Starting phenix.real_space_refine on Mon May 19 10:57:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mrm_48559/05_2025/9mrm_48559.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mrm_48559/05_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_48559/05_2025/9mrm_48559.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mrm_48559/05_2025/9mrm_48559.map" model { file = "/net/cci-nas-00/data/ceres_data/9mrm_48559/05_2025/9mrm_48559.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mrm_48559/05_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-5687/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: 11.37, per 1000 atoms: 0.62 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: 4.38 Conformation dependent library (CDL) restraints added in 2.2 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: 1.93 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: 5.86 Time building geometry restraints manager: 5.13 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: 5.710 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: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 40.670 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.080 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.160 ------------------------------------------------------------------------------- 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 : 1.902 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: 0.2949 time to fit residues: 275.2856 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 : 2.209 ------------------------------------------------------------------------------- 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 = 0.4188 r_free = 0.4188 target = 0.148176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.104769 restraints weight = 54647.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.104992 restraints weight = 43587.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.104787 restraints weight = 35274.666| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.3245 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= 0.143 Angle : 0.634 7.971 25226 Z= 0.338 Chirality : 0.044 0.261 2826 Planarity : 0.005 0.130 3102 Dihedral : 5.222 74.622 2522 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.81 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: 0.62 (0.18), residues: 2298 helix: 1.51 (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 0.009 0.001 ARG E 36 Details of bonding type rmsd hydrogen bonds : bond 0.05106 ( 975) hydrogen bonds : angle 4.86289 ( 2796) SS BOND : bond 0.00297 ( 12) SS BOND : angle 0.65552 ( 24) covalent geometry : bond 0.00300 (18686) covalent geometry : angle 0.63368 (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 : 2.013 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 424 TYR cc_start: 0.8541 (t80) cc_final: 0.7893 (t80) REVERT: A 496 MET cc_start: 0.8530 (tpt) cc_final: 0.8302 (tpp) REVERT: A 517 PHE cc_start: 0.8649 (p90) cc_final: 0.8417 (p90) REVERT: A 527 MET cc_start: 0.8062 (ttp) cc_final: 0.7657 (ttt) REVERT: A 609 THR cc_start: 0.9003 (t) cc_final: 0.8778 (t) REVERT: A 625 THR cc_start: 0.9456 (m) cc_final: 0.9141 (p) REVERT: A 642 GLN cc_start: 0.8660 (tp-100) cc_final: 0.7917 (tm-30) REVERT: A 645 ILE cc_start: 0.7007 (mm) cc_final: 0.6750 (mm) REVERT: A 657 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8568 (mp0) REVERT: A 721 MET cc_start: 0.5505 (pmm) cc_final: 0.4935 (pmm) REVERT: B 486 GLU cc_start: 0.8585 (tt0) cc_final: 0.8064 (tp30) REVERT: B 527 MET cc_start: 0.8823 (mtm) cc_final: 0.8228 (mtp) REVERT: B 674 MET cc_start: 0.4021 (mtp) cc_final: 0.3349 (ttm) REVERT: B 729 SER cc_start: 0.7434 (p) cc_final: 0.6447 (p) REVERT: B 730 LYS cc_start: 0.8825 (mmpt) cc_final: 0.8559 (tppt) REVERT: C 398 THR cc_start: 0.8158 (p) cc_final: 0.7888 (p) REVERT: C 508 GLN cc_start: 0.7082 (pp30) cc_final: 0.6694 (mm-40) REVERT: C 537 SER cc_start: 0.9341 (m) cc_final: 0.8806 (t) REVERT: C 625 THR cc_start: 0.9469 (m) cc_final: 0.9184 (p) REVERT: C 627 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8507 (mt-10) REVERT: C 642 GLN cc_start: 0.9399 (tp-100) cc_final: 0.8919 (tm-30) REVERT: C 668 ASP cc_start: 0.9338 (t0) cc_final: 0.9041 (m-30) REVERT: C 670 MET cc_start: 0.9423 (mmp) cc_final: 0.9017 (mmm) REVERT: C 702 TYR cc_start: 0.8295 (t80) cc_final: 0.7928 (t80) REVERT: D 585 MET cc_start: 0.8760 (tpp) cc_final: 0.8521 (tpp) REVERT: D 638 ASP cc_start: 0.8142 (m-30) cc_final: 0.7705 (m-30) REVERT: D 641 LYS cc_start: 0.9155 (pptt) cc_final: 0.8907 (mmtm) REVERT: D 670 MET cc_start: 0.8576 (mmp) cc_final: 0.8186 (mmm) REVERT: D 767 TRP cc_start: 0.8084 (m-90) cc_final: 0.7286 (m-90) REVERT: E 8 GLN cc_start: 0.8152 (mp10) cc_final: 0.7888 (mp10) REVERT: E 181 PHE cc_start: 0.7191 (m-80) cc_final: 0.6822 (m-80) REVERT: F 9 MET cc_start: 