Starting phenix.real_space_refine on Mon Jun 16 07:54:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mrm_48559/06_2025/9mrm_48559.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mrm_48559/06_2025/9mrm_48559.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mrm_48559/06_2025/9mrm_48559.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mrm_48559/06_2025/9mrm_48559.map" model { file = "/net/cci-nas-00/data/ceres_data/9mrm_48559/06_2025/9mrm_48559.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mrm_48559/06_2025/9mrm_48559.cif" } resolution = 4.52 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.001 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 128 5.16 5 C 11885 2.51 5 N 2967 2.21 5 O 3314 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18294 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3236 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 401} Chain breaks: 1 Chain: "B" Number of atoms: 3223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3223 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 400} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3236 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 401} Chain breaks: 1 Chain: "D" Number of atoms: 3219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3219 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 400} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1335 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 1, 'TRANS': 170} Chain breaks: 3 Chain: "F" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1335 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 1, 'TRANS': 170} Chain breaks: 3 Chain: "G" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1335 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 1, 'TRANS': 170} Chain breaks: 3 Chain: "H" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1335 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 1, 'TRANS': 170} Chain breaks: 3 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: "B" 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: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 11.94, per 1000 atoms: 0.65 Number of scatterers: 18294 At special positions: 0 Unit cell: (120.28, 115.43, 152.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 128 16.00 O 3314 8.00 N 2967 7.00 C 11885 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS E 39 " - pdb=" SG CYS E 67 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 76 " distance=2.03 Simple disulfide: pdb=" SG CYS F 39 " - pdb=" SG CYS F 67 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 76 " distance=2.03 Simple disulfide: pdb=" SG CYS G 39 " - pdb=" SG CYS G 67 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 76 " distance=2.03 Simple disulfide: pdb=" SG CYS H 39 " - pdb=" SG CYS H 67 " distance=2.03 Simple disulfide: pdb=" SG CYS H 66 " - pdb=" SG CYS H 76 " 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: 4.57 Conformation dependent library (CDL) restraints added in 2.3 seconds 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4276 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 22 sheets defined 59.0% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.03 Creating SS restraints... Processing helix chain 'A' and resid 417 through 419 No H-bonds generated for 'chain 'A' and resid 417 through 419' Processing helix chain 'A' and resid 423 through 437 removed outlier: 3.834A pdb=" N ALA A 430 " --> pdb=" O VAL A 426 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 515 through 521 Proline residue: A 520 - end of helix Processing helix chain 'A' and resid 522 through 546 removed outlier: 3.561A pdb=" N TRP A 526 " --> pdb=" O ALA A 522 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE A 531 " --> pdb=" O MET A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 569 removed outlier: 3.919A pdb=" N ASN A 569 " --> pdb=" O GLU A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 595 through 629 removed outlier: 3.704A pdb=" N SER A 614 " --> pdb=" O LEU A 610 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET A 629 " --> pdb=" O THR A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 641 Processing helix chain 'A' and resid 653 through 662 removed outlier: 3.684A pdb=" N GLU A 657 " --> pdb=" O GLY A 653 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG A 660 " --> pdb=" O LYS A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 677 Processing helix chain 'A' and resid 685 through 696 Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 742 through 756 Processing helix chain 'A' and resid 757 through 768 removed outlier: 4.542A pdb=" N LYS A 765 " --> pdb=" O LYS A 761 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TRP A 766 " --> pdb=" O LEU A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 791 Processing helix chain 'A' and resid 792 through 818 removed outlier: 4.266A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR A 797 " --> pdb=" O ALA A 793 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N MET A 807 " --> pdb=" O LEU A 803 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU A 808 " --> pdb=" O GLY A 804 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 809 " --> pdb=" O LEU A 805 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 420 Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 461 through 469 removed outlier: 3.908A pdb=" N LEU B 467 " --> pdb=" O MET B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 515 through 522 Proline residue: B 520 - end of helix Processing helix chain 'B' and resid 523 through 546 removed outlier: 3.946A pdb=" N MET B 527 " --> pdb=" O TYR B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 585 removed outlier: 3.740A pdb=" N PHE B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET B 585 " --> pdb=" O LEU B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 624 removed outlier: 3.681A pdb=" N VAL B 604 " --> pdb=" O ILE B 600 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N TRP B 605 " --> pdb=" O VAL B 601 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TRP B 606 " --> pdb=" O GLY B 602 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 642 removed outlier: 3.581A pdb=" N LEU B 639 " --> pdb=" O SER B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 662 removed outlier: 3.734A pdb=" N GLU B 657 " --> pdb=" O GLY B 653 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG B 661 " --> pdb=" O GLU B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 677 Processing helix chain 'B' and resid 685 through 697 removed outlier: 3.546A pdb=" N VAL B 693 " --> pdb=" O GLY B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 713 removed outlier: 3.637A pdb=" N TYR B 711 " --> pdb=" O THR B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 757 removed outlier: 3.781A pdb=" N ALA B 749 " --> pdb=" O PRO B 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 767 removed outlier: 3.939A pdb=" N LYS B 761 " --> pdb=" O GLY B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 771 Processing helix chain 'B' and resid 773 through 778 removed outlier: 3.535A pdb=" N LYS B 776 " --> pdb=" O CYS B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 792 Processing helix chain 'B' and resid 793 through 817 removed outlier: 3.807A pdb=" N TYR B 797 " --> pdb=" O ALA B 793 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B 808 " --> pdb=" O GLY B 804 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL B 809 " --> pdb=" O LEU B 805 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA B 810 " --> pdb=" O ALA B 806 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 811 " --> pdb=" O MET B 807 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 515 through 519 Processing helix chain 'C' and resid 521 through 545 removed outlier: 4.204A pdb=" N ILE C 525 " --> pdb=" O LEU C 521 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TRP C 526 " --> pdb=" O ALA C 522 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE C 534 " --> pdb=" O VAL C 530 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY C 535 " --> pdb=" O PHE C 531 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL C 536 " --> pdb=" O ALA C 532 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER C 537 " --> pdb=" O TYR C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 586 removed outlier: 3.988A pdb=" N SER C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY C 582 " --> pdb=" O TRP C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 629 removed outlier: 3.589A pdb=" N ILE C 600 " --> pdb=" O LEU C 596 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER C 614 " --> pdb=" O LEU C 610 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N MET C 629 " --> pdb=" O THR C 625 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 641 Processing helix chain 'C' and resid 653 through 662 removed outlier: 3.808A pdb=" N GLU C 657 " --> pdb=" O GLY C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 677 Processing helix chain 'C' and resid 685 through 697 Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 