Starting phenix.real_space_refine on Mon Jul 6 16:08:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ovv_70920/07_2026/9ovv_70920_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ovv_70920/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9ovv_70920/07_2026/9ovv_70920_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ovv_70920/07_2026/9ovv_70920_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ovv_70920/07_2026/9ovv_70920.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ovv_70920/07_2026/9ovv_70920.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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, 188 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'FWF': 1, 'POV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain breaks: 1 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: 6.84, 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: 3.51 Conformation dependent library (CDL) restraints added in 1.0 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: 0.79 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: 8.02 Time building geometry restraints manager: 4.78 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: 5.030 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: 0.230 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 34.060 Find NCS groups from input model: 0.780 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6511 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/Z covalent geometry : bond 0.00927 / 0.43 (18678) covalent geometry : angle 1.18331 / 0.55 (25132) SS BOND : bond 0.00364 / 0.18 ( 4) SS BOND : angle 2.07326 / 1.16 ( 8) hydrogen bonds : bond 0.30365 / 20.12 ( 709) hydrogen bonds : angle 10.45373 / 7.08 ( 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 : 0.931 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: 0.3449 time to fit residues: 279.3764 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 : 0.929 ------------------------------------------------------------------------------- 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... B 726 ASN B 747 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.196315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.163347 restraints weight = 74082.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.165688 restraints weight = 63140.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.167655 restraints weight = 45022.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.167849 restraints weight = 34817.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.168740 restraints weight = 35178.340| |-----------------------------------------------------------------------------| r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3948 r_free = 0.3948 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 = 0.3941 r_free = 0.3941 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (12 function evaluations) r_final: 0.3941 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.4018 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 : 0.656 6.494 25140 Z= 0.342 Chirality : 0.040 0.151 2690 Planarity : 0.006 0.109 3010 Dihedral : 16.601 168.920 3122 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.33 % Allowed : 10.76 % Favored : 88.91 % Rotamer: Outliers : 2.21 % Allowed : 11.18 % Favored : 86.61 % 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: -3.75 (0.16), residues: 2146 helix: -1.90 (0.13), residues: 1172 sheet: -3.27 (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 0.011 0.001 TYR B 523 PHE 0.018 0.002 PHE A 619 TRP 0.014 0.001 TRP G 87 HIS 0.009 0.002 HIS F 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (18678) covalent geometry : angle 0.65569 / 0.34 (25132) SS BOND : bond 0.00091 / 0.04 ( 4) SS BOND : angle 0.59122 / 0.29 ( 8) hydrogen bonds : bond 0.05378 / 3.56 ( 709) hydrogen bonds : angle 5.43787 / 3.72 ( 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 382 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 341 time to evaluate : 0.893 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: 0.7413 (t0) cc_final: 0.7174 (t0) REVERT: B 404 PRO cc_start: 0.8550 (Cg_endo) cc_final: 0.8259 (Cg_exo) REVERT: C 787 ASN cc_start: 0.7498 (t0) cc_final: 0.7248 (t0) REVERT: D 404 PRO cc_start: 0.8677 (Cg_endo) cc_final: 0.8338 (Cg_exo) REVERT: D 546 PHE cc_start: 0.5204 (p90) cc_final: 0.4398 (p90) REVERT: E 128 LEU cc_start: 0.6081 (mt) cc_final: 0.5776 (mt) REVERT: F 72 TRP cc_start: 0.6616 (m-10) cc_final: 0.5520 (t60) REVERT: F 95 MET cc_start: 0.3543 (tpt) cc_final: 0.1425 (mpp) REVERT: F 120 TRP cc_start: 0.4924 (m100) cc_final: 0.4326 (m100) REVERT: F 135 TYR cc_start: 0.4243 (m-80) cc_final: 0.3781 (m-80) REVERT: G 22 PHE cc_start: 0.6680 (OUTLIER) cc_final: 0.5921 (t80) REVERT: G 90 MET cc_start: 0.5149 (mpp) cc_final: 0.4934 (mpp) REVERT: H 27 HIS cc_start: 0.5287 (m-70) cc_final: 0.5082 (m90) REVERT: H 77 LEU cc_start: 