0.7522 (mtm) cc_final: 0.6984 (tmm) REVERT: F 58 THR cc_start: 0.7263 (m) cc_final: 0.7035 (p) REVERT: F 173 TYR cc_start: 0.8108 (p90) cc_final: 0.7818 (p90) REVERT: F 205 LYS cc_start: 0.8858 (tttt) cc_final: 0.8394 (tptt) REVERT: G 23 MET cc_start: 0.8627 (tpt) cc_final: 0.8248 (tpt) REVERT: G 97 LEU cc_start: 0.7501 (tt) cc_final: 0.6854 (mt) REVERT: G 124 SER cc_start: 0.7014 (t) cc_final: 0.6630 (m) REVERT: G 175 TYR cc_start: 0.8962 (m-80) cc_final: 0.8717 (m-80) REVERT: G 199 MET cc_start: 0.9100 (ptp) cc_final: 0.8843 (ptp) REVERT: H 63 TRP cc_start: 0.7027 (m100) cc_final: 0.6655 (m100) REVERT: H 190 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8736 (mm-30) outliers start: 3 outliers final: 0 residues processed: 411 average time/residue: 0.2870 time to fit residues: 179.1410 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 : 1.922 ------------------------------------------------------------------------------- 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: 0.0770 chunk 86 optimal weight: 7.9990 chunk 164 optimal weight: 0.8980 chunk 180 optimal weight: 4.9990 chunk 223 optimal weight: 4.9990 chunk 152 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 37 optimal weight: 0.0000 chunk 187 optimal weight: 6.9990 overall best weight: 0.7946 ------------------------------------------------------------------------------- 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 = 0.4175 r_free = 0.4175 target = 0.147636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.104438 restraints weight = 55987.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.103392 restraints weight = 47368.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.103199 restraints weight = 41456.286| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18698 Z= 0.134 Angle : 0.575 8.033 25226 Z= 0.308 Chirality : 0.042 0.224 2826 Planarity : 0.004 0.047 3102 Dihedral : 4.986 83.504 2522 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.48 % Favored : 96.30 % Rotamer: Outliers : 0.05 % Allowed : 2.40 % Favored : 97.54 % 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: 0.79 (0.18), residues: 2298 helix: 1.66 (0.15), residues: 1211 sheet: -0.82 (0.40), residues: 157 loop : -0.73 (0.21), residues: 930 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 0.022 0.001 PHE G 181 TYR 0.021 0.001 TYR B 450 ARG 0.007 0.000 ARG B 545 Details of bonding type rmsd hydrogen bonds : bond 0.04737 ( 975) hydrogen bonds : angle 4.65262 ( 2796) SS BOND : bond 0.00255 ( 12) SS BOND : angle 0.63917 ( 24) covalent geometry : bond 0.00286 (18686) covalent geometry : angle 0.57532 (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 366 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 365 time to evaluate : 2.095 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: 0.8883 (p90) cc_final: 0.8455 (p90) REVERT: A 527 MET cc_start: 0.8229 (ttp) cc_final: 0.7846 (ttt) REVERT: A 642 GLN cc_start: 0.8816 (tp-100) cc_final: 0.7978 (tm-30) REVERT: A 657 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8570 (mp0) REVERT: A 702 TYR cc_start: 0.8061 (t80) cc_final: 0.7806 (t80) REVERT: A 721 MET cc_start: 0.5365 (pmm) cc_final: 0.4653 (pmm) REVERT: B 503 MET cc_start: 0.8109 (ttm) cc_final: 0.7815 (ttm) REVERT: B 670 MET cc_start: 0.8415 (mmp) cc_final: 0.8215 (mmm) REVERT: C 508 GLN cc_start: 0.7149 (pp30) cc_final: 0.6821 (mm-40) REVERT: C 537 SER cc_start: 0.9371 (m) cc_final: 0.8811 (t) REVERT: C 619 ASN cc_start: 0.9282 (t0) cc_final: 0.8998 (t0) REVERT: C 625 THR cc_start: 0.9450 (m) cc_final: 0.9144 (p) REVERT: C 627 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8526 (mt-10) REVERT: C 642 GLN cc_start: 0.9379 (tp-100) cc_final: 0.9144 (tp-100) REVERT: C 668 ASP cc_start: 0.9312 (t0) cc_final: 0.9064 (m-30) REVERT: C 670 MET cc_start: 0.9417 (mmp) cc_final: 0.8935 (mmm) REVERT: C 702 TYR cc_start: 0.8019 (t80) cc_final: 0.7504 (t80) REVERT: D 546 PHE cc_start: 0.6597 (t80) cc_final: 0.6144 (t80) REVERT: D 638 ASP cc_start: 0.8046 (m-30) cc_final: 0.7556 (m-30) REVERT: D 641 LYS cc_start: 0.9139 (pptt) cc_final: 0.8870 (mmtm) REVERT: D 659 PHE cc_start: 0.7468 (m-80) cc_final: 0.7148 (m-80) REVERT: D 670 MET cc_start: 0.8520 (mmp) cc_final: 0.8298 (mmm) REVERT: D 767 TRP cc_start: 0.8189 (m-90) cc_final: 0.7422 (m-90) REVERT: E 8 GLN cc_start: 0.8259 (mp10) cc_final: 0.7933 (mp10) REVERT: E 30 ASP cc_start: 0.7456 (p0) cc_final: 0.7240 (p0) REVERT: F 9 MET cc_start: 0.7353 (mtm) cc_final: 0.6931 (tmm) REVERT: F 81 HIS cc_start: 0.8303 (m90) cc_final: 0.7967 (m-70) REVERT: F 205 LYS cc_start: 0.8940 (tttt) cc_final: 0.8407 (tptp) REVERT: G 97 LEU cc_start: 0.7555 (tt) cc_final: 0.6846 (mt) REVERT: G 103 SER cc_start: 0.9167 (t) cc_final: 0.8869 (p) REVERT: G 124 SER cc_start: 0.6976 (t) cc_final: 0.6660 (m) REVERT: G 173 TYR cc_start: 0.7421 (p90) cc_final: 0.7200 (p90) REVERT: H 63 TRP cc_start: 0.7056 (m100) cc_final: 0.6786 (m100) REVERT: H 181 PHE cc_start: 0.7256 (m-80) cc_final: 0.6894 (m-80) outliers start: 1 outliers final: 0 residues processed: 366 average time/residue: 0.2761 time to fit residues: 156.3239 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 : 2.012 ------------------------------------------------------------------------------- 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: 9.9990 chunk 99 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 117 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 227 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.4140 r_free = 0.4140 target = 0.145131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.100328 restraints weight = 54577.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.101179 restraints weight = 42125.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.101115 restraints weight = 33509.045| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18698 Z= 0.151 Angle : 0.585 7.919 25226 Z= 0.313 Chirality : 0.042 0.178 2826 Planarity : 0.004 0.046 3102 Dihedral : 4.902 83.480 2522 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.83 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % 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: 0.78 (0.18), residues: 2298 helix: 1.63 (0.15), residues: 1215 sheet: -0.87 (0.39), residues: 157 loop : -0.71 (0.21), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 671 HIS 0.007 0.001 HIS B 435 PHE 0.022 0.002 PHE C 659 TYR 0.017 0.001 TYR C 533 ARG 0.005 0.000 ARG B 545 Details of bonding type rmsd hydrogen bonds : bond 0.04794 ( 975) hydrogen bonds : angle 4.63231 ( 2796) SS BOND : bond 0.00254 ( 12) SS BOND : angle 0.91841 ( 24) covalent geometry : bond 0.00324 (18686) covalent geometry : angle 0.58460 (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 340 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 340 time to evaluate : 2.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 ASP cc_start: 0.9187 (m-30) cc_final: 0.8982 (m-30) REVERT: A 431 GLU cc_start: 0.8744 (pt0) cc_final: 0.8494 (pm20) REVERT: A 463 MET cc_start: 0.8239 (mtt) cc_final: 0.7876 (mmt) REVERT: A 471 LYS cc_start: 0.7656 (mtmt) cc_final: 0.7272 (tppt) REVERT: A 496 MET cc_start: 0.8431 (tpt) cc_final: 0.8174 (tpp) REVERT: A 527 MET cc_start: 0.8323 (ttp) cc_final: 0.8068 (ttt) REVERT: A 642 GLN cc_start: 0.8892 (tp-100) cc_final: 0.7966 (tm-30) REVERT: A 657 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8600 (mp0) REVERT: A 721 MET cc_start: 0.5792 (pmm) cc_final: 0.5013 (pmm) REVERT: B 503 MET cc_start: 0.8124 (ttm) cc_final: 0.7912 (ttm) REVERT: B 674 MET cc_start: 0.4283 (mtp) cc_final: 0.3007 (tmm) REVERT: B 729 SER cc_start: 0.7343 (p) cc_final: 0.6359 (p) REVERT: B 730 LYS cc_start: 0.8889 (mmpt) cc_final: 0.8513 (tppt) REVERT: C 508 GLN cc_start: 0.7143 (pp30) cc_final: 0.6923 (mm-40) REVERT: C 537 SER cc_start: 0.9480 (m) cc_final: 0.8937 (t) REVERT: C 619 ASN cc_start: 0.9239 (t0) cc_final: 0.8938 (t0) REVERT: C 625 THR cc_start: 0.9389 (m) cc_final: 0.9102 (p) REVERT: C 627 GLU cc_start: 0.9027 (mm-30) cc_final: 0.8533 (mt-10) REVERT: C 642 GLN cc_start: 0.9332 (tp-100) cc_final: 0.7978 (pp30) REVERT: C 668 ASP cc_start: 0.9360 (t0) cc_final: 0.9093 (m-30) REVERT: C 670 MET cc_start: 0.9489 (mmp) cc_final: 0.9010 (mmm) REVERT: C 702 TYR cc_start: 0.8228 (t80) cc_final: 0.7688 (t80) REVERT: C 726 ASN cc_start: 0.9033 (m-40) cc_final: 0.8774 (m-40) REVERT: C 748 LEU cc_start: 0.9474 (mt) cc_final: 0.9267 (pp) REVERT: D 659 PHE cc_start: 0.7607 (m-80) cc_final: 0.7237 (m-80) REVERT: D 670 MET cc_start: 0.8627 (mmp) cc_final: 0.8398 (mmm) REVERT: D 674 MET cc_start: 0.6520 (mtm) cc_final: 0.6296 (mtt) REVERT: D 767 TRP cc_start: 0.8282 (m-90) cc_final: 0.7489 (m-90) REVERT: E 8 GLN cc_start: 0.8618 (mp10) cc_final: 0.8263 (mp10) REVERT: E 177 TRP cc_start: 0.7487 (p90) cc_final: 0.6626 (p90) REVERT: F 81 HIS cc_start: 0.8430 (m90) cc_final: 0.8117 (m-70) REVERT: F 190 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8881 (mm-30) REVERT: F 205 LYS cc_start: 0.8897 (tttt) cc_final: 0.8393 (tptp) REVERT: G 124 SER cc_start: 0.7090 (t) cc_final: 0.6691 (m) REVERT: H 177 TRP cc_start: 0.7681 (p90) cc_final: 0.6873 (p90) outliers start: 0 outliers final: 0 residues processed: 340 average time/residue: 0.2740 time to fit residues: 143.4644 Evaluate side-chains 259 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 1.822 ------------------------------------------------------------------------------- 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: 10.0000 chunk 142 optimal weight: 0.1980 chunk 161 optimal weight: 2.9990 chunk 196 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 117 optimal weight: 0.1980 chunk 121 optimal weight: 0.8980 chunk 42 optimal weight: 9.9990 chunk 209 optimal weight: 1.9990 chunk 38 optimal weight: 0.0050 overall best weight: 0.4596 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.147143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.101811 restraints weight = 54784.