742 through 756 Processing helix chain 'C' and resid 757 through 767 removed outlier: 3.678A pdb=" N LYS C 763 " --> pdb=" O LEU C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 782 through 786 removed outlier: 4.388A pdb=" N SER C 785 " --> pdb=" O GLU C 782 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 791 Processing helix chain 'C' and resid 792 through 818 removed outlier: 4.365A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR C 797 " --> pdb=" O ALA C 793 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET C 807 " --> pdb=" O LEU C 803 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU C 808 " --> pdb=" O GLY C 804 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 421 removed outlier: 3.679A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 428 removed outlier: 3.926A pdb=" N LEU D 428 " --> pdb=" O TYR D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 437 Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 515 through 520 Proline residue: D 520 - end of helix Processing helix chain 'D' and resid 521 through 545 removed outlier: 4.192A pdb=" N ILE D 525 " --> pdb=" O LEU D 521 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N VAL D 530 " --> pdb=" O TRP D 526 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE D 531 " --> pdb=" O MET D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 626 removed outlier: 3.576A pdb=" N VAL D 604 " --> pdb=" O ILE D 600 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TRP D 605 " --> pdb=" O VAL D 601 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR D 625 " --> pdb=" O ALA D 621 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL D 626 " --> pdb=" O ALA D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 641 Processing helix chain 'D' and resid 653 through 662 removed outlier: 3.767A pdb=" N GLU D 657 " --> pdb=" O GLY D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 677 Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 706 through 714 removed outlier: 3.578A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 757 removed outlier: 3.840A pdb=" N ASN D 747 " --> pdb=" O GLY D 743 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU D 748 " --> pdb=" O THR D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 768 removed outlier: 4.300A pdb=" N TRP D 766 " --> pdb=" O LEU D 762 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 791 Processing helix chain 'D' and resid 792 through 817 removed outlier: 4.352A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR D 797 " --> pdb=" O ALA D 793 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET D 807 " --> pdb=" O LEU D 803 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU D 808 " --> pdb=" O GLY D 804 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL D 809 " --> pdb=" O LEU D 805 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA D 810 " --> pdb=" O ALA D 806 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 28 removed outlier: 3.600A pdb=" N LEU E 11 " --> pdb=" O VAL E 7 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N VAL E 14 " --> pdb=" O LEU E 10 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY E 15 " --> pdb=" O LEU E 11 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ALA E 16 " --> pdb=" O THR E 12 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N PHE E 17 " --> pdb=" O THR E 13 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA E 18 " --> pdb=" O VAL E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 96 removed outlier: 3.902A pdb=" N PHE E 96 " --> pdb=" O ALA E 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 93 through 96' Processing helix chain 'E' and resid 97 through 104 removed outlier: 3.844A pdb=" N ARG E 101 " --> pdb=" O LEU E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 124 removed outlier: 3.938A pdb=" N ILE E 108 " --> pdb=" O SER E 104 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE E 121 " --> pdb=" O GLY E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 160 removed outlier: 4.269A pdb=" N LEU E 135 " --> pdb=" O HIS E 131 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER E 136 " --> pdb=" O ASN E 132 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ALA E 137 " --> pdb=" O ILE E 133 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLY E 138 " --> pdb=" O ILE E 134 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE E 139 " --> pdb=" O LEU E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 209 removed outlier: 4.038A pdb=" N TYR E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N HIS E 204 " --> pdb=" O PHE E 200 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU E 207 " --> pdb=" O ARG E 203 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR E 208 " --> pdb=" O HIS E 204 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY E 209 " --> pdb=" O LYS E 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 28 Processing helix chain 'F' and resid 94 through 104 removed outlier: 4.459A pdb=" N ALA F 99 " --> pdb=" O TYR F 95 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL F 100 " --> pdb=" O PHE F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 122 removed outlier: 4.250A pdb=" N CYS F 120 " --> pdb=" O MET F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 126 Processing helix chain 'F' and resid 131 through 159 removed outlier: 3.917A pdb=" N ALA F 137 " --> pdb=" O ILE F 133 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY F 138 " --> pdb=" O ILE F 134 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ILE F 139 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE F 140 " --> pdb=" O SER F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 206 removed outlier: 3.979A pdb=" N TYR F 180 " --> pdb=" O GLY F 176 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY F 193 " --> pdb=" O ALA F 189 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL F 194 " --> pdb=" O GLU F 190 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU F 195 " --> pdb=" O MET F 191 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN F 206 " --> pdb=" O ASP F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 209 No H-bonds generated for 'chain 'F' and resid 207 through 209' Processing helix chain 'G' and resid 7 through 28 Processing helix chain 'G' and resid 94 through 104 removed outlier: 4.694A pdb=" N ALA G 99 " --> pdb=" O TYR G 95 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N VAL G 100 " --> pdb=" O PHE G 96 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG G 101 " --> pdb=" O LEU G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 123 removed outlier: 3.527A pdb=" N ILE G 108 " --> pdb=" O SER G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 126 No H-bonds generated for 'chain 'G' and resid 124 through 126' Processing helix chain 'G' and resid 131 through 161 removed outlier: 3.812A pdb=" N LEU G 135 " --> pdb=" O HIS G 131 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN G 148 " --> pdb=" O ALA G 144 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE G 149 " --> pdb=" O GLY G 145 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE G 150 " --> pdb=" O LEU G 146 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA G 160 " --> pdb=" O ILE G 156 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY G 161 " --> pdb=" O SER G 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 206 removed outlier: 3.946A pdb=" N TYR G 180 " --> pdb=" O GLY G 176 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY G 193 " --> pdb=" O ALA G 189 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL G 194 " --> pdb=" O GLU G 190 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU G 195 " --> pdb=" O MET G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 209 No H-bonds generated for 'chain 'G' and resid 207 through 209' Processing helix chain 'H' and resid 6 through 28 removed outlier: 4.198A pdb=" N LEU H 10 " --> pdb=" O GLY H 6 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU H 11 " --> pdb=" O VAL H 7 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N VAL H 14 " --> pdb=" O LEU H 10 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLY H 15 " --> pdb=" O LEU H 11 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ALA H 16 " --> pdb=" O THR H 12 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N PHE H 17 " --> pdb=" O THR H 13 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA H 18 " --> pdb=" O VAL H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 96 removed outlier: 3.943A pdb=" N PHE H 96 " --> pdb=" O ALA H 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 93 through 96' Processing helix chain 'H' and resid 97 through 104 removed outlier: 3.831A pdb=" N ARG H 101 " --> pdb=" O LEU H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.987A pdb=" N ILE H 108 " --> pdb=" O SER H 104 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE H 121 " --> pdb=" O GLY H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 160 removed outlier: 4.219A pdb=" N LEU H 135 " --> pdb=" O HIS H 131 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N