0.8292 (mt) cc_final: 0.7772 (tt) outliers start: 41 outliers final: 27 residues processed: 370 average time/residue: 0.2937 time to fit residues: 167.9540 Evaluate side-chains 305 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 277 time to evaluate : 0.836 ------------------------------------------------------------------------------- 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 543 SER 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 525 ILE 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: 4.9990 chunk 212 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 186 optimal weight: 4.9990 chunk 16 optimal weight: 0.0010 chunk 126 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4079 r_free = 0.4079 target = 0.179119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.146983 restraints weight = 71963.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.146467 restraints weight = 94488.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.149766 restraints weight = 80241.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.149242 restraints weight = 52308.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.150134 restraints weight = 48255.513| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3754 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3754 r_free = 0.3754 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3753 r_free = 0.3753 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3753 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.5677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18682 Z= 0.162 Angle : 0.616 8.364 25140 Z= 0.325 Chirality : 0.039 0.164 2690 Planarity : 0.005 0.095 3010 Dihedral : 14.665 137.153 3122 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.02 % Favored : 89.84 % Rotamer: Outliers : 2.11 % Allowed : 12.37 % Favored : 85.53 % 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: -2.93 (0.17), residues: 2146 helix: -1.02 (0.14), residues: 1214 sheet: -3.27 (0.41), residues: 128 loop : -3.09 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 628 TYR 0.013 0.001 TYR F 89 PHE 0.020 0.002 PHE E 23 TRP 0.008 0.001 TRP D 671 HIS 0.008 0.001 HIS F 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (18678) covalent geometry : angle 0.61567 / 0.32 (25132) SS BOND : bond 0.00843 / 0.41 ( 4) SS BOND : angle 1.57817 / 0.90 ( 8) hydrogen bonds : bond 0.05137 / 3.41 ( 709) hydrogen bonds : angle 4.67213 / 3.23 ( 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 321 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 282 time to evaluate : 0.939 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 704 MET cc_start: 0.7737 (mpp) cc_final: 0.7491 (mtt) REVERT: B 404 PRO cc_start: 0.8511 (Cg_endo) cc_final: 0.8277 (Cg_exo) REVERT: D 404 PRO cc_start: 0.8579 (Cg_endo) cc_final: 0.8334 (Cg_exo) REVERT: D 546 PHE cc_start: 0.5408 (p90) cc_final: 0.4489 (p90) REVERT: E 128 LEU cc_start: 0.5967 (mt) cc_final: 0.5766 (mt) REVERT: F 72 TRP cc_start: 0.6532 (m-10) cc_final: 0.5325 (t60) REVERT: F 95 MET cc_start: 0.3649 (tpt) cc_final: 0.1375 (mpp) REVERT: F 120 TRP cc_start: 0.4863 (m100) cc_final: 0.4546 (m100) REVERT: H 77 LEU cc_start: 0.8166 (mt) cc_final: 0.7724 (tt) REVERT: H 90 MET cc_start: 0.6408 (mmp) cc_final: 0.5948 (ptp) outliers start: 39 outliers final: 27 residues processed: 300 average time/residue: 0.2945 time to fit residues: 137.7518 Evaluate side-chains 264 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 237 time to evaluate : 0.943 ------------------------------------------------------------------------------- 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 666 MET 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 815 CYS Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 676 SER Chi-restraints excluded: chain C residue 803 MET 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 D residue 815 CYS 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: 1.9990 chunk 47 optimal weight: 0.7980 chunk 137 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 175 optimal weight: 7.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 582 GLN B 575 ASN B 587 GLN H 27 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.169396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.134030 restraints weight = 71103.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.132073 restraints weight = 91691.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.134415 restraints weight = 90476.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.134607 restraints weight = 59777.