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.103962 restraints weight = 38045.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.104675 restraints weight = 27854.753| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 18698 Z= 0.114 Angle : 0.559 8.737 25226 Z= 0.294 Chirality : 0.041 0.195 2826 Planarity : 0.003 0.049 3102 Dihedral : 4.663 85.465 2522 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.26 % Favored : 96.48 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % 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: 0.81 (0.18), residues: 2298 helix: 1.75 (0.15), residues: 1220 sheet: -0.94 (0.37), residues: 167 loop : -0.82 (0.21), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 671 HIS 0.004 0.001 HIS B 435 PHE 0.016 0.001 PHE E 186 TYR 0.014 0.001 TYR A 702 ARG 0.005 0.000 ARG B 545 Details of bonding type rmsd hydrogen bonds : bond 0.04195 ( 975) hydrogen bonds : angle 4.38169 ( 2796) SS BOND : bond 0.00260 ( 12) SS BOND : angle 0.83017 ( 24) covalent geometry : bond 0.00238 (18686) covalent geometry : angle 0.55875 (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 352 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 2.037 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: 0.8285 (mtt) cc_final: 0.7942 (mmt) REVERT: A 471 LYS cc_start: 0.7787 (mtmt) cc_final: 0.7381 (tppt) REVERT: A 496 MET cc_start: 0.8334 (tpt) cc_final: 0.8074 (tpp) REVERT: A 642 GLN cc_start: 0.8816 (tp-100) cc_final: 0.7757 (pp30) REVERT: A 702 TYR cc_start: 0.8135 (t80) cc_final: 0.7823 (t80) REVERT: A 721 MET cc_start: 0.5697 (pmm) cc_final: 0.5175 (pmm) REVERT: B 503 MET cc_start: 0.7986 (ttm) cc_final: 0.7774 (ttm) REVERT: B 674 MET cc_start: 0.4443 (mtp) cc_final: 0.3284 (tmm) REVERT: B 729 SER cc_start: 0.7169 (p) cc_final: 0.6274 (p) REVERT: B 730 LYS cc_start: 0.8941 (mmpt) cc_final: 0.8574 (tppt) REVERT: C 537 SER cc_start: 0.9314 (m) cc_final: 0.8876 (t) REVERT: C 619 ASN cc_start: 0.9216 (t0) cc_final: 0.8901 (t0) REVERT: C 627 GLU cc_start: 0.8960 (mm-30) cc_final: 0.8431 (mt-10) REVERT: C 642 GLN cc_start: 0.9340 (tp-100) cc_final: 0.8408 (pp30) REVERT: C 668 ASP cc_start: 0.9303 (t0) cc_final: 0.9054 (m-30) REVERT: C 670 MET cc_start: 0.9462 (mmp) cc_final: 0.8994 (mmm) REVERT: C 702 TYR cc_start: 0.8309 (t80) cc_final: 0.8042 (t80) REVERT: C 726 ASN cc_start: 0.9020 (m-40) cc_final: 0.8771 (m-40) REVERT: D 659 PHE cc_start: 0.7548 (m-80) cc_final: 0.7267 (m-80) REVERT: D 670 MET cc_start: 0.8585 (mmp) cc_final: 0.8349 (mmm) REVERT: D 767 TRP cc_start: 0.8214 (m-90) cc_final: 0.7412 (m-90) REVERT: E 8 GLN cc_start: 0.8645 (mp10) cc_final: 0.8330 (mp10) REVERT: E 64 ARG cc_start: 0.6247 (ptm-80) cc_final: 0.3699 (ptp-170) REVERT: E 177 TRP cc_start: 0.7422 (p90) cc_final: 0.6430 (p90) REVERT: E 199 MET cc_start: 0.9030 (ppp) cc_final: 0.8653 (ppp) REVERT: F 205 LYS cc_start: 0.8856 (tttt) cc_final: 0.8360 (tptp) REVERT: H 63 TRP cc_start: 0.6412 (m100) cc_final: 0.6020 (m100) REVERT: H 177 TRP cc_start: 0.7619 (p90) cc_final: 0.6796 (p90) outliers start: 0 outliers final: 0 residues processed: 352 average time/residue: 0.2728 time to fit residues: 148.0916 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 : 1.875 ------------------------------------------------------------------------------- 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: 0.9980 chunk 41 optimal weight: 30.0000 chunk 214 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 221 optimal weight: 7.9990 chunk 147 optimal weight: 20.0000 chunk 77 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 100 optimal weight: 0.5980 chunk 158 optimal weight: 8.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.4120 r_free = 0.4120 target = 0.143566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.099348 restraints weight = 54426.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.098909 restraints weight = 41580.