SER H 136 " --> pdb=" O ASN H 132 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ALA H 137 " --> pdb=" O ILE H 133 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLY H 138 " --> pdb=" O ILE H 134 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE H 139 " --> pdb=" O LEU H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 206 removed outlier: 4.104A pdb=" N TYR H 180 " --> pdb=" O GLY H 176 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N HIS H 204 " --> pdb=" O PHE H 200 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN H 206 " --> pdb=" O ASP H 202 " (cutoff:3.500A) Processing helix chain 'H' and resid 207 through 209 No H-bonds generated for 'chain 'H' and resid 207 through 209' Processing sheet with id=AA1, first strand: chain 'A' and resid 440 through 444 removed outlier: 3.852A pdb=" N ILE A 474 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA3, first strand: chain 'A' and resid 489 through 491 Processing sheet with id=AA4, first strand: chain 'A' and resid 496 through 498 removed outlier: 4.230A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 682 through 683 removed outlier: 8.752A pdb=" N VAL A 683 " --> pdb=" O TYR A 647 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR A 649 " --> pdb=" O VAL A 683 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LEU A 650 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 10.071A pdb=" N GLU A 705 " --> pdb=" O LEU A 650 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A 723 " --> pdb=" O ILE A 502 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 440 through 444 removed outlier: 3.751A pdb=" N ILE B 474 " --> pdb=" O VAL B 396 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 407 through 408 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 496 through 498 removed outlier: 3.566A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.639A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.652A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.950A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL B 723 " --> pdb=" O ILE B 502 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 440 through 444 removed outlier: 5.971A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL C 396 " --> pdb=" O ILE C 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB4, first strand: chain 'C' and resid 489 through 491 Processing sheet with id=AB5, first strand: chain 'C' and resid 496 through 498 removed outlier: 4.285A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.363A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.202A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 9.043A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 439 through 444 removed outlier: 7.050A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N THR D 443 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ILE D 474 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE D 476 " --> pdb=" O THR D 398 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ALA D 477 " --> pdb=" O GLY D 733 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N GLY D 733 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU D 479 " --> pdb=" O GLY D 731 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLY D 731 " --> pdb=" O LEU D 479 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 439 through 444 removed outlier: 7.050A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N THR D 443 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ILE D 474 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE D 476 " --> pdb=" O THR D 398 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ALA D 477 " --> pdb=" O GLY D 733 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N GLY D 733 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU D 479 " --> pdb=" O GLY D 731 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLY D 731 " --> pdb=" O LEU D 479 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.334A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.578A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 9.256A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL D 723 " --> pdb=" O ILE D 502 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE D 504 " --> pdb=" O MET D 721 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 76 through 78 Processing sheet with id=AC2, first strand: chain 'F' and resid 76 through 78 removed outlier: 3.605A pdb=" N LEU F 33 " --> pdb=" O SER F 60 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 76 through 78 removed outlier: 3.745A pdb=" N LEU G 33 " --> pdb=" O SER G 60 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 76 through 78 978 hydrogen bonds defined for protein. 2796 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: 5.75 Time building geometry restraints manager: 5.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5607 1.34 - 1.46: 4805 1.46 - 1.58: 8066 1.58 - 1.70: 0 1.70 - 1.82: 208 Bond restraints: 18686 Sorted by residual: bond pdb=" CG1 ILE E 188 " pdb=" CD1 ILE E 188 " ideal model delta sigma weight residual 1.513 1.432 0.081 3.90e-02 6.57e+02 4.29e+00 bond pdb=" CG1 ILE F 188 " pdb=" CD1 ILE F 188 " ideal model delta sigma weight residual 1.513 1.445 0.068 3.90e-02 6.57e+02 3.07e+00 bond pdb=" C GLN C 508 " pdb=" N LYS C 509 " ideal model delta sigma weight residual 1.333 1.350 -0.017 1.30e-02 5.92e+03 1.71e+00 bond pdb=" CA GLN B 586 " pdb=" C GLN B 586 " ideal model delta sigma weight residual 1.532 1.520 0.012 9.60e-03 1.09e+04 1.59e+00 bond pdb=" CA ASN B 726 " pdb=" CB ASN B 726 " ideal model delta sigma weight residual 1.530 1.549 -0.019 1.69e-02 3.50e+03 1.22e+00 ... (remaining 18681 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 24919 2.39 - 4.79: 260 4.79 - 7.18: 19 7.18 - 9.57: 3 9.57 - 11.96: 1 Bond angle restraints: 25202 Sorted by residual: angle pdb=" C MET B 629 " pdb=" N VAL B 630 " pdb=" CA VAL B 630 " ideal model delta sigma weight residual 121.97 130.35 -8.38 1.80e+00 3.09e-01 2.17e+01 angle pdb=" C GLY B 725 " pdb=" N ASN B 726 " pdb=" CA ASN B 726 " ideal model delta sigma weight residual 121.54 129.45 -7.91 1.91e+00 2.74e-01 1.72e+01 angle pdb=" N ILE D 476 " pdb=" CA ILE D 476 " pdb=" C ILE D 476 " ideal model delta sigma weight residual 111.77 108.16 3.61 1.04e+00 9.25e-01 1.20e+01 angle pdb=" C ARG A 715 " pdb=" N LYS A 716 " pdb=" CA LYS A 716 " ideal model delta sigma weight residual 120.58 125.11 -4.53 1.32e+00 5.74e-01 1.18e+01 angle pdb=" CA LEU H 114 " pdb=" CB LEU H 114 " pdb=" CG LEU H 114 " ideal model delta sigma weight residual 116.30 128.26 -11.96 3.50e+00 8.16e-02 1.17e+01 ... (remaining 25197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 10251 17.62 - 35.24: 606 35.24 - 52.87: 84 52.87 - 70.49: 21 70.49 - 88.11: 14 Dihedral angle restraints: 10976 sinusoidal: 4270 harmonic: 6706 Sorted by residual: dihedral pdb=" CD ARG A 628 " pdb=" NE ARG A 628 " pdb=" CZ ARG A 628 " pdb=" NH1 ARG A 628 " ideal model delta sinusoidal sigma weight residual 0.00 -63.32 63.32 1 1.00e+01 1.00e-02 5.29e+01 dihedral pdb=" CA VAL E 14 " pdb=" C VAL E 14 " pdb=" N GLY E 15 " pdb=" CA GLY E 15 " ideal model delta harmonic sigma weight residual 180.00 -156.61 -23.39 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CB CYS B 718 " pdb=" SG CYS B 718 " pdb=" SG CYS B 773 " pdb=" CB CYS B 773 " ideal model delta sinusoidal sigma weight residual 93.00 131.39 -38.39 1 1.00e+01 1.00e-02 2.08e+01 ... (remaining 10973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1968 0.042 - 0.085: 678 0.085 - 0.127: 157 0.127 - 0.170: 20 0.170 - 0.212: 3 Chirality restraints: 2826 Sorted by residual: chirality pdb=" CA THR B 744 " pdb=" N THR B 744 " pdb=" C THR B 744 " pdb=" CB THR B 744 " both_signs ideal model delta sigma weight residual False 2.53 2.31 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA THR C 744 " pdb=" N THR C 744 " pdb=" C THR C 744 " pdb=" CB THR C 744 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA THR A 744 " pdb=" N THR A 744 " pdb=" C THR A 744 " pdb=" CB THR A 744 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.87e-01 ... (remaining 2823 not shown) Planarity restraints: 3102 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 628 " -0.792 9.50e-02 1.11e+02 3.57e-01 9.06e+01 pdb=" NE ARG A 628 " 0.071 2.00e-02 2.50e+03 pdb=" CZ ARG A 628 " -0.055 2.00e-02 2.50e+03 pdb=" NH1 ARG A 628 " 0.019 2.00e-02 2.50e+03 pdb=" NH2 ARG A 628 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU F 97 " -0.013 2.00e-02 2.50e+03 2.51e-02 6.32e+00 pdb=" C LEU F 97 " 0.043 2.00e-02 2.50e+03 pdb=" O LEU F 97 " -0.016 2.00e-02 2.50e+03 pdb=" N ARG F 98 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 519 " 0.036 5.00e-02 4.00e+02 5.41e-02 4.69e+00 pdb=" N PRO C 520 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 520 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 520 " 0.030 5.00e-02 4.00e+02 ... (remaining 3099 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 308 2.67 - 3.23: 19334 3.23 - 3.79: 27468 3.79 - 4.34: 35341 4.34 - 4.90: 57916 Nonbonded interactions: 140367 Sorted by model distance: nonbonded pdb=" OE2 GLU B 657 " pdb=" NH1 ARG B 660 " model vdw 2.118 3.120 nonbonded pdb=" OE1 GLU C 705 " pdb=" OH TYR C 732 " model vdw 2.164 3.040 nonbonded pdb=" OG SER D 547 " pdb=" OE2 GLU D 566 " model vdw 2.223 3.040 nonbonded pdb=" O VAL B 397 " pdb=" OG1 THR B 443 " model vdw 2.231 3.040 nonbonded pdb=" N GLU G 94 " pdb=" OE1 GLU G 94 " model vdw 2.243 3.120 ... (remaining 140362 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 391 through 504 or (resid 505 and (name N or name CA or na \ me C or name O or name CB )) or resid 506 through 817 or (resid 818 through 819 \ and (name N or name CA or name C or name O or name CB )) or resid 1301)) selection = (chain 'B' and (resid 391 through 504 or (resid 505 and (name N or name CA or na \ me C or name O or name CB )) or resid 506 through 819 or resid 1301)) selection = (chain 'C' and (resid 391 through 504 or (resid 505 and (name N or name CA or na \ me C or name O or name CB )) or resid 506 through 817 or (resid 818 through 819 \ and (name N or name CA or name C or name O or name CB )) or resid 1301)) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 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: 7.