19 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA E 24 " --> pdb=" O LEU E 20 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE E 29 " --> pdb=" O ILE E 25 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA E 30 " --> pdb=" O TRP E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 47 Processing helix chain 'E' and resid 48 through 51 removed outlier: 3.565A pdb=" N LEU E 51 " --> pdb=" O LEU E 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 48 through 51' Processing helix chain 'E' and resid 52 through 68 removed outlier: 3.623A pdb=" N LEU E 57 " --> pdb=" O LEU E 53 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N HIS E 59 " --> pdb=" O GLU E 55 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE E 62 " --> pdb=" O ILE E 58 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N CYS E 63 " --> pdb=" O HIS E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 90 Proline residue: E 80 - end of helix removed outlier: 4.135A pdb=" N ALA E 83 " --> pdb=" O MET E 79 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N TYR E 84 " --> pdb=" O PRO E 80 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N HIS E 85 " --> pdb=" O LEU E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 117 removed outlier: 3.755A pdb=" N TYR E 114 " --> pdb=" O ASP E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 142 removed outlier: 3.544A pdb=" N LYS E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LEU E 123 " --> pdb=" O GLY E 119 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA E 124 " --> pdb=" O TRP E 120 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE E 125 " --> pdb=" O CYS E 121 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL E 140 " --> pdb=" O GLY E 136 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL E 142 " --> pdb=" O ILE E 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 38 removed outlier: 3.733A pdb=" N PHE F 8 " --> pdb=" O THR F 4 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N CYS F 9 " --> pdb=" O PHE F 5 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU F 15 " --> pdb=" O MET F 11 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ALA F 18 " --> pdb=" O LEU F 14 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA F 19 " --> pdb=" O LEU F 15 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA F 30 " --> pdb=" O TRP F 26 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU F 33 " --> pdb=" O ILE F 29 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS F 35 " --> pdb=" O PHE F 31 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N THR F 36 " --> pdb=" O ASP F 32 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP F 37 " --> pdb=" O GLU F 33 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR F 38 " --> pdb=" O LEU F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 69 removed outlier: 4.535A pdb=" N HIS F 59 " --> pdb=" O GLU F 55 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE F 62 " --> pdb=" O ILE F 58 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N CYS F 63 " --> pdb=" O HIS F 59 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL F 64 " --> pdb=" O ALA F 60 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU F 67 " --> pdb=" O CYS F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 91 Proline residue: F 80 - end of helix removed outlier: 4.025A pdb=" N TYR F 84 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 107 Processing helix chain 'F' and resid 108 through 143 removed outlier: 4.799A pdb=" N LEU F 123 " --> pdb=" O GLY F 119 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA F 124 " --> pdb=" O TRP F 120 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE F 125 " --> pdb=" O CYS F 121 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU F 141 " --> pdb=" O MET F 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 32 removed outlier: 4.386A pdb=" N TYR G 10 " --> pdb=" O ALA G 6 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU G 12 " --> pdb=" O PHE G 8 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA G 13 " --> pdb=" O CYS G 9 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU G 15 " --> pdb=" O MET G 11 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA G 18 " --> pdb=" O LEU G 14 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE G 23 " --> pdb=" O ALA G 19 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA G 24 " --> pdb=" O LEU G 20 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE G 29 " --> pdb=" O ILE G 25 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA G 30 " --> pdb=" O TRP G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 47 Processing helix chain 'G' and resid 48 through 51 removed outlier: 3.566A pdb=" N LEU G 51 " --> pdb=" O LEU G 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 48 through 51' Processing helix chain 'G' and resid 52 through 69 removed outlier: 3.622A pdb=" N LEU G 57 " --> pdb=" O LEU G 53 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N HIS G 59 " --> pdb=" O GLU G 55 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE G 62 " --> pdb=" O ILE G 58 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N CYS G 63 " --> pdb=" O HIS G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 90 Proline residue: G 80 - end of helix removed outlier: 4.134A pdb=" N ALA G 83 " --> pdb=" O MET G 79 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TYR G 84 " --> pdb=" O PRO G 80 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N HIS G 85 " --> pdb=" O LEU G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 117 removed outlier: 3.754A pdb=" N TYR G 114 " --> pdb=" O ASP G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 142 removed outlier: 3.544A pdb=" N LYS G 122 " --> pdb=" O GLU G 118 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LEU G 123 " --> pdb=" O GLY G 119 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA G 124 " --> pdb=" O TRP G 120 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE G 125 " --> pdb=" O CYS G 121 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL G 140 " --> pdb=" O GLY G 136 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL G 142 " --> pdb=" O ILE G 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 38 removed outlier: 3.733A pdb=" N PHE H 8 " --> pdb=" O THR H 4 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS H 9 " --> pdb=" O PHE H 5 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU H 15 " --> pdb=" O MET H 11 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ALA H 18 " --> pdb=" O LEU H 14 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA H 19 " --> pdb=" O LEU H 15 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA H 30 " --> pdb=" O TRP H 26 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU H 33 " --> pdb=" O ILE H 29 