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.099127 restraints weight = 36459.652| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.5147 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= 0.164 Angle : 0.604 8.175 25226 Z= 0.321 Chirality : 0.043 0.205 2826 Planarity : 0.004 0.049 3102 Dihedral : 4.811 87.098 2522 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.13 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % 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: 1.46 (0.15), residues: 1224 sheet: -0.95 (0.37), residues: 182 loop : -0.75 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 671 HIS 0.007 0.001 HIS B 435 PHE 0.031 0.002 PHE E 179 TYR 0.016 0.001 TYR C 523 ARG 0.004 0.000 ARG D 545 Details of bonding type rmsd hydrogen bonds : bond 0.04821 ( 975) hydrogen bonds : angle 4.60603 ( 2796) SS BOND : bond 0.00473 ( 12) SS BOND : angle 0.86568 ( 24) covalent geometry : bond 0.00355 (18686) covalent geometry : angle 0.60356 (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 329 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 329 time to evaluate : 2.021 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 463 MET cc_start: 0.8180 (mtt) cc_final: 0.7813 (mmt) REVERT: A 471 LYS cc_start: 0.7766 (mtmt) cc_final: 0.7348 (tppt) REVERT: A 496 MET cc_start: 0.8275 (tpt) cc_final: 0.8031 (tpp) REVERT: A 642 GLN cc_start: 0.8746 (tp-100) cc_final: 0.8347 (tm-30) REVERT: B 674 MET cc_start: 0.4657 (mtp) cc_final: 0.3525 (tmm) REVERT: B 729 SER cc_start: 0.7176 (p) cc_final: 0.6218 (p) REVERT: B 730 LYS cc_start: 0.8903 (mmpt) cc_final: 0.8594 (tppp) REVERT: C 537 SER cc_start: 0.9478 (m) cc_final: 0.9053 (t) REVERT: C 627 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8418 (mt-10) REVERT: C 642 GLN cc_start: 0.9303 (tp-100) cc_final: 0.8394 (pp30) REVERT: C 670 MET cc_start: 0.9436 (mmp) cc_final: 0.8848 (mmm) REVERT: C 674 MET cc_start: 0.9327 (tpp) cc_final: 0.9098 (tpp) REVERT: C 702 TYR cc_start: 0.8280 (t80) cc_final: 0.8009 (t80) REVERT: D 408 MET cc_start: 0.6688 (tpt) cc_final: 0.6372 (tpt) REVERT: D 670 MET cc_start: 0.8615 (mmp) cc_final: 0.8293 (mmt) REVERT: D 767 TRP cc_start: 0.8302 (m-90) cc_final: 0.7457 (m-90) REVERT: E 64 ARG cc_start: 0.6599 (ptm-80) cc_final: 0.3765 (ptp-170) REVERT: E 177 TRP cc_start: 0.7474 (p90) cc_final: 0.6883 (p90) REVERT: E 199 MET cc_start: 0.9045 (ppp) cc_final: 0.8707 (ppp) REVERT: F 62 LEU cc_start: 0.8620 (mt) cc_final: 0.8376 (mt) REVERT: F 190 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8556 (mm-30) REVERT: F 205 LYS cc_start: 0.8875 (tttt) cc_final: 0.8375 (tptp) REVERT: G 116 MET cc_start: 0.3638 (ttt) cc_final: 0.3417 (ttt) REVERT: G 190 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8605 (mm-30) REVERT: H 177 TRP cc_start: 0.7690 (p90) cc_final: 0.7036 (p90) outliers start: 0 outliers final: 0 residues processed: 329 average time/residue: 0.2691 time to fit residues: 138.6421 Evaluate side-chains 262 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 2.029 ------------------------------------------------------------------------------- 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: 4.9990 chunk 83 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 218 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 216 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 chunk 136 optimal weight: 0.8980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 78 GLN E 148 ASN ** 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 = 0.4105 r_free = 0.4105 target = 0.142197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.097403 restraints weight = 54137.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.097993 restraints weight = 42372.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.097857 restraints weight = 32988.042| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.5606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 18698 Z= 0.165 Angle : 0.605 13.156 25226 Z= 0.320 Chirality : 0.043 0.216 2826 Planarity : 0.004 0.044 3102 Dihedral : 4.726 73.490 2522 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.26 % Favored : 95.52 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % 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: 0.54 (0.18), residues: 2298 helix: 1.46 (0.15), residues: 1218 sheet: -1.11 (0.37), residues: 172 loop : -0.83 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 671 HIS 0.007 0.001 HIS F 81 PHE 0.018 0.002 PHE E 179 TYR 0.022 0.001 TYR F 34 ARG 0.004 0.000 ARG D 545 Details of bonding type rmsd hydrogen bonds : bond 0.04793 ( 975) hydrogen bonds : angle 4.59826 ( 2796) SS BOND : bond 0.00290 ( 12) SS BOND : angle 0.76083 ( 24) covalent geometry : bond 0.00353 (18686) covalent geometry : angle 0.60518 (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 322 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 1.867 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 463 MET cc_start: 0.8222 (mtt) cc_final: 0.7817 (mmt) REVERT: A 471 LYS cc_start: 0.7845 (mtmt) cc_final: 0.7419 (tppt) REVERT: A 496 MET cc_start: 0.8429 (tpt) cc_final: 0.8169 (tpp) REVERT: A 637 GLU cc_start: 0.9008 (pp20) cc_final: 0.8623 (mm-30) REVERT: A 642 GLN cc_start: 0.8805 (tp-100) cc_final: 0.7765 (tm-30) REVERT: A 645 ILE cc_start: 0.7123 (mm) cc_final: 0.6781 (mm) REVERT: A 702 TYR cc_start: 0.8282 (t80) cc_final: 0.7765 (t80) REVERT: A 721 MET cc_start: 0.6174 (pmm) cc_final: 0.5889 (pmm) REVERT: B 674 MET cc_start: 0.4776 (mtp) cc_final: 0.3349 (tmm) REVERT: C 537 SER cc_start: 0.9434 (m) cc_final: 0.8892 (t) REVERT: C 585 MET cc_start: 0.8852 (mmm) cc_final: 0.8609 (mmm) REVERT: C 627 GLU cc_start: 0.9004 (mm-30) cc_final: 0.8373 (mt-10) REVERT: C 642 GLN cc_start: 0.9269 (tp-100) cc_final: 0.7897 (pp30) REVERT: C 670 MET cc_start: 0.9420 (mmp) cc_final: 0.8906 (mmm) REVERT: C 674 MET cc_start: 0.9345 (tpp) cc_final: 0.9117 (tpp) REVERT: C 702 TYR cc_start: 0.8441 (t80) cc_final: 0.8112 (t80) REVERT: C 803 LEU cc_start: 0.9318 (mt) cc_final: 0.8989 (mm) REVERT: D 408 MET cc_start: 0.6850 (tpt) cc_final: 0.6565 (tpt) REVERT: D 546 PHE cc_start: 0.6751 (t80) cc_final: 0.6379 (t80) REVERT: D 637 GLU cc_start: 0.8567 (pm20) cc_final: 0.8289 (pm20) REVERT: D 670 MET cc_start: 0.8679 (mmp) cc_final: 0.8477 (mmm) REVERT: D 702 TYR cc_start: 0.8162 (t80) cc_final: 0.7060 (t80) REVERT: D 704 LEU cc_start: 0.9411 (tp) cc_final: 0.8968 (tp) REVERT: D 767 TRP cc_start: 0.8410 (m-90) cc_final: 0.7505 (m-90) REVERT: E 177 TRP cc_start: 0.7422 (p90) cc_final: 0.6706 (p90) REVERT: F 205 LYS cc_start: 0.8885 (tttt) cc_final: 0.8387 (tptp) REVERT: G 81 HIS cc_start: 0.8166 (m90) cc_final: 0.7907 (m-70) REVERT: G 152 ILE cc_start: 0.9243 (tp) cc_final: 0.8919 (mm) REVERT: G 190 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8622 (mm-30) REVERT: H 23 MET cc_start: 0.8208 (ttt) cc_final: 0.7603 (tpt) REVERT: H 69 GLU cc_start: 0.7519 (tm-30) cc_final: 0.7170 (tm-30) REVERT: H 177 TRP cc_start: 0.7515 (p90) cc_final: 0.7033 (p90) REVERT: H 205 LYS cc_start: 0.8854 (mttp) cc_final: 0.8542 (mmtm) outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 0.2607 time to fit residues: 131.0197 Evaluate side-chains 258 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 1.873 ------------------------------------------------------------------------------- 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: 0.0980 chunk 208 optimal weight: 0.8980 chunk 179 optimal weight: 3.9990 chunk 154 optimal weight: 0.0770 chunk 87 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 212 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 overall best weight: 0.6140 ------------------------------------------------------------------------------- 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 81 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.144192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.099845 restraints weight = 54186.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.101110 restraints weight = 39420.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.100766 restraints weight = 33653.767| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.5784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18698 Z= 0.118 Angle : 0.575 9.933 25226 Z= 0.299 Chirality : 0.042 0.212 2826 Planarity : 0.003 0.047 3102 Dihedral : 4.546 70.170 2522 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.83 % Favored : 95.91 % 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: 0.66 (0.18), residues: 2298 helix: 1.56 (0.15), residues: 1230 sheet: -1.11 (0.38), residues: 172 loop : -0.78 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 767 HIS 0.004 0.001 HIS B 435 PHE 0.016 0.001 PHE F 106 TYR 0.015 0.001 TYR C 732 ARG 0.004 0.000 ARG D 545 Details of bonding type rmsd hydrogen bonds : bond 0.04343 ( 975) hydrogen bonds : angle 4.45059 ( 2796) SS BOND : bond 0.00222 ( 12) SS BOND : angle 0.71815 ( 24) covalent geometry : bond 0.00250 (18686) covalent geometry : angle 0.57526 (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 320 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 2.003 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: A 463 MET cc_start: 0.8183 (mtt) cc_final: 0.7732 (mmt) REVERT: A 471 LYS cc_start: 0.7873 (mtmt) cc_final: 0.7436 (tppt) REVERT: A 637 GLU cc_start: 0.8912 (pp20) cc_final: 0.8634 (mm-30) REVERT: A 642 GLN cc_start: 0.8804 (tp-100) cc_final: 0.7785 (tm-30) REVERT: A 645 ILE cc_start: 0.7144 (mm) cc_final: 0.6865 (mm) REVERT: A 702 TYR cc_start: 0.8266 (t80) cc_final: 0.7658 (t80) REVERT: A 721 MET cc_start: 0.6196 (pmm) cc_final: 0.5816 (pmm) REVERT: B 408 MET cc_start: 0.7497 (tpt) cc_final: 0.7238 (tpt) REVERT: B 546 PHE cc_start: 0.8111 (t80) cc_final: 0.7796 (t80) REVERT: B 674 MET cc_start: 0.4813 (mtp) cc_final: 0.3528 (tmm) REVERT: C 537 SER cc_start: 0.9332 (m) cc_final: 0.8814 (t) REVERT: C 627 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8481 (mt-10) REVERT: C 642 GLN cc_start: 0.9256 (tp-100) cc_final: 0.7837 (pp30) REVERT: C 670 MET cc_start: 0.9399 (mmp) cc_final: 0.8879 (mmm) REVERT: C 674 MET cc_start: 0.9326 (tpp) cc_final: 0.9106 (tpp) REVERT: C 702 TYR cc_start: 0.8494 (t80) cc_final: 0.8227 (t80) REVERT: C 726 ASN cc_start: 0.9036 (m-40) cc_final: 0.8489 (t0) REVERT: C 764 ASN cc_start: 0.9084 (m110) cc_final: 