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.136763 restraints weight = 56206.962| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3582 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3582 r_free = 0.3582 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3582 r_free = 0.3582 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3582 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.7018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 18682 Z= 0.186 Angle : 0.618 13.794 25140 Z= 0.322 Chirality : 0.039 0.159 2690 Planarity : 0.005 0.084 3010 Dihedral : 14.252 117.405 3122 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.39 % Favored : 89.42 % Rotamer: Outliers : 1.78 % Allowed : 13.61 % Favored : 84.61 % 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: -2.56 (0.18), residues: 2146 helix: -0.59 (0.15), residues: 1190 sheet: -3.07 (0.40), residues: 128 loop : -3.12 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 628 TYR 0.013 0.001 TYR C 401 PHE 0.017 0.002 PHE A 491 TRP 0.009 0.001 TRP G 87 HIS 0.012 0.002 HIS H 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.19 (18678) covalent geometry : angle 0.61723 / 0.32 (25132) SS BOND : bond 0.00314 / 0.15 ( 4) SS BOND : angle 2.08245 / 1.23 ( 8) hydrogen bonds : bond 0.04447 / 2.94 ( 709) hydrogen bonds : angle 4.46059 / 3.08 ( 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 286 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 253 time to evaluate : 0.966 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 401 TYR cc_start: 0.9249 (m-80) cc_final: 0.8672 (m-80) REVERT: B 546 PHE cc_start: 0.5049 (p90) cc_final: 0.4707 (p90) REVERT: B 807 MET cc_start: 0.7788 (ttm) cc_final: 0.7552 (mtm) REVERT: D 546 PHE cc_start: 0.5499 (p90) cc_final: 0.4457 (p90) REVERT: E 137 MET cc_start: 0.7180 (ptt) cc_final: 0.6963 (ptt) REVERT: F 72 TRP cc_start: 0.6674 (m-10) cc_final: 0.5223 (t60) REVERT: F 95 MET cc_start: 0.3582 (tpt) cc_final: 0.1230 (mpp) REVERT: G 31 PHE cc_start: 0.3752 (OUTLIER) cc_final: 0.3487 (m-80) REVERT: G 90 MET cc_start: 0.5405 (mpp) cc_final: 0.5194 (mpp) REVERT: H 77 LEU cc_start: 0.8278 (mt) cc_final: 0.7740 (tt) REVERT: H 90 MET cc_start: 0.6751 (mmp) cc_final: 0.6188 (ptp) outliers start: 33 outliers final: 23 residues processed: 275 average time/residue: 0.2969 time to fit residues: 127.8249 Evaluate side-chains 254 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 230 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 593 SER 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 390 THR 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 593 SER 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 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 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: 2.9990 chunk 164 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 chunk 32 optimal weight: 0.3980 chunk 137 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 213 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 722 ASN C 710 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.163103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.119866 restraints weight = 72209.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.117616 restraints weight = 55592.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.120177 restraints weight = 58954.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.121129 restraints weight = 38024.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.122010 restraints weight = 34823.713| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3415 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3415 r_free = 0.3415 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3415 r_free = 0.3415 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3415 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.7807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18682 Z= 0.156 Angle : 0.560 5.482 25140 Z= 0.294 Chirality : 0.038 0.142 2690 Planarity : 0.005 0.083 3010 Dihedral : 13.425 109.537 3122 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.27 % Favored : 90.63 % Rotamer: Outliers : 1.84 % Allowed : 14.42 % Favored : 83.75 % 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: -2.22 (0.18), residues: 2146 helix: -0.23 (0.15), residues: 1202 sheet: -2.86 (0.43), residues: 126 loop : -3.17 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 688 TYR 0.012 0.001 TYR G 38 PHE 0.016 0.001 PHE A 491 TRP 0.006 0.001 TRP D 767 HIS 0.007 0.001 HIS G 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (18678) covalent geometry : angle 0.55952 / 0.29 (25132) SS BOND : bond 0.00359 / 0.18 ( 4) SS BOND : angle 0.75637 / 0.44 ( 8) hydrogen bonds : bond 0.04215 / 2.79 ( 709) hydrogen bonds : angle 4.20567 / 2.90 ( 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 279 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 245 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 THR cc_start: 0.9282 (OUTLIER) cc_final: 0.9019 (m) REVERT: A 492 MET cc_start: 0.9359 (mtp) cc_final: 0.9136 (ttm) REVERT: F 72 TRP cc_start: 0.6824 (m-10) cc_final: 0.4746 (t60) REVERT: F 89 TYR cc_start: 0.4996 (t80) cc_final: 0.4654 (t80) REVERT: F 95 MET cc_start: 0.3300 (tpt) cc_final: 0.0919 (mpp) REVERT: H 22 PHE cc_start: 0.6597 (t80) cc_final: 0.6343 (t80) REVERT: H 77 LEU cc_start: 0.8519 (mt) cc_final: 0.7760 (tt) REVERT: H 90 MET cc_start: 0.7547 (mmp) cc_final: 0.6477 (ptp) outliers start: 34 outliers final: 27 residues processed: 261 average time/residue: 0.2861 time to fit residues: 117.8757 Evaluate side-chains 258 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 230 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 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 592 LEU Chi-restraints excluded: chain C residue 666 MET 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 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 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: 1.9990 chunk 122 optimal weight: 5.9990 chunk 2 optimal weight: 0.6980 chunk 192 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 148 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 163 optimal weight: 0.0270 chunk 178 optimal weight: 10.0000 chunk 125 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 overall best weight: 0.8840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 710 GLN C 710 GLN C 722 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.163450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.122629 restraints weight = 71333.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.120812 restraints weight = 72485.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.123686 restraints weight = 70551.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.124253 restraints weight = 45847.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.125747 restraints weight = 43117.671| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3447 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3447 r_free = 0.3447 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 = 0.3447 r_free = 0.3447 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (12 function evaluations) r_final: 0.3447 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.8105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18682 Z= 0.118 Angle : 0.517 5.349 25140 Z= 0.271 Chirality : 0.037 0.139 2690 Planarity : 0.004 0.080 3010 Dihedral : 12.997 110.692 3122 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.27 % Favored : 90.59 % Rotamer: Outliers : 1.51 % Allowed : 15.60 % Favored : 82.88 % 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: -1.89 (0.18), residues: 2146 helix: 0.05 (0.15), residues: 1208 sheet: -2.79 (0.41), residues: 134 loop : -3.04 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 628 TYR 0.013 0.001 TYR E 38 PHE 0.014 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/Z covalent geometry : bond 0.00272 / 0.12 (18678) covalent geometry : angle 0.51708 / 0.27 (25132) SS BOND : bond 0.00173 / 0.08 ( 4) SS BOND : angle 0.94751 / 0.55 ( 8) hydrogen bonds : bond 0.03698 / 2.46 ( 709) hydrogen bonds : angle 4.02238 / 2.78 ( 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 269 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 241 time to evaluate : 0.959 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: F 72 TRP cc_start: 0.6787 (m-10) cc_final: 0.4873 (t60) REVERT: F 89 TYR cc_start: 0.4906 (t80) cc_final: 0.4566 (t80) REVERT: F 95 MET cc_start: 0.3297 (tpt) cc_final: 0.0863 (mpp) REVERT: G 10 TYR cc_start: 0.8095 (m-10) cc_final: 0.7841 (m-10) REVERT: H 77 LEU cc_start: 0.8457 (mt) cc_final: 0.7719 (tt) REVERT: H 90 MET cc_start: 0.7307 (mmp) cc_final: 0.6364 (ptp) outliers start: 28 outliers final: 21 residues processed: 256 average time/residue: 0.2770 time to fit residues: 113.4778 Evaluate side-chains 257 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 236 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 538 LEU 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 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 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 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: 0.5980 chunk 180 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 173 optimal weight: 8.9990 chunk 175 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 chunk 146 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 210 optimal weight: 6.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3885 r_free = 0.3885 target = 0.160903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.118939 restraints weight = 71790.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.117411 restraints weight = 62323.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.120059 restraints weight = 62058.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.120362 restraints weight = 42279.