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS H 35 " --> pdb=" O PHE H 31 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N THR H 36 " --> pdb=" O ASP H 32 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP H 37 " --> pdb=" O GLU H 33 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR H 38 " --> pdb=" O LEU H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 69 removed outlier: 4.535A pdb=" N HIS H 59 " --> pdb=" O GLU H 55 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE H 62 " --> pdb=" O ILE H 58 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N CYS H 63 " --> pdb=" O HIS H 59 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL H 64 " --> pdb=" O ALA H 60 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU H 67 " --> pdb=" O CYS H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 91 Proline residue: H 80 - end of helix removed outlier: 4.025A pdb=" N TYR H 84 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 107 Processing helix chain 'H' and resid 108 through 143 removed outlier: 4.799A pdb=" N LEU H 123 " --> pdb=" O GLY H 119 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA H 124 " --> pdb=" O TRP H 120 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE H 125 " --> pdb=" O CYS H 121 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU H 141 " --> pdb=" O MET H 137 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 391 through 395 Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 404 removed outlier: 3.677A pdb=" N MET A 403 " --> pdb=" O GLU A 418 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 449 through 450 removed outlier: 3.720A pdb=" N ALA A 455 " --> pdb=" O ASP A 450 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 486 through 487 Processing sheet with id=AA5, first strand: chain 'A' and resid 493 through 494 removed outlier: 3.725A pdb=" N LYS A 726 " --> pdb=" O LEU A 494 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 496 through 498 removed outlier: 6.694A pdb=" N ALA A 642 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N LEU A 699 " --> pdb=" O ALA A 642 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLY A 644 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 9.010A pdb=" N GLU A 701 " --> pdb=" O GLY A 644 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 395 through 399 Processing sheet with id=AA8, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AA9, first strand: chain 'B' and resid 497 through 498 Processing sheet with id=AB1, first strand: chain 'B' and resid 646 through 648 Processing sheet with id=AB2, first strand: chain 'C' and resid 391 through 395 Processing sheet with id=AB3, first strand: chain 'C' and resid 403 through 404 removed outlier: 3.677A pdb=" N MET C 403 " --> pdb=" O GLU C 418 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 449 through 450 removed outlier: 3.720A pdb=" N ALA C 455 " --> pdb=" O ASP C 450 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 486 through 487 Processing sheet with id=AB6, first strand: chain 'C' and resid 493 through 494 removed outlier: 3.725A pdb=" N LYS C 726 " --> pdb=" O LEU C 494 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 496 through 498 removed outlier: 6.693A pdb=" N ALA C 642 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N LEU C 699 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLY C 644 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 9.010A pdb=" N GLU C 701 " --> pdb=" O GLY C 644 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 395 through 399 Processing sheet with id=AB9, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AC1, first strand: chain 'D' and resid 497 through 498 Processing sheet with id=AC2, first strand: chain 'D' and resid 646 through 648 709 hydrogen bonds defined for protein. 2037 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: 7.02 Time building geometry restraints manager: 5.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 17402 1.03 - 1.23: 565 1.23 - 1.43: 7321 1.43 - 1.63: 10588 1.63 - 1.83: 246 Bond restraints: 36122 Sorted by residual: bond pdb=" C21 POV C 904 " pdb=" O21 POV C 904 " ideal model delta sigma weight residual 1.330 1.422 -0.092 2.00e-02 2.50e+03 2.13e+01 bond pdb=" C21 POV C 902 " pdb=" O21 POV C 902 " ideal model delta sigma weight residual 1.330 1.421 -0.091 2.00e-02 2.50e+03 2.07e+01 bond pdb=" C21 POV A 902 " pdb=" O21 POV A 902 " ideal model delta sigma weight residual 1.330 1.421 -0.091 2.00e-02 2.50e+03 2.07e+01 bond pdb=" C21 POV E 201 " pdb=" O21 POV E 201 " ideal model delta sigma weight residual 1.330 1.421 -0.091 2.00e-02 2.50e+03 2.07e+01 bond pdb=" C21 POV C 905 " pdb=" O21 POV C 905 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.03e+01 ... (remaining 36117 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 63677 2.56 - 5.11: 772 5.11 - 7.67: 147 7.67 - 10.23: 60 10.23 - 12.78: 48 Bond angle restraints: 64704 Sorted by residual: angle pdb=" N SER B 403 " pdb=" CA SER B 403 " pdb=" C SER B 403 " ideal model delta sigma weight residual 110.14 102.09 8.05 1.51e+00 4.39e-01 2.84e+01 angle pdb=" N SER D 403 " pdb=" CA SER D 403 " pdb=" C SER D 403 " ideal model delta sigma weight residual 110.14 102.11 8.03 1.51e+00 4.39e-01 2.83e+01 angle pdb=" N ASP B 590 " pdb=" CA ASP B 590 " pdb=" C ASP B 590 " ideal model delta sigma weight residual 113.55 108.01 5.54 1.26e+00 6.30e-01 1.93e+01 angle pdb=" N ASP D 590 " pdb=" CA ASP D 590 " pdb=" C ASP D 590 " ideal model delta sigma weight residual 113.55 108.01 5.54 1.26e+00 6.30e-01 1.93e+01 angle pdb=" O11 POV A 902 " pdb=" P POV A 902 " pdb=" O12 POV A 902 " ideal model delta sigma weight residual 97.67 110.45 -12.78 3.00e+00 1.11e-01 1.82e+01 ... (remaining 64699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.70: 16813 35.70 - 71.41: 522 71.41 - 107.11: 34 107.11 - 142.81: 10 142.81 - 178.51: 5 Dihedral angle restraints: 17384 sinusoidal: 9504 harmonic: 7880 Sorted by residual: dihedral pdb=" CA LYS A 712 " pdb=" C LYS A 712 " pdb=" N PRO A 713 " pdb=" CA PRO A 713 " ideal model delta harmonic sigma weight residual 180.00 134.36 45.64 0 5.00e+00 4.00e-02 8.33e+01 dihedral pdb=" CA LYS C 712 " pdb=" C LYS C 712 " pdb=" N PRO C 713 " pdb=" CA PRO C 713 " ideal model delta harmonic sigma weight residual 180.00 134.42 45.58 0 5.00e+00 4.00e-02 8.31e+01 dihedral pdb=" CA THR G 105 " pdb=" C THR G 105 " pdb=" N ILE G 106 " pdb=" CA ILE G 106 " ideal model delta harmonic sigma weight residual -180.00 -143.08 -36.92 0 5.00e+00 4.00e-02 5.45e+01 ... (remaining 17381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1716 0.039 - 0.078: 749 0.078 - 0.117: 173 0.117 - 0.156: 48 0.156 - 0.196: 4 Chirality restraints: 2690 Sorted by residual: chirality pdb=" CA ARG C 389 " pdb=" N ARG C 389 " pdb=" C ARG C 389 " pdb=" CB ARG C 389 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.57e-01 