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.720 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 42.660 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.090 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 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 : 0.003 0.081 18698 Z= 0.150 Angle : 0.650 11.965 25226 Z= 0.372 Chirality : 0.044 0.212 2826 Planarity : 0.009 0.357 3102 Dihedral : 12.052 88.110 6664 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.18 % Favored : 95.52 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.16), residues: 2298 helix: -0.04 (0.14), residues: 1170 sheet: -0.99 (0.42), residues: 142 loop : -0.97 (0.20), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 606 HIS 0.004 0.001 HIS B 435 PHE 0.023 0.002 PHE C 531 TYR 0.019 0.003 TYR C 533 ARG 0.064 0.003 ARG A 628 Details of bonding type rmsd hydrogen bonds : bond 0.15874 ( 975) hydrogen bonds : angle 6.47774 ( 2796) SS BOND : bond 0.00319 ( 12) SS BOND : angle 0.66658 ( 24) covalent geometry : bond 0.00304 (18686) covalent geometry : angle 0.64951 (25202) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 626 time to evaluate : 2.008 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: A 424 TYR cc_start: 0.8668 (t80) cc_final: 0.8040 (t80) REVERT: A 463 MET cc_start: 0.8471 (mtm) cc_final: 0.8002 (mmt) REVERT: A 534 ILE cc_start: 0.9624 (mt) cc_final: 0.9407 (mm) REVERT: A 537 SER cc_start: 0.9601 (m) cc_final: 0.9311 (t) REVERT: A 609 THR cc_start: 0.9102 (t) cc_final: 0.8894 (t) REVERT: A 625 THR cc_start: 0.9474 (m) cc_final: 0.9162 (p) REVERT: A 642 GLN cc_start: 0.8764 (tp-100) cc_final: 0.7819 (tm-30) REVERT: A 645 ILE cc_start: 0.7079 (mm) cc_final: 0.6858 (mm) REVERT: A 657 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8567 (mp0) REVERT: A 702 TYR cc_start: 0.8020 (t80) cc_final: 0.7625 (t80) REVERT: B 486 GLU cc_start: 0.8500 (tt0) cc_final: 0.8077 (tp30) REVERT: B 527 MET cc_start: 0.8878 (mtm) cc_final: 0.7987 (mtt) REVERT: B 609 THR cc_start: 0.9226 (t) cc_final: 0.8942 (t) REVERT: B 674 MET cc_start: 0.3470 (mtp) cc_final: 0.2054 (tmm) REVERT: B 769 ASP cc_start: 0.8981 (m-30) cc_final: 0.8393 (p0) REVERT: C 474 ILE cc_start: 0.8670 (tt) cc_final: 0.8398 (tp) REVERT: C 508 GLN cc_start: 0.7299 (pp30) cc_final: 0.6497 (mm110) REVERT: C 537 SER cc_start: 0.9338 (m) cc_final: 0.8736 (t) REVERT: C 627 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8407 (mt-10) REVERT: C 642 GLN cc_start: 0.9270 (tp-100) cc_final: 0.8858 (tm-30) REVERT: C 668 ASP cc_start: 0.9282 (t0) cc_final: 0.8943 (m-30) REVERT: D 503 MET cc_start: 0.7320 (ttp) cc_final: 0.6624 (ttm) REVERT: D 609 THR cc_start: 0.9236 (t) cc_final: 0.8837 (t) REVERT: D 612 ILE cc_start: 0.9574 (mm) cc_final: 0.9319 (tp) REVERT: D 614 SER cc_start: 0.9526 (m) cc_final: 0.9233 (t) REVERT: D 651 ASP cc_start: 0.7071 (t0) cc_final: 0.6421 (p0) REVERT: D 767 TRP cc_start: 0.8676 (m-90) cc_final: 0.8208 (m-90) REVERT: E 8 GLN cc_start: 0.7573 (mp10) cc_final: 0.7333 (mp10) REVERT: E 35 SER cc_start: 0.7267 (m) cc_final: 0.7048 (t) REVERT: F 60 SER cc_start: 0.9012 (m) cc_final: 0.8718 (t) REVERT: F 149 ILE cc_start: 0.8153 (mt) cc_final: 0.7863 (mt) REVERT: F 173 TYR cc_start: 0.8115 (p90) cc_final: 0.7563 (p90) REVERT: F 205 LYS cc_start: 0.8811 (tttt) cc_final: 0.8311 (tptt) REVERT: G 23 MET cc_start: 0.8528 (tpt) cc_final: 0.8253 (tpt) REVERT: G 97 LEU cc_start: 0.7491 (tt) cc_final: 0.6799 (mt) REVERT: G 116 MET cc_start: 0.3319 (mmm) cc_final: 0.3093 (mmm) REVERT: G 124 SER cc_start: 0.7051 (t) cc_final: 0.6588 (m) REVERT: H 23 MET cc_start: 0.8688 (tpt) cc_final: 0.8382 (ttt) REVERT: H 63 TRP cc_start: 0.6850 (m100) cc_final: 0.6616 (m100) outliers start: 0 outliers final: 0 residues processed: 626 average time/residue: 0.2945 time to fit residues: 275.2779 Evaluate side-chains 334 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 334 time to evaluate : 2.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 0.8980 chunk 175 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 118 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 135 optimal weight: 0.3980 chunk 210 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 586 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.148408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.108627 restraints weight = 55010.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.106389 restraints weight = 47510.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.106526 restraints weight = 41577.285| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 18698 Z= 0.141 Angle : 0.633 7.988 25226 Z= 0.338 Chirality : 0.044 0.261 2826 Planarity : 0.005 0.133 3102 Dihedral : 5.223 74.557 2522 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.57 % Favored : 96.21 % Rotamer: Outliers : 0.15 % Allowed : 3.27 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.18), residues: 2298 helix: 1.50 (0.15), residues: 1198 sheet: -0.88 (0.39), residues: 160 loop : -0.76 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 671 HIS 0.005 0.001 HIS B 435 PHE 0.040 0.002 PHE H 179 TYR 0.026 0.002 TYR C 732 ARG 0.017 0.001 ARG E 36 Details of bonding type rmsd hydrogen bonds : bond 0.05115 ( 975) hydrogen bonds : angle 4.86661 ( 2796) SS BOND : bond 0.00245 ( 12) SS BOND : angle 0.64245 ( 24) covalent geometry : bond 0.00297 (18686) covalent geometry : angle 0.63288 (25202) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 409 time to evaluate : 2.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 TYR cc_start: 0.8425 (t80) cc_final: 0.7738 (t80) REVERT: A 517 PHE cc_start: 0.8702 (p90) cc_final: 0.8391 (p90) REVERT: A 527 MET cc_start: 0.7866 (ttp) cc_final: 0.7530 (ttt) REVERT: A 537 SER cc_start: 0.9693 (m) cc_final: 0.9376 (t) REVERT: A 609 THR cc_start: 0.8994 (t) cc_final: 0.8759 (t) REVERT: A 625 THR cc_start: 0.9453 (m) cc_final: 0.9154 (p) REVERT: A 642 GLN cc_start: 0.8567 (tp-100) cc_final: 0.7998 (tm-30) REVERT: A 657 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8549 (mp0) REVERT: A 721 MET cc_start: 0.5331 (pmm) cc_final: 0.4830 (pmm) REVERT: B 486 GLU cc_start: 0.8363 (tt0) cc_final: 0.7955 (tp30) REVERT: B 527 MET cc_start: 0.8670 (mtm) cc_final: 0.8068 (mtp) REVERT: B 674 MET cc_start: 0.3998 (mtp) cc_final: 0.3353 (ttm) REVERT: B 729 SER cc_start: 0.7241 (p) cc_final: 0.6236 (p) REVERT: C 398 THR cc_start: 0.7994 (p) cc_final: 0.7742 (p) REVERT: C 508 GLN cc_start: 0.7036 (pp30) cc_final: 0.6651 (mm-40) REVERT: C 537 SER cc_start: 0.9273 (m) cc_final: 0.8716 (t) REVERT: C 585 MET cc_start: 0.8607 (mmt) cc_final: 0.8384 (mmt) REVERT: C 625 THR cc_start: 0.9511 (m) cc_final: 0.9237 (p) REVERT: C 627 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8515 (mt-10) REVERT: C 642 GLN cc_start: 0.9374 (tp-100) cc_final: 0.9027 (tm-30) REVERT: C 668 ASP cc_start: 0.9251 (t0) cc_final: 0.9020 (m-30) REVERT: C 670 MET cc_start: 0.9410 (mmp) cc_final: 0.8978 (mmm) REVERT: C 702 TYR cc_start: 0.8076 (t80) cc_final: 0.7640 (t80) REVERT: D 585 MET cc_start: 0.8641 (tpp) cc_final: 0.8390 (tpp) REVERT: D 670 MET cc_start: 0.8365 (mmp) cc_final: 0.8018 (mmm) REVERT: D 767 TRP cc_start: 0.8066 (m-90) cc_final: 0.7273 (m-90) REVERT: E 8 GLN cc_start: 0.8000 (mp10) cc_final: 0.7773 (mp10) REVERT: E 181 PHE cc_start: 0.6980 (m-80) cc_final: 0.6610 (m-80) REVERT: F 9 MET cc_start: 0.7384 (mtm) cc_final: 0.6929 (tmm) REVERT: F 58 THR cc_start: 0.7482 (m) cc_final: 0.7259 (p) REVERT: F 173 TYR cc_start: 0.7989 (p90) cc_final: 0.7722 (p90) REVERT: F 205 LYS cc_start: 0.8863 (tttt) cc_final: 0.8393 (tptt) REVERT: G 23 MET cc_start: 0.8577 (tpt) cc_final: 0.8201 (tpt) REVERT: G 97 LEU cc_start: 0.7531 (tt) cc_final: 0.6898 (mt) REVERT: G 124 SER cc_start: 0.6887 (t) cc_final: 0.6530 (m) REVERT: H 63 TRP cc_start: 0.6980 (m100) cc_final: 0.6637 (m100) REVERT: H 190 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8709 (mm-30) outliers start: 3 outliers final: 0 residues processed: 411 average time/residue: 0.2845 time to fit residues: 178.2031 Evaluate side-chains 282 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 2.