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.121246 restraints weight = 39796.059| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3394 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3394 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.8544 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= 0.146 Angle : 0.535 5.608 25140 Z= 0.280 Chirality : 0.037 0.144 2690 Planarity : 0.004 0.079 3010 Dihedral : 12.816 107.968 3122 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.21 % Favored : 89.66 % Rotamer: Outliers : 1.73 % Allowed : 15.77 % Favored : 82.51 % 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: -1.75 (0.18), residues: 2146 helix: 0.25 (0.15), residues: 1210 sheet: -2.81 (0.40), residues: 138 loop : -3.11 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 661 TYR 0.011 0.001 TYR C 728 PHE 0.017 0.001 PHE A 491 TRP 0.007 0.001 TRP G 87 HIS 0.005 0.001 HIS F 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (18678) covalent geometry : angle 0.53500 / 0.28 (25132) SS BOND : bond 0.00231 / 0.11 ( 4) SS BOND : angle 0.85861 / 0.51 ( 8) hydrogen bonds : bond 0.03857 / 2.55 ( 709) hydrogen bonds : angle 4.01073 / 2.78 ( 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 285 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 253 time to evaluate : 0.896 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: B 772 GLU cc_start: 0.7183 (mp0) cc_final: 0.6925 (mp0) REVERT: B 788 SER cc_start: 0.9151 (t) cc_final: 0.8670 (p) REVERT: C 395 THR cc_start: 0.9270 (OUTLIER) cc_final: 0.8993 (m) REVERT: D 597 SER cc_start: 0.9382 (p) cc_final: 0.8771 (m) REVERT: F 95 MET cc_start: 0.3451 (tpt) cc_final: 0.1564 (mpp) REVERT: H 77 LEU cc_start: 0.8459 (mt) cc_final: 0.7708 (tt) REVERT: H 90 MET cc_start: 0.7340 (mmp) cc_final: 0.6513 (ptp) outliers start: 32 outliers final: 28 residues processed: 267 average time/residue: 0.2828 time to fit residues: 121.1181 Evaluate side-chains 270 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 241 time to evaluate : 0.978 ------------------------------------------------------------------------------- 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 592 LEU Chi-restraints excluded: chain B residue 407 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 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 592 LEU 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 815 CYS Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 138 ILE 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 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: 6.9990 chunk 29 optimal weight: 1.9990 chunk 186 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 125 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 31 optimal weight: 0.2980 chunk 44 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3894 r_free = 0.3894 target = 0.161566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.120634 restraints weight = 71723.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.118731 restraints weight = 68968.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.121899 restraints weight = 62900.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.122077 restraints weight = 42590.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.122756 restraints weight = 41718.030| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3414 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3414 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.8796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18682 Z= 0.115 Angle : 0.508 5.614 25140 Z= 0.265 Chirality : 0.036 0.138 2690 Planarity : 0.004 0.075 3010 Dihedral : 12.333 107.224 3122 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.90 % Favored : 90.96 % Rotamer: Outliers : 1.35 % Allowed : 16.58 % 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: -1.46 (0.18), residues: 2146 helix: 0.49 (0.15), residues: 1214 sheet: -2.75 (0.40), residues: 138 loop : -3.02 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 586 TYR 0.010 0.001 TYR A 728 PHE 0.012 0.001 PHE A 491 TRP 0.005 0.001 TRP G 87 HIS 0.005 0.001 HIS F 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (18678) covalent geometry : angle 0.50739 / 0.26 (25132) SS BOND : bond 0.00137 / 0.07 ( 4) SS BOND : angle 0.85099 / 0.50 ( 8) hydrogen bonds : bond 0.03468 / 2.30 ( 709) hydrogen bonds : angle 3.85711 / 2.68 ( 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 284 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 259 time to evaluate : 0.988 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 630 GLU cc_start: 0.6883 (mm-30) cc_final: 0.6454 (mm-30) REVERT: B 439 LYS cc_start: 0.7935 (mttt) cc_final: 0.7673 (mttm) REVERT: B 788 SER cc_start: 0.9134 (t) cc_final: 0.8677 (p) REVERT: C 395 THR cc_start: 0.9232 (OUTLIER) cc_final: 0.9031 (m) REVERT: D 597 SER cc_start: 0.9351 (p) cc_final: 0.8724 (m) REVERT: E 10 TYR cc_start: 0.8353 (m-10) cc_final: 0.8036 (m-80) REVERT: E 51 LEU cc_start: 0.7000 (mm) cc_final: 0.6687 (pp) REVERT: F 39 LYS cc_start: 0.5736 (OUTLIER) cc_final: 0.4499 (tppt) REVERT: F 95 MET cc_start: 0.3409 (tpt) cc_final: 