chirality pdb=" CA ARG A 389 " pdb=" N ARG A 389 " pdb=" C ARG A 389 " pdb=" CB ARG A 389 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.35e-01 chirality pdb=" CB VAL C 532 " pdb=" CA VAL C 532 " pdb=" CG1 VAL C 532 " pdb=" CG2 VAL C 532 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.74e-01 ... (remaining 2687 not shown) Planarity restraints: 5092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 571 " 0.165 2.00e-02 2.50e+03 1.87e-01 5.22e+02 pdb=" CG ASN C 571 " -0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN C 571 " -0.158 2.00e-02 2.50e+03 pdb=" ND2 ASN C 571 " 0.003 2.00e-02 2.50e+03 pdb="HD21 ASN C 571 " -0.272 2.00e-02 2.50e+03 pdb="HD22 ASN C 571 " 0.287 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 747 " 0.163 2.00e-02 2.50e+03 1.85e-01 5.14e+02 pdb=" CG ASN B 747 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN B 747 " -0.158 2.00e-02 2.50e+03 pdb=" ND2 ASN B 747 " 0.006 2.00e-02 2.50e+03 pdb="HD21 ASN B 747 " -0.271 2.00e-02 2.50e+03 pdb="HD22 ASN B 747 " 0.283 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 571 " -0.161 2.00e-02 2.50e+03 1.82e-01 4.95e+02 pdb=" CG ASN A 571 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN A 571 " 0.154 2.00e-02 2.50e+03 pdb=" ND2 ASN A 571 " -0.003 2.00e-02 2.50e+03 pdb="HD21 ASN A 571 " 0.265 2.00e-02 2.50e+03 pdb="HD22 ASN A 571 " -0.279 2.00e-02 2.50e+03 ... (remaining 5089 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.30: 7030 2.30 - 2.88: 79352 2.88 - 3.45: 87027 3.45 - 4.03: 117927 4.03 - 4.60: 183001 Nonbonded interactions: 474337 Sorted by model distance: nonbonded pdb=" O ASP G 102 " pdb=" H THR G 105 " model vdw 1.727 2.450 nonbonded pdb=" O ASP E 102 " pdb=" H THR E 105 " model vdw 1.728 2.450 nonbonded pdb=" H ALA C 642 " pdb=" O LYS C 695 " model vdw 1.740 2.450 nonbonded pdb=" H ALA A 642 " pdb=" O LYS A 695 " model vdw 1.740 2.450 nonbonded pdb=" O SER A 702 " pdb=" H ASN A 705 " model vdw 1.745 2.450 ... (remaining 474332 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 387 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB \ 3 or name HG2 or name HG3 or name HE21 or name HE22)) or resid 390 or resid 393 \ through 398 or resid 400 through 403 or resid 405 through 407 or resid 412 throu \ gh 414 or resid 416 through 422 or resid 424 through 431 or resid 433 or resid 4 \ 36 or resid 438 or resid 440 through 441 or resid 443 through 450 or resid 452 t \ hrough 454 or resid 456 through 466 or resid 468 through 469 or resid 471 or res \ id 473 through 546 or resid 565 through 581 or resid 583 through 635 or resid 63 \ 7 through 646 or resid 649 through 663 or resid 665 through 670 or resid 672 thr \ ough 682 or resid 684 through 685 or resid 688 through 736 or resid 738 or resid \ 741 through 759 or resid 761 through 770 or resid 779 through 795 or resid 797 \ through 904)) selection = (chain 'B' and ((resid 392 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB \ 3 or name HG2 or name HG3 or name HE21 or name HE22)) or resid 394 or resid 397 \ through 402 or resid 404 through 407 or resid 409 through 411 or resid 416 throu \ gh 418 or resid 420 through 426 or resid 428 through 435 or resid 437 or resid 4 \ 40 or resid 442 or resid 444 through 445 or resid 447 through 454 or resid 456 t \ hrough 458 or resid 460 through 470 or resid 472 through 473 or resid 475 or res \ id 477 through 550 or resid 569 through 585 or resid 587 through 625 or resid 63 \ 1 through 639 or resid 641 through 650 or resid 653 through 667 or resid 669 thr \ ough 674 or resid 676 through 686 or resid 688 through 689 or resid 692 through \ 740 or resid 742 or resid 745 through 763 or resid 765 through 799 or resid 801 \ through 904)) selection = (chain 'C' and ((resid 387 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB \ 3 or name HG2 or name HG3 or name HE21 or name HE22)) or resid 390 or resid 393 \ through 398 or resid 400 through 403 or resid 405 through 407 or resid 412 throu \ gh 414 or resid 416 through 422 or resid 424 through 431 or resid 433 or resid 4 \ 36 or resid 438 or resid 440 through 441 or resid 443 through 450 or resid 452 t \ hrough 454 or resid 456 through 466 or resid 468 through 469 or resid 471 or res \ id 473 through 546 or resid 565 through 581 or resid 583 through 635 or resid 63 \ 7 through 646 or resid 649 through 663 or resid 665 through 670 or resid 672 thr \ ough 682 or resid 684 through 685 or resid 688 through 736 or resid 738 or resid \ 741 through 759 or resid 761 through 770 or resid 779 through 795 or resid 797 \ through 904)) selection = (chain 'D' and ((resid 392 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB \ 3 or name HG2 or name HG3 or name HE21 or name HE22)) or resid 394 or resid 397 \ through 402 or resid 404 through 407 or resid 409 through 411 or resid 416 throu \ gh 418 or resid 420 through 426 or resid 428 through 435 or resid 437 or resid 4 \ 40 or resid 442 or resid 444 through 445 or resid 447 through 454 or resid 456 t \ hrough 458 or resid 460 through 470 or resid 472 through 473 or resid 475 or res \ id 477 through 550 or resid 569 through 585 or resid 587 through 625 or resid 63 \ 1 through 639 or resid 641 through 650 or resid 653 through 667 or resid 669 thr \ ough 674 or resid 676 through 686 or resid 688 through 689 or resid 692 through \ 740 or resid 742 or resid 745 through 763 or resid 765 through 799 or resid 801 \ through 904)) } ncs_group { reference = (chain 'E' and resid 2 through 143) 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=0.45 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: 6.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.210 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 32.310 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6369 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 : 0.009 0.092 18682 Z= 0.431 Angle : 1.184 12.784 25140 Z= 0.552 Chirality : 0.045 0.196 2690 Planarity : 0.006 0.096 3010 Dihedral : 16.176 178.514 7112 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.47 % Allowed : 11.70 % Favored : 87.84 % Rotamer: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.10 % 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: -4.98 (0.15), residues: 2146 helix: -3.43 (0.11), residues: 1070 sheet: -4.08 (0.35), residues: 126 loop : -2.89 (0.20), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 661 TYR 0.023 0.002 TYR D 732 PHE 0.019 0.002 PHE B 546 TRP 0.011 0.001 TRP A 601 HIS 0.008 0.002 HIS H 85 Details of bonding type rmsd covalent geometry : bond 0.00927 (18678) covalent geometry : angle 1.18331 (25132) SS BOND : bond 0.00364 ( 4) SS BOND : angle 2.07326 ( 8) hydrogen bonds : bond 0.30365 ( 709) hydrogen bonds : angle 10.45373 ( 2037) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 545 time to evaluate : 0.816 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: 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: B 404 PRO cc_start: 0.8605 (Cg_endo) cc_final: 0.8317 (Cg_exo) REVERT: C 700 LEU cc_start: 0.5886 (pt) cc_final: 0.5682 (pt) REVERT: E 65 MET cc_start: 0.6035 (ttp) cc_final: 0.5583 (ttp) REVERT: F 72 TRP cc_start: 0.6525 (m-10) cc_final: 0.5770 (t60) REVERT: F 95 MET cc_start: 0.3492 (tpt) cc_final: 0.1489 (mpp) REVERT: H 77 LEU cc_start: 0.8184 (mt) cc_final: 0.7560 (tt) REVERT: H 90 MET cc_start: 0.7078 (mmp) cc_final: 0.6304 (ptp) outliers start: 0 outliers final: 0 residues processed: 545 average time/residue: 0.3301 time to fit residues: 264.5897 Evaluate side-chains 315 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 0.0270 chunk 77 optimal weight: 2.