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 121 optimal weight: 1.9990 chunk 124 optimal weight: 0.0870 chunk 86 optimal weight: 7.9990 chunk 164 optimal weight: 0.0870 chunk 180 optimal weight: 4.9990 chunk 223 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 187 optimal weight: 0.7980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.147888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.107617 restraints weight = 55527.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.105999 restraints weight = 46461.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.105948 restraints weight = 41623.946| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18698 Z= 0.130 Angle : 0.574 8.013 25226 Z= 0.307 Chirality : 0.042 0.229 2826 Planarity : 0.004 0.048 3102 Dihedral : 4.973 83.845 2522 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.48 % Favored : 96.30 % Rotamer: Outliers : 0.05 % Allowed : 2.56 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.18), residues: 2298 helix: 1.65 (0.15), residues: 1217 sheet: -0.85 (0.39), residues: 157 loop : -0.71 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 671 HIS 0.005 0.001 HIS B 435 PHE 0.023 0.001 PHE G 181 TYR 0.019 0.001 TYR B 450 ARG 0.007 0.000 ARG B 545 Details of bonding type rmsd hydrogen bonds : bond 0.04650 ( 975) hydrogen bonds : angle 4.62458 ( 2796) SS BOND : bond 0.00235 ( 12) SS BOND : angle 0.64152 ( 24) covalent geometry : bond 0.00278 (18686) covalent geometry : angle 0.57434 (25202) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 368 time to evaluate : 2.086 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 517 PHE cc_start: 0.8875 (p90) cc_final: 0.8460 (p90) REVERT: A 527 MET cc_start: 0.8205 (ttp) cc_final: 0.7776 (ttt) REVERT: A 537 SER cc_start: 0.9700 (m) cc_final: 0.9141 (t) REVERT: A 642 GLN cc_start: 0.8712 (tp-100) cc_final: 0.8428 (tm-30) REVERT: A 657 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8512 (mp0) REVERT: A 702 TYR cc_start: 0.7918 (t80) cc_final: 0.7648 (t80) REVERT: A 721 MET cc_start: 0.5039 (pmm) cc_final: 0.4577 (pmm) REVERT: B 414 MET cc_start: 0.9129 (pmm) cc_final: 0.8910 (pmm) REVERT: B 670 MET cc_start: 0.8258 (mmp) cc_final: 0.8057 (mmm) REVERT: C 398 THR cc_start: 0.8043 (p) cc_final: 0.7834 (p) REVERT: C 508 GLN cc_start: 0.7101 (pp30) cc_final: 0.6874 (mm-40) REVERT: C 537 SER cc_start: 0.9348 (m) cc_final: 0.8793 (t) REVERT: C 619 ASN cc_start: 0.9274 (t0) cc_final: 0.8989 (t0) REVERT: C 627 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8526 (mt-10) REVERT: C 670 MET cc_start: 0.9394 (mmp) cc_final: 0.8906 (mmm) REVERT: D 546 PHE cc_start: 0.6644 (t80) cc_final: 0.6182 (t80) REVERT: D 629 MET cc_start: 0.6509 (tmm) cc_final: 0.6294 (tmm) REVERT: D 638 ASP cc_start: 0.7832 (m-30) cc_final: 0.7491 (m-30) REVERT: D 641 LYS cc_start: 0.9110 (pptt) cc_final: 0.8845 (mmtm) REVERT: D 659 PHE cc_start: 0.7293 (m-80) cc_final: 0.6982 (m-80) REVERT: D 670 MET cc_start: 0.8366 (mmp) cc_final: 0.8154 (mmm) REVERT: D 767 TRP cc_start: 0.8171 (m-90) cc_final: 0.7429 (m-90) REVERT: E 8 GLN cc_start: 0.8161 (mp10) cc_final: 0.7884 (mp10) REVERT: E 30 ASP cc_start: 0.7402 (p0) cc_final: 0.7187 (p0) REVERT: F 9 MET cc_start: 0.7264 (mtm) cc_final: 0.6846 (tmm) REVERT: F 81 HIS cc_start: 0.8139 (m90) cc_final: 0.7842 (m-70) REVERT: F 173 TYR cc_start: 0.7981 (p90) cc_final: 0.7766 (p90) REVERT: F 205 LYS cc_start: 0.8892 (tttt) cc_final: 0.8393 (tptp) REVERT: G 97 LEU cc_start: 0.7541 (tt) cc_final: 0.6813 (mt) REVERT: G 124 SER cc_start: 0.6864 (t) cc_final: 0.6563 (m) REVERT: H 63 TRP cc_start: 0.7014 (m100) cc_final: 0.6775 (m100) outliers start: 1 outliers final: 0 residues processed: 369 average time/residue: 0.3264 time to fit residues: 189.8309 Evaluate side-chains 264 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 2.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 147 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 117 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 714 GLN ** E 78 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 = 0.4116 r_free = 0.4116 target = 0.143575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.098698 restraints weight = 54715.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.099806 restraints weight = 42377.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.099637 restraints weight = 31466.781| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 18698 Z= 0.187 Angle : 0.623 8.343 25226 Z= 0.335 Chirality : 0.043 0.177 2826 Planarity : 0.004 0.045 3102 Dihedral : 5.031 85.925 2522 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.96 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.18), residues: 2298 helix: 1.45 (0.15), residues: 1213 sheet: -0.82 (0.39), residues: 157 loop : -0.75 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 671 HIS 0.008 0.001 HIS B 435 PHE 0.023 0.002 PHE D 546 TYR 0.019 0.002 TYR C 523 ARG 0.005 0.001 ARG B 545 Details of bonding type rmsd hydrogen bonds : bond 0.05214 ( 975) hydrogen bonds : angle 4.78085 ( 2796) SS BOND : bond 0.00293 ( 12) SS BOND : angle 0.95459 ( 24) covalent geometry : bond 0.00402 (18686) covalent geometry : angle 0.62259 (25202) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 338 time to evaluate : 3.003 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 431 GLU cc_start: 0.8770 (pt0) cc_final: 0.8525 (pm20) REVERT: A 463 MET cc_start: 0.8264 (mtt) cc_final: 0.7886 (mmt) REVERT: A 471 LYS cc_start: 0.7636 (mtmt) cc_final: 0.7255 (tppt) REVERT: A 496 MET cc_start: 0.8449 (tpt) cc_final: 0.8209 (tpp) REVERT: A 527 MET cc_start: 0.8387 (ttp) cc_final: 0.8097 (ttt) REVERT: A 537 SER cc_start: 0.9713 (m) cc_final: 0.9499 (t) REVERT: A 642 GLN cc_start: 0.8894 (tp-100) cc_final: 0.7963 (tm-30) REVERT: A 721 MET cc_start: 0.5956 (pmm) cc_final: 0.5261 (pmm) REVERT: B 486 GLU cc_start: 0.8519 (tt0) cc_final: 0.8081 (tp30) REVERT: B 503 MET cc_start: 0.8267 (ttm) cc_final: 0.7982 (ttt) REVERT: B 674 MET cc_start: 0.4494 (mtp) cc_final: 0.3148 (tmm) REVERT: C 508 GLN cc_start: 0.7208 (pp30) cc_final: 0.6964 (mm-40) REVERT: C 537 SER cc_start: 0.9526 (m) cc_final: 0.8988 (t) REVERT: C 619 ASN cc_start: 0.9267 (t0) cc_final: 0.8962 (t0) REVERT: C 627 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8464 (mt-10) REVERT: C 642 GLN cc_start: 0.9304 (tp-100) cc_final: 0.7957 (pp30) REVERT: C 670 MET cc_start: 0.9452 (mmp) cc_final: 0.9097 (mmm) REVERT: C 674 MET cc_start: 0.9343 (tpp) cc_final: 0.9142 (tpp) REVERT: C 702 TYR cc_start: 0.8562 (t80) cc_final: 0.8156 (t80) REVERT: C 726 ASN cc_start: 0.9008 (m-40) cc_final: 0.8752 (m-40) REVERT: D 629 MET cc_start: 0.6718 (tmm) cc_final: 0.6451 (tmm) REVERT: D 638 ASP cc_start: 0.7963 (m-30) cc_final: 0.7660 (m-30) REVERT: D 641 LYS cc_start: 0.9307 (pptt) cc_final: 0.9064 (mmtm) REVERT: D 659 PHE cc_start: 0.7604 (m-80) cc_final: 0.7239 (m-80) REVERT: D 670 MET cc_start: 0.8612 (mmp) cc_final: 0.8388 (mmm) REVERT: D 674 MET cc_start: 0.6662 (mtm) cc_final: 0.6458 (mtt) REVERT: D 767 TRP cc_start: 0.8282 (m-90) cc_final: 0.7486 (m-90) REVERT: E 8 GLN cc_start: 0.8663 (mp10) cc_final: 0.8279 (mp10) REVERT: E 177 TRP cc_start: 0.7575 (p90) cc_final: 0.6722 (p90) REVERT: F 9 MET cc_start: 0.7681 (mtm) cc_final: 0.6927 (tmm) REVERT: F 62 LEU cc_start: 0.8583 (mt) cc_final: 0.8256 (mt) REVERT: F 190 GLU cc_start: 0.9057 (mm-30) cc_final: 0.8820 (mm-30) REVERT: F 205 LYS cc_start: 0.8937 (tttt) cc_final: 0.8414 (tptp) REVERT: G 103 SER cc_start: 0.9140 (t) cc_final: 0.8753 (p) REVERT: G 124 SER cc_start: 0.6923 (t) cc_final: 0.6617 (m) REVERT: G 190 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8707 (mm-30) REVERT: H 177 TRP cc_start: 0.7667 (p90) cc_final: 0.6891 (p90) outliers start: 0 outliers final: 0 residues processed: 338 average time/residue: 0.2877 time to fit residues: 151.8783 Evaluate side-chains 268 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 2.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 82 optimal weight: 8.9990 chunk 142 optimal weight: 0.9990 chunk 161 optimal weight: 3.9990 chunk 196 optimal weight: 2.9990 chunk 207 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 117 optimal weight: 0.0000 chunk 121 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 209 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.140398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.096540 restraints weight = 55826.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.096199 restraints weight = 43658.