0.0826 (mpp) REVERT: H 77 LEU cc_start: 0.8439 (mt) cc_final: 0.7689 (tt) REVERT: H 90 MET cc_start: 0.7297 (mmp) cc_final: 0.6394 (ptm) outliers start: 25 outliers final: 19 residues processed: 272 average time/residue: 0.2782 time to fit residues: 122.1129 Evaluate side-chains 267 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 246 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 THR 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 395 THR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 592 LEU 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 110 optimal weight: 1.9990 chunk 199 optimal weight: 9.9990 chunk 100 optimal weight: 0.8980 chunk 52 optimal weight: 0.0770 chunk 98 optimal weight: 0.6980 chunk 183 optimal weight: 8.9990 chunk 145 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 212 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.160781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.119801 restraints weight = 71708.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.117355 restraints weight = 70291.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.119963 restraints weight = 74452.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.120488 restraints weight = 48767.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.121201 restraints weight = 45970.794| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3395 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (13 function evaluations) r_final: 0.3395 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.9008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18682 Z= 0.122 Angle : 0.517 5.992 25140 Z= 0.269 Chirality : 0.037 0.139 2690 Planarity : 0.004 0.079 3010 Dihedral : 12.171 106.697 3122 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.41 % Favored : 90.45 % Rotamer: Outliers : 1.57 % Allowed : 16.25 % Favored : 82.18 % 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: -1.31 (0.19), residues: 2146 helix: 0.63 (0.15), residues: 1212 sheet: -2.76 (0.40), residues: 138 loop : -2.96 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 661 TYR 0.010 0.001 TYR H 139 PHE 0.014 0.001 PHE A 491 TRP 0.005 0.000 TRP H 120 HIS 0.005 0.001 HIS F 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (18678) covalent geometry : angle 0.51649 / 0.27 (25132) SS BOND : bond 0.00229 / 0.11 ( 4) SS BOND : angle 0.78234 / 0.46 ( 8) hydrogen bonds : bond 0.03482 / 2.31 ( 709) hydrogen bonds : angle 3.85689 / 2.68 ( 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 : 0.936 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: B 439 LYS cc_start: 0.7999 (mttt) cc_final: 0.7731 (mttm) REVERT: B 772 GLU cc_start: 0.7004 (mp0) cc_final: 0.6733 (mp0) REVERT: B 788 SER cc_start: 0.9130 (t) cc_final: 0.8702 (p) REVERT: D 597 SER cc_start: 0.9346 (p) cc_final: 0.8723 (m) REVERT: E 10 TYR cc_start: 0.8367 (m-10) cc_final: 0.8132 (m-80) REVERT: E 51 LEU cc_start: 0.7055 (mm) cc_final: 0.6785 (mm) REVERT: F 39 LYS cc_start: 0.5672 (OUTLIER) cc_final: 0.4460 (tppt) REVERT: F 95 MET cc_start: 0.3383 (tpt) cc_final: 0.1400 (mpp) REVERT: F 120 TRP cc_start: 0.6476 (m100) cc_final: 0.6210 (m100) REVERT: H 77 LEU cc_start: 0.8454 (mt) cc_final: 0.7692 (tt) REVERT: H 90 MET cc_start: 0.7267 (mmp) cc_final: 0.6384 (ptm) REVERT: H 117 LYS cc_start: 0.4970 (OUTLIER) cc_final: 0.4224 (mmtt) outliers start: 29 outliers final: 21 residues processed: 260 average time/residue: 0.2751 time to fit residues: 115.4391 Evaluate side-chains 265 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 242 time to evaluate : 0.932 ------------------------------------------------------------------------------- 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 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 392 ILE Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 803 MET Chi-restraints excluded: chain D residue 422 GLU 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 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 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: 3.9990 chunk 146 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 176 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 710 GLN ** B 714 GLN ** 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 = 0.3835 r_free = 0.3835 target = 0.156374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.114564 restraints weight = 72910.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.111664 restraints weight = 68921.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.114418 restraints weight = 64964.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.115349 restraints weight = 43961.