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 726 ASN B 747 ASN D 726 ASN D 747 ASN E 40 ASN ** H 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.196265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.162825 restraints weight = 74078.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.166570 restraints weight = 62137.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.168182 restraints weight = 40435.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.168216 restraints weight = 33070.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.168792 restraints weight = 32210.860| |-----------------------------------------------------------------------------| r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3944 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3944 r_free = 0.3944 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3937 r_free = 0.3937 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3937 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18682 Z= 0.152 Angle : 0.652 6.504 25140 Z= 0.341 Chirality : 0.040 0.151 2690 Planarity : 0.006 0.108 3010 Dihedral : 16.585 168.856 3122 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.33 % Allowed : 10.76 % Favored : 88.91 % Rotamer: Outliers : 2.05 % Allowed : 11.45 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.10 % 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: -3.74 (0.16), residues: 2146 helix: -1.89 (0.13), residues: 1172 sheet: -3.28 (0.37), residues: 152 loop : -3.05 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 690 TYR 0.012 0.001 TYR F 114 PHE 0.018 0.001 PHE A 619 TRP 0.014 0.001 TRP G 87 HIS 0.009 0.002 HIS F 85 Details of bonding type rmsd covalent geometry : bond 0.00337 (18678) covalent geometry : angle 0.65187 (25132) SS BOND : bond 0.00154 ( 4) SS BOND : angle 0.58667 ( 8) hydrogen bonds : bond 0.05390 ( 709) hydrogen bonds : angle 5.43231 ( 2037) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 340 time to evaluate : 0.888 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 787 ASN cc_start: 0.7391 (t0) cc_final: 0.7166 (t0) REVERT: B 404 PRO cc_start: 0.8556 (Cg_endo) cc_final: 0.8264 (Cg_exo) REVERT: C 787 ASN cc_start: 0.7502 (t0) cc_final: 0.7253 (t0) REVERT: D 404 PRO cc_start: 0.8684 (Cg_endo) cc_final: 0.8339 (Cg_exo) REVERT: D 546 PHE cc_start: 0.5222 (p90) cc_final: 0.4408 (p90) REVERT: D 585 MET cc_start: 0.7963 (mmt) cc_final: 0.7245 (mtt) REVERT: E 128 LEU cc_start: 0.6105 (mt) cc_final: 0.5795 (mt) REVERT: F 72 TRP cc_start: 0.6639 (m-10) cc_final: 0.5515 (t60) REVERT: F 95 MET cc_start: 0.3545 (tpt) cc_final: 0.1428 (mpp) REVERT: F 120 TRP cc_start: 0.4936 (m100) cc_final: 0.4357 (m100) REVERT: F 135 TYR cc_start: 0.4271 (m-80) cc_final: 0.3805 (m-80) REVERT: G 22 PHE cc_start: 0.6690 (OUTLIER) cc_final: 0.5927 (t80) REVERT: G 90 MET cc_start: 0.5151 (mpp) cc_final: 0.4936 (mpp) REVERT: H 27 HIS cc_start: 0.5312 (m-70) cc_final: 0.5106 (m90) REVERT: H 77 LEU cc_start: 0.8302 (mt) cc_final: 0.7779 (tt) outliers start: 38 outliers final: 25 residues processed: 366 average time/residue: 0.2994 time to fit residues: 168.2156 Evaluate side-chains 302 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 276 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 645 ILE Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 521 ILE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 422 GLU Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 645 ILE Chi-restraints excluded: chain D residue 815 CYS Chi-restraints excluded: chain E residue 9 CYS Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 22 PHE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 107 MET Chi-restraints excluded: chain A residue 901 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 167 optimal weight: 5.9990 chunk 212 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 186 optimal weight: 4.9990 chunk 16 optimal weight: 0.0870 chunk 126 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 GLN A 710 GLN F 44 GLN G 40 ASN ** H 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.182285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.151450 restraints weight = 72009.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.151470 restraints weight = 83757.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.154335 restraints weight = 68873.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.153899 restraints weight = 47803.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.154380 restraints weight = 46718.412| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3802 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3802 r_free = 0.3802 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3802 r_free = 0.3802 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3802 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.5465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18682 Z= 0.137 Angle : 0.593 7.954 25140 Z= 0.309 Chirality : 0.038 0.166 2690 Planarity : 0.005 0.095 3010 Dihedral : 14.630 137.970 3122 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.69 % Favored : 90.17 % Rotamer: Outliers : 1.94 % Allowed : 12.47 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.05 % 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: -2.92 (0.17), residues: 2146 helix: -1.03 (0.14), residues: 1214 sheet: -3.00 (0.39), residues: 150 loop : -3.08 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 688 TYR 0.015 0.001 TYR F 89 PHE 0.017 0.001 PHE E 23 TRP 0.007 0.001 TRP D 767 HIS 0.009 0.001 HIS F 59 Details of bonding type rmsd covalent geometry : bond 0.00311 (18678) covalent geometry : angle 0.59285 (25132) SS BOND : bond 0.00611 ( 4) SS BOND : angle 0.92945 ( 8) hydrogen bonds : bond 0.04907 ( 709) hydrogen bonds : angle 4.66718 ( 2037) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 280 time to evaluate : 0.910 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: symmetry clash revert: symmetry clash REVERT: A 492 MET cc_start: 0.9368 (mtp) cc_final: 0.9100 (ttm) REVERT: B 404 PRO cc_start: 0.8595 (Cg_endo) cc_final: 0.8323 (Cg_exo) REVERT: D 404 PRO cc_start: 0.8656 (Cg_endo) cc_final: 0.8367 (Cg_exo) REVERT: D 546 PHE cc_start: 0.5394 (p90) cc_final: 0.4511 (p90) REVERT: F 72 TRP cc_start: 0.6528 (m-10) cc_final: 0.5256 (t60) REVERT: F 95 MET cc_start: 0.3605 (tpt) cc_final: 0.1359 (mpp) REVERT: F 120 TRP cc_start: 0.4866 (m100) cc_final: 0.4555 (m100) REVERT: H 77 LEU cc_start: 0.8226 (mt) cc_final: 0.7720 (tt) REVERT: H 90 MET cc_start: 0.6519 (mmp) cc_final: 0.5985 (ptp) outliers start: 36 outliers final: 25 residues processed: 296 average time/residue: 0.2826 time to fit residues: 129.4213 Evaluate side-chains 273 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 248 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 803 MET Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain C residue 462 GLU Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 676 SER Chi-restraints excluded: chain D residue 422 GLU Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain E residue 9 CYS Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain F residue 44 GLN Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain H residue 9 CYS Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 107 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 18 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 150 optimal weight: 0.3980 chunk 63 optimal weight: 0.6980 chunk 175 optimal weight: 6.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 638 GLN ** H 59 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 = 0.3994 r_free = 0.3994 target = 0.171210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.133288 restraints weight = 71271.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.131371 restraints weight = 75951.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.134048 restraints weight = 72070.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.134292 restraints weight = 49711.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.135070 restraints weight = 47801.952| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3575 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3575 r_free = 0.3575 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3574 r_free = 0.3574 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3574 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.6649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 18682 Z= 0.161 Angle : 0.589 13.456 25140 Z= 0.306 Chirality : 0.038 0.161 2690 Planarity : 0.005 0.084 3010 Dihedral : 14.017 117.458 3122 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.34 % Favored : 89.47 % Rotamer: Outliers : 1.67 % Allowed : 13.28 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 2.44 % 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: -2.49 (0.18), residues: 2146 helix: -0.58 (0.15), residues: 1196 sheet: -3.04 (0.42), residues: 128 loop : -3.02 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 628 TYR 0.011 0.001 TYR D 450 PHE 0.017 0.001 PHE A 491 TRP 0.008 0.001 TRP E 87 HIS 0.010 0.002 HIS H 27 Details of bonding type rmsd covalent geometry : bond 0.00377 (18678) covalent geometry : angle 0.58806 (25132) SS BOND : bond 0.00130 ( 4) SS BOND : angle 2.13044 ( 8) hydrogen bonds : bond 0.04253 ( 709) hydrogen bonds : angle 4.37766 ( 2037) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 253 time to evaluate : 1.033 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 492 MET cc_start: 0.9370 (mtp) cc_final: 0.9077 (ttm) REVERT: B 404 PRO cc_start: 0.8941 (Cg_endo) cc_final: 0.8615 (Cg_exo) REVERT: B 546 PHE cc_start: 0.5308 (p90) cc_final: 0.4937 (p90) REVERT: B 807 MET cc_start: 0.7908 (ttm) cc_final: 0.7635 (mtm) REVERT: D 546 PHE cc_start: 0.5481 (p90) cc_final: 0.4353 (p90) REVERT: E 10 TYR cc_start: 0.8420 (m-10) cc_final: 0.8163 (m-10) REVERT: E 137 MET cc_start: 0.7306 (ptt) cc_final: 0.7076 (ptt) REVERT: F 72 TRP cc_start: 0.6715 (m-10) cc_final: 0.5276 (t60) REVERT: F 95 MET cc_start: 0.3644 (tpt) cc_final: 0.1368 (mpp) REVERT: G 15 LEU cc_start: 0.6450 (OUTLIER) cc_final: 0.5911 (mp) REVERT: G 31 PHE cc_start: 0.3925 (OUTLIER) cc_final: 0.3629 (m-80) REVERT: G 90 MET cc_start: 0.5496 (mpp) cc_final: 0.5295 (mpp) REVERT: H 27 HIS cc_start: 0.5428 (m-70) cc_final: 0.5177 (m90) REVERT: H 77 LEU cc_start: 0.8389 (mt) cc_final: 0.7689 (tt) REVERT: H 90 MET cc_start: 0.7056 (mmp) cc_final: 0.6311 (ptp) outliers start: 31 outliers final: 21 residues processed: 270 average time/residue: 0.2996 time to fit residues: 126.8224 Evaluate side-chains 245 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 222 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 803 MET Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 521 ILE Chi-restraints excluded: chain C residue 529 TYR Chi-restraints excluded: chain D residue 422 GLU Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 815 CYS Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 31 PHE Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 107 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 132 optimal weight: 3.9990 chunk 164 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 116 optimal weight: 8.9990 chunk 213 optimal weight: 10.0000 chunk 27 optimal weight: 0.0470 chunk 4 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 722 ASN C 710 GLN H 27 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.163910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.120348 restraints weight = 71838.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.118118 restraints weight = 55378.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.120487 restraints weight = 59041.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.121799 restraints weight = 39414.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.123170 restraints weight = 35575.511| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3432 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.3432 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.7691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18682 Z= 0.164 Angle : 0.576 6.086 25140 Z= 0.303 Chirality : 0.038 0.145 2690 Planarity : 0.005 0.085 3010 Dihedral : 13.463 109.673 3122 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.37 % Favored : 90.54 % Rotamer: Outliers : 2.11 % Allowed : 13.82 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.05 % 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: -2.17 (0.18), residues: 2146 helix: -0.25 (0.15), residues: 1212 sheet: -2.84 (0.44), residues: 126 loop : -3.08 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 416 TYR 0.012 0.001 TYR D 523 PHE 0.017 0.001 PHE A 491 TRP 0.007 0.001 TRP C 763 HIS 0.007 0.001 HIS F 59 Details of bonding type rmsd covalent geometry : bond 0.00383 (18678) covalent geometry : angle 0.57628 (25132) SS BOND : bond 0.00409 ( 4) SS BOND : angle 0.73882 ( 8) hydrogen bonds : bond 0.04307 ( 709) hydrogen bonds : angle 4.23361 ( 2037) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 251 time to evaluate : 0.946 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 492 MET cc_start: 0.9369 (mtp) cc_final: 0.9167 (ttm) REVERT: A 704 MET cc_start: 0.8717 (mtt) cc_final: 0.8441 (mtt) REVERT: F 72 TRP cc_start: 0.6830 (m-10) cc_final: 0.4767 (t60) REVERT: F 89 TYR cc_start: 0.4963 (t80) cc_final: 0.4628 (t80) REVERT: F 95 MET cc_start: 0.3285 (tpt) cc_final: 0.0924 (mpp) REVERT: H 77 LEU cc_start: 0.8520 (mt) cc_final: 0.7981 (tt) REVERT: H 90 MET cc_start: 0.7516 (mmp) cc_final: 0.6472 (ptp) outliers start: 39 outliers final: 31 residues processed: 273 average time/residue: 0.2652 time to fit residues: 113.9132 Evaluate side-chains 262 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 231 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 803 MET Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 769 ASP Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 529 TYR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 803 MET Chi-restraints excluded: chain D residue 422 GLU Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 769 ASP Chi-restraints excluded: chain D residue 815 CYS Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 107 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 181 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 192 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 163 optimal weight: 9.9990 chunk 178 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 GLN A 722 ASN C 710 GLN C 722 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.162151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.123822 restraints weight = 71021.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.121517 restraints weight = 81262.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.124082 restraints weight = 77484.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.124679 restraints weight = 50420.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.125099 restraints weight = 48028.747| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3439 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3439 r_free = 0.3439 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3439 r_free = 0.3439 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3439 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.8241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 18682 Z= 0.152 Angle : 0.545 5.733 25140 Z= 0.286 Chirality : 0.037 0.143 2690 Planarity : 0.005 0.079 3010 Dihedral : 13.161 108.228 3122 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.51 % Favored : 90.35 % Rotamer: Outliers : 1.73 % Allowed : 15.06 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.18), residues: 2146 helix: 0.03 (0.15), residues: 1206 sheet: -2.84 (0.41), residues: 134 loop : -3.06 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 657 TYR 0.017 0.001 TYR E 38 PHE 0.016 0.001 PHE A 491 TRP 0.006 0.001 TRP E 87 HIS 0.005 0.001 HIS F 59 Details of bonding type rmsd covalent geometry : bond 0.00359 (18678) covalent geometry : angle 0.54500 (25132) SS BOND : bond 0.00149 ( 4) SS BOND : angle 1.11501 ( 8) hydrogen bonds : bond 0.03930 ( 709) hydrogen bonds : angle 4.11345 ( 2037) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 246 time to evaluate : 0.934 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 395 THR cc_start: 0.9291 (OUTLIER) cc_final: 0.9017 (m) REVERT: A 704 MET cc_start: 0.8899 (mtt) cc_final: 0.8561 (mtt) REVERT: B 597 SER cc_start: 0.9460 (p) cc_final: 0.9061 (m) REVERT: D 597 SER cc_start: 0.9235 (p) cc_final: 0.8723 (m) REVERT: E 10 TYR cc_start: 0.8557 (m-10) cc_final: 0.8236 (m-10) REVERT: F 25 ILE cc_start: 0.8218 (mm) cc_final: 0.7975 (mt) REVERT: F 72 TRP cc_start: 0.6773 (m-10) cc_final: 0.4911 (t60) REVERT: F 89 TYR cc_start: 0.4808 (t80) cc_final: 0.4472 (t80) REVERT: F 95 MET cc_start: 0.3296 (tpt) cc_final: 0.0816 (mpp) REVERT: H 22 PHE cc_start: 0.6914 (t80) cc_final: 0.6590 (t80) REVERT: H 27 HIS cc_start: 0.5374 (m90) cc_final: 0.5138 (m-70) REVERT: H 77 LEU cc_start: 0.8439 (mt) cc_final: 0.7854 (tt) REVERT: H 90 MET cc_start: 0.7107 (mmp) cc_final: 0.6304 (ptp) outliers start: 32 outliers final: 24 residues processed: 263 average time/residue: 0.2610 time to fit residues: 109.2981 Evaluate side-chains 260 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 235 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 521 ILE Chi-restraints excluded: chain C residue 529 TYR Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 422 GLU Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 815 CYS Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 107 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 63 optimal weight: 0.7980 chunk 180 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 173 optimal weight: 8.9990 chunk 175 optimal weight: 4.9990 chunk 122 optimal weight: 0.6980 chunk 146 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 41 optimal weight: 0.0870 chunk 210 optimal weight: 6.9990 overall best weight: 1.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 GLN C 710 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.160406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.120246 restraints weight = 71596.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.118918 restraints weight = 66807.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.121115 restraints weight = 69685.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.121710 restraints weight = 45177.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.122456 restraints weight = 42699.226| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3410 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3410 r_free = 0.3410 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3410 r_free = 0.3410 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3410 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.8690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 18682 Z= 0.150 Angle : 0.543 5.661 25140 Z= 0.285 Chirality : 0.037 0.142 2690 Planarity : 0.005 0.082 3010 Dihedral : 12.837 107.803 3122 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.79 % Favored : 90.12 % Rotamer: Outliers : 1.89 % Allowed : 15.82 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.18), residues: 2146 helix: 0.20 (0.15), residues: 1218 sheet: -2.80 (0.40), residues: 138 loop : -3.04 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 657 TYR 0.012 0.001 TYR D 523 PHE 0.016 0.001 PHE A 491 TRP 0.006 0.001 TRP G 87 HIS 0.005 0.001 HIS F 59 Details of bonding type rmsd covalent geometry : bond 0.00354 (18678) covalent