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.095568 restraints weight = 38284.243| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.5254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 18698 Z= 0.219 Angle : 0.662 8.620 25226 Z= 0.359 Chirality : 0.045 0.208 2826 Planarity : 0.004 0.045 3102 Dihedral : 5.117 78.470 2522 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.35 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.18), residues: 2298 helix: 1.17 (0.15), residues: 1216 sheet: -0.99 (0.40), residues: 157 loop : -0.85 (0.21), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 671 HIS 0.019 0.002 HIS F 81 PHE 0.036 0.002 PHE D 546 TYR 0.022 0.002 TYR C 523 ARG 0.005 0.001 ARG G 101 Details of bonding type rmsd hydrogen bonds : bond 0.05548 ( 975) hydrogen bonds : angle 4.92351 ( 2796) SS BOND : bond 0.00500 ( 12) SS BOND : angle 1.03203 ( 24) covalent geometry : bond 0.00478 (18686) covalent geometry : angle 0.66139 (25202) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 328 time to evaluate : 2.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 MET cc_start: 0.8222 (mtt) cc_final: 0.7792 (mmt) REVERT: A 471 LYS cc_start: 0.7770 (mtmt) cc_final: 0.7356 (tppt) REVERT: A 496 MET cc_start: 0.8442 (tpt) cc_final: 0.8168 (tpp) REVERT: A 527 MET cc_start: 0.8367 (ttp) cc_final: 0.8122 (ttt) REVERT: A 533 TYR cc_start: 0.8918 (t80) cc_final: 0.8707 (t80) REVERT: A 537 SER cc_start: 0.9700 (m) cc_final: 0.9255 (t) REVERT: A 642 GLN cc_start: 0.8865 (tp-100) cc_final: 0.8122 (tm-30) REVERT: A 702 TYR cc_start: 0.8122 (t80) cc_final: 0.7921 (t80) REVERT: B 486 GLU cc_start: 0.8350 (tt0) cc_final: 0.7991 (tp30) REVERT: B 503 MET cc_start: 0.8598 (ttm) cc_final: 0.8047 (mtt) REVERT: B 674 MET cc_start: 0.4977 (mtp) cc_final: 0.3571 (tmm) REVERT: C 537 SER cc_start: 0.9553 (m) cc_final: 0.9065 (t) REVERT: C 627 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8413 (mt-10) REVERT: C 642 GLN cc_start: 0.9242 (tp-100) cc_final: 0.8637 (tm-30) REVERT: C 670 MET cc_start: 0.9477 (mmp) cc_final: 0.9010 (mmm) REVERT: C 674 MET cc_start: 0.9355 (tpp) cc_final: 0.9126 (tpp) REVERT: C 726 ASN cc_start: 0.9067 (m-40) cc_final: 0.8840 (m-40) REVERT: D 408 MET cc_start: 0.6982 (tpt) cc_final: 0.6644 (tpt) REVERT: D 638 ASP cc_start: 0.7879 (m-30) cc_final: 0.7403 (m-30) REVERT: D 641 LYS cc_start: 0.9315 (pptt) cc_final: 0.9025 (mmtm) REVERT: D 659 PHE cc_start: 0.7298 (m-80) cc_final: 0.6909 (m-80) REVERT: D 670 MET cc_start: 0.8759 (mmp) cc_final: 0.8523 (mmm) REVERT: D 702 TYR cc_start: 0.8360 (t80) cc_final: 0.7178 (t80) REVERT: D 708 MET cc_start: 0.9270 (ptp) cc_final: 0.9026 (ptt) REVERT: D 767 TRP cc_start: 0.8349 (m-90) cc_final: 0.7570 (m-90) REVERT: E 8 GLN cc_start: 0.8876 (mp10) cc_final: 0.8483 (mp10) REVERT: E 181 PHE cc_start: 0.7551 (m-80) cc_final: 0.7290 (m-80) REVERT: F 22 LEU cc_start: 0.8661 (mt) cc_final: 0.8336 (mt) REVERT: F 190 GLU cc_start: 0.9013 (mm-30) cc_final: 0.8679 (mm-30) REVERT: F 205 LYS cc_start: 0.8905 (tttt) cc_final: 0.8385 (tptp) REVERT: G 81 HIS cc_start: 0.8275 (m90) cc_final: 0.8054 (m-70) REVERT: G 124 SER cc_start: 0.7087 (t) cc_final: 0.6793 (m) REVERT: G 177 TRP cc_start: 0.7417 (m100) cc_final: 0.7116 (m100) REVERT: G 190 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8728 (mm-30) REVERT: H 78 GLN cc_start: 0.7837 (mm-40) cc_final: 0.7423 (tp40) REVERT: H 177 TRP cc_start: 0.7701 (p90) cc_final: 0.7009 (p90) outliers start: 0 outliers final: 0 residues processed: 328 average time/residue: 0.2692 time to fit residues: 137.6206 Evaluate side-chains 263 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 10 optimal weight: 0.8980 chunk 41 optimal weight: 20.0000 chunk 214 optimal weight: 3.9990 chunk 79 optimal weight: 0.0870 chunk 61 optimal weight: 0.9990 chunk 221 optimal weight: 4.9990 chunk 147 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 158 optimal weight: 10.0000 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 ASN F 8 GLN G 8 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.143233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.096155 restraints weight = 54100.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.098528 restraints weight = 37654.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.100016 restraints weight = 29907.997| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.5546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 18698 Z= 0.131 Angle : 0.594 10.832 25226 Z= 0.312 Chirality : 0.042 0.217 2826 Planarity : 0.003 0.047 3102 Dihedral : 4.823 73.328 2522 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.87 % Favored : 95.91 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.18), residues: 2298 helix: 1.42 (0.15), residues: 1223 sheet: -1.01 (0.37), residues: 177 loop : -0.88 (0.21), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D 460 HIS 0.006 0.001 HIS C 412 PHE 0.020 0.001 PHE D 658 TYR 0.015 0.001 TYR B 673 ARG 0.005 0.000 ARG E 64 Details of bonding type rmsd hydrogen bonds : bond 0.04797 ( 975) hydrogen bonds : angle 4.57673 ( 2796) SS BOND : bond 0.00526 ( 12) SS BOND : angle 1.55240 ( 24) covalent geometry : bond 0.00278 (18686) covalent geometry : angle 0.59233 (25202) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 340 time to evaluate : 2.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 MET cc_start: 0.8156 (mtt) cc_final: 0.7735 (mmt) REVERT: A 471 LYS cc_start: 0.7785 (mtmt) cc_final: 0.7381 (tppt) REVERT: A 496 MET cc_start: 0.8382 (tpt) cc_final: 0.8090 (tpp) REVERT: A 533 TYR cc_start: 0.8776 (t80) cc_final: 0.8380 (t80) REVERT: A 537 SER cc_start: 0.9685 (m) cc_final: 0.9459 (t) REVERT: A 637 GLU cc_start: 0.9018 (pp20) cc_final: 0.8571 (mm-30) REVERT: A 642 GLN cc_start: 0.8805 (tp-100) cc_final: 0.8109 (tm-30) REVERT: A 721 MET cc_start: 0.6033 (pmm) cc_final: 0.5767 (pmm) REVERT: B 486 GLU cc_start: 0.8461 (tt0) cc_final: 0.8062 (tp30) REVERT: B 534 ILE cc_start: 0.9419 (mt) cc_final: 0.9015 (tp) REVERT: B 634 GLU cc_start: 0.7410 (tm-30) cc_final: 0.7175 (pp20) REVERT: B 670 MET cc_start: 0.8642 (mmp) cc_final: 0.8428 (mmm) REVERT: B 674 MET cc_start: 0.4868 (mtp) cc_final: 0.3394 (tmm) REVERT: C 537 SER cc_start: 0.9298 (m) cc_final: 0.8773 (t) REVERT: C 627 GLU cc_start: 0.8975 (mm-30) cc_final: 0.8458 (mt-10) REVERT: C 642 GLN cc_start: 0.9217 (tp-100) cc_final: 0.8710 (tm-30) REVERT: C 670 MET cc_start: 0.9407 (mmp) cc_final: 0.8942 (mmm) REVERT: C 674 MET cc_start: 0.9302 (tpp) cc_final: 0.9000 (tpp) REVERT: C 702 TYR cc_start: 0.8601 (t80) cc_final: 0.8230 (t80) REVERT: D 473 ASP cc_start: 0.8867 (t0) cc_final: 0.8655 (t70) REVERT: D 638 ASP cc_start: 0.7993 (m-30) cc_final: 0.7436 (m-30) REVERT: D 641 LYS cc_start: 0.9357 (pptt) cc_final: 0.9084 (mmtt) REVERT: D 658 PHE cc_start: 0.8022 (t80) cc_final: 0.7817 (t80) REVERT: D 702 TYR cc_start: 0.8345 (t80) cc_final: 0.7219 (t80) REVERT: D 708 MET cc_start: 0.9281 (ptp) cc_final: 0.9076 (ptt) REVERT: D 767 TRP cc_start: 0.8182 (m-90) cc_final: 0.7417 (m-90) REVERT: E 63 TRP cc_start: 0.6594 (m100) cc_final: 0.5910 (m100) REVERT: E 177 TRP cc_start: 0.7443 (p90) cc_final: 0.6834 (p90) REVERT: F 205 LYS cc_start: 0.8844 (tttt) cc_final: 0.8344 (tptp) REVERT: G 81 HIS cc_start: 0.8073 (m90) cc_final: 0.7830 (m-70) REVERT: G 116 MET cc_start: 0.3876 (tpp) cc_final: 0.3615 (tpp) REVERT: G 124 SER cc_start: 0.6868 (t) cc_final: 0.6567 (m) REVERT: G 152 ILE cc_start: 0.9205 (tp) cc_final: 0.8894 (mm) REVERT: G 177 TRP cc_start: 0.7279 (m100) cc_final: 0.7006 (m100) REVERT: G 190 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8658 (mm-30) REVERT: H 148 ASN cc_start: 0.9257 (m-40) cc_final: 0.9006 (m-40) REVERT: H 177 TRP cc_start: 0.7552 (p90) cc_final: 0.6810 (p90) outliers start: 0 outliers final: 0 residues processed: 340 average time/residue: 0.2778 time to fit residues: 146.2916 Evaluate side-chains 273 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 2.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 128 optimal weight: 0.0770 chunk 83 optimal weight: 0.0980 chunk 5 optimal weight: 10.0000 chunk 218 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 73 optimal weight: 8.9990 chunk 216 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 114 optimal weight: 8.9990 chunk 136 optimal weight: 0.7980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 586 GLN C 791 ASN E 148 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.144523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.097026 restraints weight = 54542.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.099646 restraints weight = 37076.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.101274 restraints weight = 28966.595| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.5724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 18698 Z= 0.115 Angle : 0.582 9.868 25226 Z= 0.304 Chirality : 0.042 0.178 2826 Planarity : 0.003 0.049 3102 Dihedral : 4.673 70.356 2522 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.87 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.18), residues: 2298 helix: 1.54 (0.15), residues: 1228 sheet: -0.87 (0.38), residues: 167 loop : -0.84 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP D 460 HIS 0.004 0.001 HIS B 435 PHE 0.025 0.001 PHE E 179 TYR 0.016 0.001 TYR A 702 ARG 0.014 0.000 ARG E 64 Details of bonding type rmsd hydrogen bonds : bond 0.04388 ( 975) hydrogen bonds : angle 4.42825 ( 2796) SS BOND : bond 0.00403 ( 12) SS BOND : angle 1.32572 ( 24) covalent geometry : bond 0.00241 (18686) covalent geometry : angle 0.58124 (25202) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 1.