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.115810 restraints weight = 41683.165| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3322 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3322 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.9314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 18682 Z= 0.222 Angle : 0.608 6.268 25140 Z= 0.321 Chirality : 0.039 0.147 2690 Planarity : 0.005 0.077 3010 Dihedral : 12.807 107.765 3122 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.32 % Favored : 88.49 % Rotamer: Outliers : 1.35 % Allowed : 16.47 % Favored : 82.18 % 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: -1.59 (0.18), residues: 2146 helix: 0.43 (0.15), residues: 1206 sheet: -2.66 (0.45), residues: 110 loop : -3.16 (0.20), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 586 TYR 0.012 0.001 TYR C 401 PHE 0.021 0.002 PHE D 546 TRP 0.008 0.001 TRP H 120 HIS 0.005 0.001 HIS F 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.22 (18678) covalent geometry : angle 0.60794 / 0.32 (25132) SS BOND : bond 0.00440 / 0.22 ( 4) SS BOND : angle 1.02760 / 0.61 ( 8) hydrogen bonds : bond 0.04413 / 2.90 ( 709) hydrogen bonds : angle 4.23966 / 2.94 ( 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 274 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 249 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 630 GLU cc_start: 0.6751 (mm-30) cc_final: 0.6315 (mm-30) REVERT: B 439 LYS cc_start: 0.8059 (mttt) cc_final: 0.7793 (mttm) REVERT: B 524 GLU cc_start: 0.8030 (tt0) cc_final: 0.7815 (tt0) REVERT: B 597 SER cc_start: 0.9331 (p) cc_final: 0.8894 (m) REVERT: B 788 SER cc_start: 0.9161 (t) cc_final: 0.8808 (p) REVERT: D 524 GLU cc_start: 0.7850 (tt0) cc_final: 0.7583 (tt0) REVERT: D 597 SER cc_start: 0.9398 (p) cc_final: 0.8884 (m) REVERT: E 56 TYR cc_start: 0.6891 (m-80) cc_final: 0.6548 (m-80) REVERT: F 39 LYS cc_start: 0.5782 (OUTLIER) cc_final: 0.4597 (tppt) REVERT: F 95 MET cc_start: 0.3135 (tpt) cc_final: 0.1088 (mpp) REVERT: H 77 LEU cc_start: 0.8481 (mt) cc_final: 0.7707 (tt) REVERT: H 90 MET cc_start: 0.7483 (mmp) cc_final: 0.6527 (ptp) REVERT: H 117 LYS cc_start: 0.5011 (OUTLIER) cc_final: 0.4238 (mmtt) outliers start: 25 outliers final: 23 residues processed: 260 average time/residue: 0.2911 time to fit residues: 119.9183 Evaluate side-chains 263 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 238 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 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 478 THR Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 803 MET Chi-restraints excluded: chain D residue 422 GLU Chi-restraints excluded: chain D residue 815 CYS Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 138 ILE 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 21 ILE 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 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: 2.9990 chunk 43 optimal weight: 3.9990 chunk 186 optimal weight: 5.9990 chunk 18 optimal weight: 0.2980 chunk 85 optimal weight: 0.8980 chunk 112 optimal weight: 0.6980 chunk 178 optimal weight: 0.2980 chunk 17 optimal weight: 0.6980 chunk 181 optimal weight: 0.3980 chunk 179 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 710 GLN C 583 GLN C 710 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.160645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.118459 restraints weight = 71759.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.117168 restraints weight = 61211.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.119876 restraints weight = 62471.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.120408 restraints weight = 39244.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.120981 restraints weight = 36883.770| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3386 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3386 r_free = 0.3386 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3386 r_free = 0.3386 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3386 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.9427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 18682 Z= 0.099 Angle : 0.515 5.890 25140 Z= 0.268 Chirality : 0.036 0.135 2690 Planarity : 0.004 0.076 3010 Dihedral : 12.065 106.919 3122 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.67 % Favored : 91.24 % Rotamer: Outliers : 1.03 % Allowed : 17.12 % Favored : 81.86 % 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: -1.20 (0.19), residues: 2146 helix: 0.67 (0.15), residues: 1222 sheet: -2.45 (0.37), residues: 160 loop : -2.90 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 545 TYR 0.014 0.001 TYR G 89 PHE 0.013 0.001 PHE A 491 TRP 0.008 0.001 TRP F 26 HIS 0.005 0.001 HIS F 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (18678) covalent geometry : angle 0.51452 / 0.27 (25132) SS BOND : bond 0.00169 / 0.08 ( 4) SS BOND : angle 0.83873 / 0.48 ( 8) hydrogen bonds : bond 0.03372 / 2.25 ( 709) hydrogen bonds : angle 3.80661 / 2.65 ( 2037) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5505.21 seconds wall clock time: 94 minutes 55.70 seconds (5695.70 seconds total)