geometry : angle 0.54291 (25132) SS BOND : bond 0.00265 ( 4) SS BOND : angle 0.87575 ( 8) hydrogen bonds : bond 0.03932 ( 709) hydrogen bonds : angle 4.04574 ( 2037) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 254 time to evaluate : 0.986 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: A 395 THR cc_start: 0.9278 (OUTLIER) cc_final: 0.9014 (m) REVERT: A 704 MET cc_start: 0.8992 (mtt) cc_final: 0.8758 (mtt) REVERT: B 597 SER cc_start: 0.9502 (p) cc_final: 0.9089 (m) REVERT: B 788 SER cc_start: 0.9121 (t) cc_final: 0.8680 (p) REVERT: D 597 SER cc_start: 0.9335 (p) cc_final: 0.8769 (m) REVERT: E 10 TYR cc_start: 0.8484 (m-10) cc_final: 0.8152 (m-10) REVERT: F 95 MET cc_start: 0.3408 (tpt) cc_final: 0.1428 (mpp) REVERT: H 22 PHE cc_start: 0.7033 (t80) cc_final: 0.6752 (t80) REVERT: H 77 LEU cc_start: 0.8466 (mt) cc_final: 0.7874 (tt) REVERT: H 90 MET cc_start: 0.7219 (mmp) cc_final: 0.6344 (ptm) outliers start: 35 outliers final: 28 residues processed: 270 average time/residue: 0.2560 time to fit residues: 110.7674 Evaluate side-chains 268 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 239 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 529 TYR Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 422 GLU Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 815 CYS Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 31 PHE Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 107 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 158 optimal weight: 1.9990 chunk 174 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 186 optimal weight: 5.9990 chunk 47 optimal weight: 0.2980 chunk 132 optimal weight: 0.1980 chunk 125 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.161203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.119413 restraints weight = 71726.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.117038 restraints weight = 66289.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.120354 restraints weight = 63159.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.120498 restraints weight = 41090.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.121394 restraints weight = 38922.889| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3391 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3391 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.8908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18682 Z= 0.115 Angle : 0.512 5.965 25140 Z= 0.267 Chirality : 0.037 0.139 2690 Planarity : 0.004 0.076 3010 Dihedral : 12.383 107.364 3122 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.95 % Favored : 90.91 % Rotamer: Outliers : 1.51 % Allowed : 16.58 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.18), residues: 2146 helix: 0.46 (0.15), residues: 1214 sheet: -2.65 (0.41), residues: 136 loop : -2.96 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 657 TYR 0.009 0.001 TYR A 728 PHE 0.013 0.001 PHE A 491 TRP 0.005 0.001 TRP E 87 HIS 0.005 0.001 HIS F 59 Details of bonding type rmsd covalent geometry : bond 0.00268 (18678) covalent geometry : angle 0.51228 (25132) SS BOND : bond 0.00146 ( 4) SS BOND : angle 0.85003 ( 8) hydrogen bonds : bond 0.03535 ( 709) hydrogen bonds : angle 3.89086 ( 2037) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 249 time to evaluate : 0.951 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 704 MET cc_start: 0.9009 (mtt) cc_final: 0.8791 (mtt) REVERT: B 597 SER cc_start: 0.9524 (p) cc_final: 0.9078 (m) REVERT: B 788 SER cc_start: 0.9155 (t) cc_final: 0.8682 (p) REVERT: C 395 THR cc_start: 0.9264 (OUTLIER) cc_final: 0.9004 (m) REVERT: E 10 TYR cc_start: 0.8381 (m-10) cc_final: 0.8109 (m-10) REVERT: E 51 LEU cc_start: 0.7192 (mm) cc_final: 0.6706 (pp) REVERT: F 39 LYS cc_start: 0.5770 (OUTLIER) cc_final: 0.4514 (tppt) REVERT: F 95 MET cc_start: 0.3390 (tpt) cc_final: 0.0813 (mpp) REVERT: H 77 LEU cc_start: 0.8472 (mt) cc_final: 0.7893 (tt) REVERT: H 90 MET cc_start: 0.7341 (mmp) cc_final: 0.6391 (ptm) REVERT: H 117 LYS cc_start: 0.4966 (OUTLIER) cc_final: 0.4279 (mmtt) outliers start: 28 outliers final: 18 residues processed: 262 average time/residue: 0.2552 time to fit residues: 107.6020 Evaluate side-chains 260 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 239 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 666 MET Chi-restraints excluded: chain D residue 422 GLU Chi-restraints excluded: chain D residue 439 LYS Chi-restraints excluded: chain D residue 815 CYS Chi-restraints excluded: chain F residue 39 LYS Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 117 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 110 optimal weight: 2.9990 chunk 199 optimal weight: 9.9990 chunk 100 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 chunk 183 optimal weight: 8.9990 chunk 145 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 212 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 710 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.160227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.118948 restraints weight = 71516.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.117085 restraints weight = 62496.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.119069 restraints weight = 68797.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.120186 restraints weight = 44159.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.120672 restraints weight = 40314.419| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3390 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3390 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.9112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18682 Z= 0.127 Angle : 0.522 5.874 25140 Z= 0.272 Chirality : 0.037 0.140 2690 Planarity : 0.004 0.080 3010 Dihedral : 12.212 107.031 3122 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.46 % Favored : 90.45 % Rotamer: Outliers : 1.57 % Allowed : 16.41 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.19), residues: 2146 helix: 0.59 (0.15), residues: 1220 sheet: -2.60 (0.40), residues: 136 loop : -2.92 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 657 TYR 0.014 0.001 TYR D 523 PHE 0.015 0.001 PHE A 491 TRP 0.005 0.001 TRP H 120 HIS 0.005 0.001 HIS F 59 Details of bonding type rmsd covalent geometry : bond 0.00300 (18678) covalent geometry : angle 0.52166 (25132) SS BOND : bond 0.00236 ( 4) SS BOND : angle 0.79032 ( 8) hydrogen bonds : bond 0.03579 ( 709) hydrogen bonds : angle 3.85821 ( 2037) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 245 time to evaluate : 0.991 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 704 MET cc_start: 0.9024 (mtt) cc_final: 0.8817 (mtt) REVERT: B 439 LYS cc_start: 0.8044 (mttt) cc_final: 0.7790 (mttm) REVERT: B 597 SER cc_start: 0.9508 (p) cc_final: 0.9082 (m) REVERT: B 788 SER cc_start: 0.9148 (t) cc_final: 0.8712 (p) REVERT: C 395 THR cc_start: 0.9241 (OUTLIER) cc_final: 0.9026 (m) REVERT: E 10 TYR cc_start: 0.8379 (m-10) cc_final: 0.8087 (m-10) REVERT: E 56 TYR cc_start: 0.6905 (m-80) cc_final: 0.6533 (m-80) REVERT: F 39 LYS cc_start: 0.5705 (OUTLIER) cc_final: 0.4489 (tppt) REVERT: F 95 MET cc_start: 0.3288 (tpt) cc_final: 0.1291 (mpp) REVERT: H 77 LEU cc_start: 0.8477 (mt) cc_final: 0.7740 (tt) REVERT: H 90 MET cc_start: 0.7239 (mmp) cc_final: 0.6361 (ptm) REVERT: H 117 LYS cc_start: 0.4998 (OUTLIER) cc_final: 0.4209 (mmtt) outliers start: 29 outliers final: 21 residues processed: 259 average time/residue: 0.2619 time to fit residues: 107.4273 Evaluate side-chains 260 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 236 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 422 GLU Chi-restraints excluded: chain D residue 439 LYS Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 815 CYS Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain F residue 39 LYS Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 117 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 174 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 192 optimal weight: 9.9990 chunk 146 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 2 optimal weight: 0.3980 chunk 85 optimal weight: 0.0770 chunk 188 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 176 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.2944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 GLN C 710 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.159204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.117511 restraints weight = 71977.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.115933 restraints weight = 61972.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.118079 restraints weight = 67612.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.119316 restraints weight = 42808.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.120192 restraints weight = 38808.911| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3378 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3378 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.9318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18682 Z= 0.148 Angle : 0.541 6.437 25140 Z= 0.283 Chirality : 0.037 0.140 2690 Planarity : 0.005 0.075 3010 Dihedral : 12.193 106.797 3122 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.41 % Favored : 90.45 % Rotamer: Outliers : 1.24 % Allowed : 16.68 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.18), residues: 2146 helix: 0.61 (0.15), residues: 1212 sheet: -2.60 (0.40), residues: 136 loop : -2.92 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 545 TYR 0.010 0.001 TYR C 401 PHE 0.019 0.001 PHE F 130 TRP 0.006 0.001 TRP H 120 HIS 0.005 0.001 HIS F 59 Details of bonding type rmsd covalent geometry : bond 0.00352 (18678) covalent geometry : angle 0.54070 (25132) SS BOND : bond 0.00269 ( 4) SS BOND : angle 0.86400 ( 8) hydrogen bonds : bond 0.03741 ( 709) hydrogen bonds : angle 3.94391 ( 2037) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4292 Ramachandran restraints generated. 2146 Oldfield, 0 Emsley, 2146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 239 time to evaluate : 0.940 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 704 MET cc_start: 0.9082 (mtt) cc_final: 0.8875 (mtt) REVERT: B 439 LYS cc_start: 0.8015 (mttt) cc_final: 0.7778 (mttm) REVERT: B 597 SER cc_start: 0.9497 (p) cc_final: 0.9092 (m) REVERT: B 788 SER cc_start: 0.9141 (t) cc_final: 0.8750 (p) REVERT: D 524 GLU cc_start: 0.7747 (tt0) cc_final: 0.7465 (tt0) REVERT: D 597 SER cc_start: 0.9308 (p) cc_final: 0.8779 (m) REVERT: E 10 TYR cc_start: 0.8388 (m-10) cc_final: 0.8038 (m-10) REVERT: E 56 TYR cc_start: 0.6771 (m-80) cc_final: 0.6422 (m-80) REVERT: F 39 LYS cc_start: 0.5651 (OUTLIER) cc_final: 0.4505 (tppt) REVERT: F 95 MET cc_start: 0.3127 (tpt) cc_final: 0.1086 (mpp) REVERT: G 90 MET cc_start: 0.5684 (mpp) cc_final: 0.5481 (mmt) REVERT: H 77 LEU cc_start: 0.8470 (mt) cc_final: 0.7719 (tt) REVERT: H 90 MET cc_start: 0.7209 (mmp) cc_final: 0.6347 (ptm) REVERT: H 117 LYS cc_start: 0.5007 (OUTLIER) cc_final: 0.4219 (mmtt) outliers start: 23 outliers final: 18 residues processed: 250 average time/residue: 0.2561 time to fit residues: 103.6025 Evaluate side-chains 255 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 235 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 815 CYS Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 422 GLU Chi-restraints excluded: chain D residue 439 LYS Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 815 CYS Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain F residue 39 LYS Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 117 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 16 optimal weight: 3.9990 chunk 206 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 186 optimal weight: 6.9990 chunk 18 optimal weight: 0.3980 chunk 85 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 181 optimal weight: 3.9990 chunk 179 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 GLN C 583 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.158889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.117085 restraints weight = 71808.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.115478 restraints weight = 62125.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.117907 restraints weight = 65596.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.118627 restraints weight = 43033.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.119686 restraints weight = 40122.735| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3374 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3374 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.9484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18682 Z= 0.142 Angle : 0.534 5.447 25140 Z= 0.279 Chirality : 0.037 0.140 2690 Planarity : 0.005 0.079 3010 Dihedral : 12.119 106.535 3122 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.51 % Favored : 90.35 % Rotamer: Outliers : 1.30 % Allowed : 16.63 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.19), residues: 2146 helix: 0.64 (0.15), residues: 1218 sheet: -2.62 (0.39), residues: 136 loop : -2.86 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 545 TYR 0.012 0.001 TYR D 523 PHE 0.023 0.001 PHE F 130 TRP 0.006 0.001 TRP H 120 HIS 0.006 0.001 HIS G 27 Details of bonding type rmsd covalent geometry : bond 0.00337 (18678) covalent geometry : angle 0.53384 (25132) SS BOND : bond 0.00198 ( 4) SS BOND : angle 0.81154 ( 8) hydrogen bonds : bond 0.03695 ( 709) hydrogen bonds : angle 3.90727 ( 2037) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5131.96 seconds wall clock time: 88 minutes 21.48 seconds (5301.48 seconds total)