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 MET cc_start: 0.8154 (mtt) cc_final: 0.7737 (mmt) REVERT: A 471 LYS cc_start: 0.7798 (mtmt) cc_final: 0.7418 (tppt) REVERT: A 496 MET cc_start: 0.8393 (tpt) cc_final: 0.8158 (tpp) REVERT: A 533 TYR cc_start: 0.8716 (t80) cc_final: 0.8397 (t80) REVERT: A 537 SER cc_start: 0.9689 (m) cc_final: 0.9461 (t) REVERT: A 637 GLU cc_start: 0.8963 (pp20) cc_final: 0.8585 (mm-30) REVERT: A 642 GLN cc_start: 0.8832 (tp-100) cc_final: 0.8064 (tm-30) REVERT: A 702 TYR cc_start: 0.8248 (t80) cc_final: 0.7663 (t80) REVERT: A 721 MET cc_start: 0.6225 (pmm) cc_final: 0.5901 (pmm) REVERT: B 486 GLU cc_start: 0.8528 (tt0) cc_final: 0.8113 (tp30) REVERT: B 534 ILE cc_start: 0.9422 (mt) cc_final: 0.9005 (tp) REVERT: B 634 GLU cc_start: 0.7481 (tm-30) cc_final: 0.7221 (pp20) REVERT: B 674 MET cc_start: 0.4869 (mtp) cc_final: 0.3509 (tmm) REVERT: C 537 SER cc_start: 0.9252 (m) cc_final: 0.8701 (t) REVERT: C 627 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8386 (mt-10) REVERT: C 642 GLN cc_start: 0.9217 (tp-100) cc_final: 0.8745 (tm-30) REVERT: C 670 MET cc_start: 0.9387 (mmp) cc_final: 0.8951 (mmm) REVERT: C 674 MET cc_start: 0.9299 (tpp) cc_final: 0.9076 (tpp) REVERT: C 803 LEU cc_start: 0.9232 (mt) cc_final: 0.9002 (mm) REVERT: D 473 ASP cc_start: 0.8803 (t0) cc_final: 0.8598 (t70) REVERT: D 637 GLU cc_start: 0.8399 (pm20) cc_final: 0.7944 (pm20) REVERT: D 638 ASP cc_start: 0.7933 (m-30) cc_final: 0.7217 (m-30) REVERT: D 659 PHE cc_start: 0.7502 (m-80) cc_final: 0.7198 (m-80) REVERT: D 670 MET cc_start: 0.8716 (mmp) cc_final: 0.8501 (mmm) REVERT: D 702 TYR cc_start: 0.8341 (t80) cc_final: 0.7219 (t80) REVERT: D 767 TRP cc_start: 0.8197 (m-90) cc_final: 0.7396 (m-90) REVERT: E 116 MET cc_start: -0.1490 (mmm) cc_final: -0.1939 (mmm) REVERT: E 177 TRP cc_start: 0.7342 (p90) cc_final: 0.6681 (p90) REVERT: F 173 TYR cc_start: 0.7929 (p90) cc_final: 0.7670 (p90) REVERT: F 205 LYS cc_start: 0.8855 (tttt) cc_final: 0.8354 (tptp) REVERT: G 81 HIS cc_start: 0.8076 (m90) cc_final: 0.7828 (m-70) REVERT: G 124 SER cc_start: 0.6709 (t) cc_final: 0.6470 (m) REVERT: G 177 TRP cc_start: 0.7238 (m100) cc_final: 0.7010 (m100) REVERT: G 190 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8584 (mm-30) REVERT: H 148 ASN cc_start: 0.9245 (m-40) cc_final: 0.8989 (m-40) REVERT: H 177 TRP cc_start: 0.7501 (p90) cc_final: 0.6781 (p90) REVERT: H 205 LYS cc_start: 0.8845 (mttp) cc_final: 0.8527 (mmtm) outliers start: 0 outliers final: 0 residues processed: 336 average time/residue: 0.2695 time to fit residues: 142.0090 Evaluate side-chains 273 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 193 optimal weight: 1.9990 chunk 208 optimal weight: 0.5980 chunk 179 optimal weight: 2.9990 chunk 154 optimal weight: 0.0470 chunk 87 optimal weight: 0.0970 chunk 81 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 144 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 212 optimal weight: 0.6980 chunk 95 optimal weight: 0.2980 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 435 HIS B 756 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.145527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.101735 restraints weight = 53399.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.101756 restraints weight = 42990.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.101796 restraints weight = 33435.232| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.5941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 18698 Z= 0.109 Angle : 0.579 8.963 25226 Z= 0.299 Chirality : 0.042 0.177 2826 Planarity : 0.003 0.051 3102 Dihedral : 4.464 65.395 2522 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.52 % Favored : 96.21 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.18), residues: 2298 helix: 1.56 (0.15), residues: 1235 sheet: -0.86 (0.39), residues: 152 loop : -0.83 (0.21), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP H 177 HIS 0.010 0.001 HIS H 59 PHE 0.024 0.001 PHE E 179 TYR 0.012 0.001 TYR A 702 ARG 0.009 0.000 ARG E 64 Details of bonding type rmsd hydrogen bonds : bond 0.03956 ( 975) hydrogen bonds : angle 4.31132 ( 2796) SS BOND : bond 0.00355 ( 12) SS BOND : angle 1.07253 ( 24) covalent geometry : bond 0.00221 (18686) covalent geometry : angle 0.57834 (25202) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 2.225 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 463 MET cc_start: 0.8160 (mtt) cc_final: 0.7719 (mmt) REVERT: A 471 LYS cc_start: 0.7874 (mtmt) cc_final: 0.7498 (tppt) REVERT: A 496 MET cc_start: 0.8373 (tpt) cc_final: 0.8140 (tpp) REVERT: A 537 SER cc_start: 0.9658 (m) cc_final: 0.9368 (t) REVERT: A 637 GLU cc_start: 0.8913 (pp20) cc_final: 0.8670 (mm-30) REVERT: A 642 GLN cc_start: 0.8810 (tp-100) cc_final: 0.8400 (tm-30) REVERT: A 702 TYR cc_start: 0.8249 (t80) cc_final: 0.7561 (t80) REVERT: A 721 MET cc_start: 0.6333 (pmm) cc_final: 0.5990 (pmm) REVERT: A 734 ILE cc_start: 0.7452 (tp) cc_final: 0.7133 (tp) REVERT: B 408 MET cc_start: 0.7499 (tpt) cc_final: 0.7260 (tpt) REVERT: B 441 LYS cc_start: 0.6299 (mmmt) cc_final: 0.5974 (tptp) REVERT: B 463 MET cc_start: 0.5016 (mmm) cc_final: 0.4710 (mmt) REVERT: B 486 GLU cc_start: 0.8443 (tt0) cc_final: 0.8042 (tp30) REVERT: B 534 ILE cc_start: 0.9390 (mt) cc_final: 0.8989 (tp) REVERT: B 634 GLU cc_start: 0.7380 (tm-30) cc_final: 0.7133 (pp20) REVERT: B 674 MET cc_start: 0.4797 (mtp) cc_final: 0.3758 (tmm) REVERT: C 537 SER cc_start: 0.9213 (m) cc_final: 0.8666 (t) REVERT: C 619 ASN cc_start: 0.9396 (t0) cc_final: 0.9002 (t0) REVERT: C 627 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8271 (mt-10) REVERT: C 642 GLN cc_start: 0.9241 (tp-100) cc_final: 0.8399 (pp30) REVERT: C 670 MET cc_start: 0.9366 (mmp) cc_final: 0.8833 (mmm) REVERT: C 682 PHE cc_start: 0.7242 (m-10) cc_final: 0.6898 (m-80) REVERT: C 702 TYR cc_start: 0.8771 (t80) cc_final: 0.8323 (t80) REVERT: C 726 ASN cc_start: 0.9057 (m-40) cc_final: 0.8817 (m-40) REVERT: C 807 MET cc_start: 0.9016 (mmm) cc_final: 0.8364 (mmt) REVERT: D 659 PHE cc_start: 0.7573 (m-80) cc_final: 0.7283 (m-80) REVERT: D 670 MET cc_start: 0.8677 (mmp) cc_final: 0.8445 (mmm) REVERT: D 702 TYR cc_start: 0.8305 (t80) cc_final: 0.7162 (t80) REVERT: D 767 TRP cc_start: 0.8286 (m-90) cc_final: 0.7421 (m-90) REVERT: E 104 SER cc_start: 0.8827 (t) cc_final: 0.8589 (p) REVERT: E 116 MET cc_start: -0.0961 (mmm) cc_final: -0.1254 (mmm) REVERT: E 177 TRP cc_start: 0.7055 (p90) cc_final: 0.6597 (p90) REVERT: F 173 TYR cc_start: 0.8014 (p90) cc_final: 0.7801 (p90) REVERT: F 205 LYS cc_start: 0.8872 (tttt) cc_final: 0.8371 (tptp) REVERT: G 81 HIS cc_start: 0.8291 (m90) cc_final: 0.8007 (m-70) REVERT: G 97 LEU cc_start: 0.7813 (tt) cc_final: 0.7157 (mt) REVERT: G 177 TRP cc_start: 0.7204 (m100) cc_final: 0.6958 (m100) REVERT: G 190 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8593 (mm-30) REVERT: H 30 ASP cc_start: 0.7098 (p0) cc_final: 0.6851 (p0) REVERT: H 140 PHE cc_start: 0.8328 (m-80) cc_final: 0.7527 (m-80) REVERT: H 205 LYS cc_start: 0.8873 (mttp) cc_final: 0.8505 (mmmt) outliers start: 0 outliers final: 0 residues processed: 351 average time/residue: 0.2925 time to fit residues: 158.8205 Evaluate side-chains 272 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 2.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 84 optimal weight: 0.8980 chunk 208 optimal weight: 0.3980 chunk 217 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 216 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 171 optimal weight: 0.0970 chunk 121 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 756 GLN E 131 HIS ** F 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.143700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.100362 restraints weight = 55175.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.099354 restraints weight = 41247.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.098920 restraints weight = 38112.811| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.6150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 18698 Z= 0.134 Angle : 0.597 8.343 25226 Z= 0.313 Chirality : 0.042 0.181 2826 Planarity : 0.004 0.050 3102 Dihedral : 4.494 59.481 2522 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.87 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.18), residues: 2298 helix: 1.56 (0.15), residues: 1235 sheet: -1.08 (0.38), residues: 162 loop : -0.74 (0.21), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP H 177 HIS 0.007 0.001 HIS E 59 PHE 0.017 0.001 PHE E 179 TYR 0.024 0.001 TYR F 34 ARG 0.006 0.000 ARG E 64 Details of bonding type rmsd hydrogen bonds : bond 0.04269 ( 975) hydrogen bonds : angle 4.42626 ( 2796) SS BOND : bond 0.00413 ( 12) SS BOND : angle 1.01164 ( 24) covalent geometry : bond 0.00290 (18686) covalent geometry : angle 0.59606 (25202) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 333 time to evaluate : 1.952 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: A 463 MET cc_start: 0.8225 (mtt) cc_final: 0.7757 (mmt) REVERT: A 471 LYS cc_start: 0.7912 (mtmt) cc_final: 0.7617 (tppt) REVERT: A 496 MET cc_start: 0.8445 (tpt) cc_final: 0.8129 (tpp) REVERT: A 537 SER cc_start: 0.9632 (m) cc_final: 0.9346 (t) REVERT: A 585 MET cc_start: 0.8869 (mmm) cc_final: 0.8613 (mmt) REVERT: A 619 ASN cc_start: 0.9260 (t0) cc_final: 0.9042 (t0) REVERT: A 642 GLN cc_start: 0.8834 (tp-100) cc_final: 0.8321 (tm-30) REVERT: A 702 TYR cc_start: 0.8254 (t80) cc_final: 0.7557 (t80) REVERT: A 721 MET cc_start: 0.6682 (pmm) cc_final: 0.6301 (pmm) REVERT: A 734 ILE cc_start: 0.7429 (tp) cc_final: 0.7201 (tp) REVERT: B 408 MET cc_start: 0.7634 (tpt) cc_final: 0.7408 (tpt) REVERT: B 486 GLU cc_start: 0.8566 (tt0) cc_final: 0.8174 (tp30) REVERT: B 534 ILE cc_start: 0.9465 (mt) cc_final: 0.9060 (tp) REVERT: B 634 GLU cc_start: 0.7583 (tm-30) cc_final: 0.7246 (pp20) REVERT: B 674 MET cc_start: 0.5056 (mtp) cc_final: 0.3987 (tmm) REVERT: C 537 SER cc_start: 0.9402 (m) cc_final: 0.8876 (t) REVERT: C 619 ASN cc_start: 0.9377 (t0) cc_final: 0.8950 (t0) REVERT: C 627 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8413 (mt-10) REVERT: C 642 GLN cc_start: 0.9288 (tp-100) cc_final: 0.8314 (pp30) REVERT: C 670 MET cc_start: 0.9386 (mmp) cc_final: 0.8838 (mmm) REVERT: C 702 TYR cc_start: 0.8451 (t80) cc_final: 0.7683 (t80) REVERT: C 726 ASN cc_start: 0.9028 (m-40) cc_final: 0.8745 (m-40) REVERT: D 463 MET cc_start: 0.3937 (mmt) cc_final: 0.3658 (mmp) REVERT: D 503 MET cc_start: 0.7794 (ttp) cc_final: 0.7478 (ttp) REVERT: D 637 GLU cc_start: 0.8330 (pm20) cc_final: 0.7957 (pm20) REVERT: D 651 ASP cc_start: 0.7138 (t0) cc_final: 0.6709 (p0) REVERT: D 659 PHE cc_start: 0.7601 (m-80) cc_final: 0.7350 (m-80) REVERT: D 670 MET cc_start: 0.8784 (mmp) cc_final: 0.8527 (mmm) REVERT: D 702 TYR cc_start: 0.8119 (t80) cc_final: 0.7157 (t80) REVERT: D 704 LEU cc_start: 0.9307 (tp) cc_final: 0.9030 (tp) REVERT: D 767 TRP cc_start: 0.8288 (m-90) cc_final: 0.7414 (m-90) REVERT: E 116 MET cc_start: -0.1012 (mmm) cc_final: -0.1333 (mmm) REVERT: F 173 TYR cc_start: 0.7993 (p90) cc_final: 0.7743 (p90) REVERT: F 205 LYS cc_start: 0.8911 (tttt) cc_final: 0.8386 (tptp) REVERT: G 97 LEU cc_start: 0.7810 (tt) cc_final: 0.7187 (mt) REVERT: G 152 ILE cc_start: 0.9206 (tp) cc_final: 0.8871 (mm) REVERT: G 177 TRP cc_start: 0.7276 (m100) cc_final: 0.6924 (m100) REVERT: G 190 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8630 (mm-30) REVERT: H 140 PHE cc_start: 0.8384 (m-80) cc_final: 0.7941 (m-80) REVERT: H 205 LYS cc_start: 0.9025 (mttp) cc_final: 0.8620 (mmtp) outliers start: 0 outliers final: 0 residues processed: 333 average time/residue: 0.2754 time to fit residues: 143.9088 Evaluate side-chains 273 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 1.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 42 optimal weight: 0.7980 chunk 171 optimal weight: 0.0470 chunk 5 optimal weight: 9.9990 chunk 203 optimal weight: 7.9990 chunk 190 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 0.0870 chunk 85 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 198 optimal weight: 0.1980 chunk 113 optimal weight: 10.0000 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 756 GLN E 78 GLN E 81 HIS E 131 HIS F 81 HIS ** H 78 GLN ** 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 = 0.4129 r_free = 0.4129 target = 0.144106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.097585 restraints weight = 53614.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.100172 restraints weight = 36421.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.101667 restraints weight = 28333.460| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.6283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18698 Z= 0.121 Angle : 0.599 8.255 25226 Z= 0.313 Chirality : 0.042 0.190 2826 Planarity : 0.003 0.050 3102 Dihedral : 4.431 55.253 2522 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.57 % Favored : 96.17 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.18), residues: 2298 helix: 1.59 (0.15), residues: 1228 sheet: -1.02 (0.38), residues: 162 loop : -0.75 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 671 HIS 0.011 0.001 HIS E 59 PHE 0.025 0.001 PHE H 181 TYR 0.015 0.001 TYR D 816 ARG 0.003 0.000 ARG B 660 Details of bonding type rmsd hydrogen bonds : bond 0.04205 ( 975) hydrogen bonds : angle 4.39764 ( 2796) SS BOND : bond 0.00391 ( 12) SS BOND : angle 0.92029 ( 24) covalent geometry : bond 0.00258 (18686) covalent geometry : angle 0.59878 (25202) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 323 time to evaluate : 2.156 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: A 411 ASN cc_start: 0.8227 (m110) cc_final: 0.8008 (m110) REVERT: A 463 MET cc_start: 0.7988 (mtt) cc_final: 0.7534 (mmt) REVERT: A 471 LYS cc_start: 0.7753 (mtmt) cc_final: 0.7527 (tppt) REVERT: A 537 SER cc_start: 0.9594 (m) cc_final: 0.9361 (t) REVERT: A 585 MET cc_start: 0.8895 (mmm) cc_final: 0.8648 (mmt) REVERT: A 642 GLN cc_start: 0.8811 (tp-100) cc_final: 0.8381 (tm-30) REVERT: A 702 TYR cc_start: 0.8277 (t80) cc_final: 0.7553 (t80) REVERT: A 734 ILE cc_start: 0.7250 (tp) cc_final: 0.6980 (tp) REVERT: B 408 MET cc_start: 0.7789 (tpt) cc_final: 0.7576 (tpt) REVERT: B 486 GLU cc_start: 0.8534 (tt0) cc_final: 0.8066 (tp30) REVERT: B 534 ILE cc_start: 0.9424 (mt) cc_final: 0.9029 (tp) REVERT: B 634 GLU cc_start: 0.7426 (tm-30) cc_final: 0.7107 (pp20) REVERT: B 671 TRP cc_start: 0.5955 (t-100) cc_final: 0.5669 (t-100) REVERT: B 674 MET cc_start: 0.4948 (mtp) cc_final: 0.3857 (tmm) REVERT: C 537 SER cc_start: 0.9328 (m) cc_final: 0.8888 (t) REVERT: C 619 ASN cc_start: 0.9362 (t0) cc_final: 0.8954 (t0) REVERT: C 627 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8316 (mt-10) REVERT: C 642 GLN cc_start: 0.9249 (tp-100) cc_final: 0.8397 (pp30) REVERT: C 670 MET cc_start: 0.9379 (mmp) cc_final: 0.9149 (mmm) REVERT: C 726 ASN cc_start: 0.9013 (m-40) cc_final: 0.8740 (m-40) REVERT: D 651 ASP cc_start: 0.7033 (t0) cc_final: 0.6648 (p0) REVERT: D 670 MET cc_start: 0.8733 (mmp) cc_final: 0.8486 (mmm) REVERT: D 702 TYR cc_start: 0.8066 (t80) cc_final: 0.7104 (t80) REVERT: D 704 LEU cc_start: 0.9237 (tp) cc_final: 0.8921 (tt) REVERT: D 767 TRP cc_start: 0.8194 (m-90) cc_final: 0.7304 (m-90) REVERT: E 69 GLU cc_start: 0.7397 (tm-30) cc_final: 0.7165 (tm-30) REVERT: E 104 SER cc_start: 0.8849 (t) cc_final: 0.8608 (p) REVERT: F 173 TYR cc_start: 0.7924 (p90) cc_final: 0.7655 (p90) REVERT: F 205 LYS cc_start: 0.8799 (tttt) cc_final: 0.8305 (tptp) REVERT: G 97 LEU cc_start: 0.7899 (tt) cc_final: 0.7222 (mt) REVERT: G 116 MET cc_start: 0.3873 (tpt) cc_final: 0.3628 (tpt) REVERT: G 177 TRP cc_start: 0.7232 (m100) cc_final: 0.6900 (m100) REVERT: G 190 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8629 (mm-30) REVERT: H 140 PHE cc_start: 0.8413 (m-80) cc_final: 0.7737 (m-80) REVERT: H 205 LYS cc_start: 0.9009 (mttp) cc_final: 0.8606 (mmtp) outliers start: 0 outliers final: 0 residues processed: 323 average time/residue: 0.3033 time to fit residues: 156.1243 Evaluate side-chains 272 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 2.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 66 optimal weight: 0.6980 chunk 151 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 95 optimal weight: 0.5980 chunk 172 optimal weight: 3.9990 chunk 186 optimal weight: 5.9990 chunk 174 optimal weight: 5.9990 chunk 164 optimal weight: 0.3980 chunk 53 optimal weight: 0.5980 chunk 18 optimal weight: 0.0570 chunk 36 optimal weight: 1.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 756 GLN E 131 HIS F 81 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.144893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.100081 restraints weight = 53591.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.102013 restraints weight = 38453.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.102666 restraints weight = 28203.725| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.6440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 18698 Z= 0.115 Angle : 0.593 10.094 25226 Z= 0.309 Chirality : 0.042 0.202 2826 Planarity : 0.003 0.051 3102 Dihedral : 4.306 49.732 2522 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.74 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.18), residues: 2298 helix: 1.62 (0.15), residues: 1228 sheet: -0.93 (0.39), residues: 162 loop : -0.78 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 671 HIS 0.006 0.001 HIS B 435 PHE 0.013 0.001 PHE E 179 TYR 0.016 0.001 TYR H 31 ARG 0.003 0.000 ARG D 420 Details of bonding type rmsd hydrogen bonds : bond 0.04024 ( 975) hydrogen bonds : angle 4.33529 ( 2796) SS BOND : bond 0.00312 ( 12) SS BOND : angle 0.82647 ( 24) covalent geometry : bond 0.00239 (18686) covalent geometry : angle 0.59284 (25202) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6483.14 seconds wall clock time: 114 minutes 36.07 seconds (6876.07 seconds total)