0.8530 (p0) REVERT: C 803 LEU cc_start: 0.9265 (mt) cc_final: 0.8995 (mm) REVERT: D 408 MET cc_start: 0.6750 (tpt) cc_final: 0.6488 (tpt) REVERT: D 651 ASP cc_start: 0.6846 (t0) cc_final: 0.6476 (p0) REVERT: D 659 PHE cc_start: 0.7582 (m-80) cc_final: 0.7275 (m-80) REVERT: D 670 MET cc_start: 0.8637 (mmp) cc_final: 0.8407 (mmm) REVERT: D 702 TYR cc_start: 0.8085 (t80) cc_final: 0.6998 (t80) REVERT: D 704 LEU cc_start: 0.9373 (tp) cc_final: 0.8868 (tp) REVERT: D 767 TRP cc_start: 0.8413 (m-90) cc_final: 0.7502 (m-90) REVERT: E 64 ARG cc_start: 0.6625 (ptm-80) cc_final: 0.4366 (ptp90) REVERT: E 78 GLN cc_start: 0.8363 (mm-40) cc_final: 0.7502 (mm-40) REVERT: E 177 TRP cc_start: 0.7258 (p90) cc_final: 0.6735 (p90) REVERT: F 190 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8590 (mm-30) REVERT: F 205 LYS cc_start: 0.8860 (tttt) cc_final: 0.8365 (tptp) REVERT: G 97 LEU cc_start: 0.7894 (tt) cc_final: 0.7256 (mt) REVERT: G 152 ILE cc_start: 0.9209 (tp) cc_final: 0.8864 (mm) REVERT: G 190 GLU cc_start: 0.8880 (mm-30) cc_final: 0.8582 (mm-30) REVERT: H 23 MET cc_start: 0.8123 (ttt) cc_final: 0.7274 (tpt) REVERT: H 140 PHE cc_start: 0.8366 (m-80) cc_final: 0.7664 (m-80) REVERT: H 148 ASN cc_start: 0.8912 (m110) cc_final: 0.8704 (m110) REVERT: H 177 TRP cc_start: 0.7455 (p90) cc_final: 0.6928 (p90) REVERT: H 205 LYS cc_start: 0.8902 (mttp) cc_final: 0.8604 (mmtm) outliers start: 0 outliers final: 0 residues processed: 320 average time/residue: 0.2712 time to fit residues: 135.3965 Evaluate side-chains 265 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 2.005 ------------------------------------------------------------------------------- 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: 0.6980 chunk 208 optimal weight: 0.6980 chunk 217 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 chunk 216 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 chunk 87 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 131 HIS G 8 GLN ** H 78 GLN ** 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 = 0.4121 r_free = 0.4121 target = 0.143372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.100967 restraints weight = 54389.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.099789 restraints weight = 42647.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.099126 restraints weight = 40004.084| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.5985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18698 Z= 0.125 Angle : 0.586 8.533 25226 Z= 0.304 Chirality : 0.042 0.218 2826 Planarity : 0.003 0.047 3102 Dihedral : 4.481 66.025 2522 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.61 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % 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: 0.67 (0.18), residues: 2298 helix: 1.55 (0.15), residues: 1230 sheet: -1.12 (0.38), residues: 164 loop : -0.75 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 671 HIS 0.008 0.001 HIS E 59 PHE 0.028 0.001 PHE E 179 TYR 0.016 0.001 TYR D 816 ARG 0.007 0.000 ARG B 660 Details of bonding type rmsd hydrogen bonds : bond 0.04346 ( 975) hydrogen bonds : angle 4.45996 ( 2796) SS BOND : bond 0.00241 ( 12) SS BOND : angle 0.81173 ( 24) covalent geometry : bond 0.00269 (18686) covalent geometry : angle 0.58603 (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 308 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 2.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 MET cc_start: 0.8133 (mtt) cc_final: 0.7741 (mmt) REVERT: A 471 LYS cc_start: 0.7884 (mtmt) cc_final: 0.7500 (tppt) REVERT: A 637 GLU cc_start: 0.8908 (pp20) cc_final: 0.8636 (mm-30) REVERT: A 642 GLN cc_start: 0.8787 (tp-100) cc_final: 0.7721 (tm-30) REVERT: A 645 ILE cc_start: 0.7171 (mm) cc_final: 0.6889 (mm) REVERT: A 702 TYR cc_start: 0.8287 (t80) cc_final: 0.7592 (t80) REVERT: A 734 ILE cc_start: 0.7287 (tp) cc_final: 0.6998 (tp) REVERT: B 408 MET cc_start: 0.7446 (tpt) cc_final: 0.7209 (tpt) REVERT: B 463 MET cc_start: 0.5142 (mmm) cc_final: 0.4868 (mmt) REVERT: B 534 ILE cc_start: 0.9450 (mt) cc_final: 0.8936 (tp) REVERT: B 546 PHE cc_start: 0.8124 (t80) cc_final: 0.7847 (t80) REVERT: B 674 MET cc_start: 0.4976 (mtp) cc_final: 0.3963 (tmm) REVERT: C 537 SER cc_start: 0.9361 (m) cc_final: 0.8804 (t) REVERT: C 627 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8368 (mt-10) REVERT: C 642 GLN cc_start: 0.9257 (tp-100) cc_final: 0.8367 (pp30) REVERT: C 670 MET cc_start: 0.9392 (mmp) cc_final: 0.8848 (mmm) REVERT: C 674 MET cc_start: 0.9350 (tpp) cc_final: 0.9097 (tpp) REVERT: C 702 TYR cc_start: 0.8559 (t80) cc_final: 0.8232 (t80) REVERT: C 726 ASN cc_start: 0.9005 (m-40) cc_final: 0.8369 (t0) REVERT: C 764 ASN cc_start: 0.8980 (m110) cc_final: 0.8531 (p0) REVERT: C 803 LEU cc_start: 0.9308 (mt) cc_final: 0.8973 (mm) REVERT: D 408 MET cc_start: 0.6782 (tpt) cc_final: 0.6555 (tpt) REVERT: D 651 ASP cc_start: 0.6878 (t0) cc_final: 0.6512 (p0) REVERT: D 659 PHE cc_start: 0.7509 (m-80) cc_final: 0.7220 (m-80) REVERT: D 670 MET cc_start: 0.8629 (mmp) cc_final: 0.8407 (mmm) REVERT: D 702 TYR cc_start: 0.8096 (t80) cc_final: 0.7082 (t80) REVERT: D 704 LEU cc_start: 0.9224 (tp) cc_final: 0.8740 (tp) REVERT: D 767 TRP cc_start: 0.8503 (m-90) cc_final: 0.7569 (m-90) REVERT: E 64 ARG cc_start: 0.6674 (ptm-80) cc_final: 0.4309 (ptp90) REVERT: F 205 LYS cc_start: 0.8905 (tttt) cc_final: 0.8413 (tptp) REVERT: G 97 LEU cc_start: 0.7964 (tt) cc_final: 0.7347 (mt) REVERT: G 152 ILE cc_start: 0.9178 (tp) cc_final: 0.8912 (mm) REVERT: G 190 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8569 (mm-30) REVERT: H 23 MET cc_start: 0.8106 (ttt) cc_final: 0.7471 (tpt) REVERT: H 127 TYR cc_start: 0.6862 (m-80) cc_final: 0.6372 (m-80) REVERT: H 148 ASN cc_start: 0.8879 (m110) cc_final: 0.8660 (m110) REVERT: H 177 TRP cc_start: 0.7445 (p90) cc_final: 0.6958 (p90) REVERT: H 205 LYS cc_start: 0.8892 (mttp) cc_final: 0.8538 (mmmt) outliers start: 0 outliers final: 0 residues processed: 308 average time/residue: 0.2695 time to fit residues: 130.0391 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 : 1.923 ------------------------------------------------------------------------------- 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: 9.9990 chunk 171 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 203 optimal weight: 0.0570 chunk 190 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 0.0470 chunk 85 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 198 optimal weight: 0.5980 chunk 113 optimal weight: 10.0000 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 791 ASN E 131 HIS F 8 GLN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.144313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.097824 restraints weight = 54181.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.100236 restraints weight = 37571.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.101727 restraints weight = 29752.600| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.6127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 18698 Z= 0.113 Angle : 0.588 8.031 25226 Z= 0.304 Chirality : 0.042 0.217 2826 Planarity : 0.003 0.048 3102 Dihedral : 4.394 61.962 2522 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.61 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: 0.67 (0.18), residues: 2298 helix: 1.56 (0.15), residues: 1231 sheet: -1.15 (0.36), residues: 176 loop : -0.77 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP E 177 HIS 0.004 0.001 HIS E 59 PHE 0.018 0.001 PHE H 140 TYR 0.015 0.001 TYR D 816 ARG 0.004 0.000 ARG D 545 Details of bonding type rmsd hydrogen bonds : bond 0.04111 ( 975) hydrogen bonds : angle 4.43270 ( 2796) SS BOND : bond 0.00280 ( 12) SS BOND : angle 0.71826 ( 24) covalent geometry : bond 0.00236 (18686) covalent geometry : angle 0.58821 (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 318 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 2.059 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: 0.8039 (mtt) cc_final: 0.7626 (mmt) REVERT: A 471 LYS cc_start: 0.7941 (mtmt) cc_final: 0.7565 (tppt) REVERT: A 496 MET cc_start: 0.8394 (tpt) cc_final: 0.8153 (tpp) REVERT: A 503 MET cc_start: 0.6280 (mmt) cc_final: 0.6013 (mmt) REVERT: A 642 GLN cc_start: 0.8779 (tp-100) cc_final: 0.7731 (tm-30) REVERT: A 645 ILE cc_start: 0.7178 (mm) cc_final: 0.6887 (mm) REVERT: A 702 TYR cc_start: 0.8308 (t80) cc_final: 0.7590 (t80) REVERT: A 721 MET cc_start: 0.6238 (pmm) cc_final: 0.6033 (pmm) REVERT: A 734 ILE cc_start: 0.7354 (tp) cc_final: 0.7066 (tp) REVERT: B 408 MET cc_start: 0.7750 (tpt) cc_final: 0.7521 (tpt) REVERT: B 534 ILE cc_start: 0.9415 (mt) cc_final: 0.8981 (tp) REVERT: B 546 PHE cc_start: 0.8100 (t80) cc_final: 0.7809 (t80) REVERT: B 671 TRP cc_start: 0.6041 (t-100) cc_final: 0.5672 (t-100) REVERT: B 674 MET cc_start: 0.4946 (mtp) cc_final: 0.3848 (tmm) REVERT: C 537 SER cc_start: 0.9315 (m) cc_final: 0.8867 (t) REVERT: C 627 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8392 (mt-10) REVERT: C 642 GLN cc_start: 0.9243 (tp-100) cc_final: 0.8325 (pp30) REVERT: C 670 MET cc_start: 0.9387 (mmp) cc_final: 0.8858 (mmm) REVERT: C 674 MET cc_start: 0.9334 (tpp) cc_final: 0.9068 (tpp) REVERT: C 702 TYR cc_start: 0.8578 (t80) cc_final: 0.8212 (t80) REVERT: C 726 ASN cc_start: 0.9005 (m-40) cc_final: 0.8327 (t0) REVERT: C 803 LEU cc_start: 0.9246 (mt) cc_final: 0.8960 (mm) REVERT: D 408 MET cc_start: 0.7077 (tpt) cc_final: 0.6856 (tpt) REVERT: D 546 PHE cc_start: 0.6588 (t80) cc_final: 0.6324 (t80) REVERT: D 659 PHE cc_start: 0.7482 (m-80) cc_final: 0.7246 (m-80) REVERT: D 670 MET cc_start: 0.8685 (mmp) cc_final: 0.8452 (mmm) REVERT: D 702 TYR cc_start: 0.8101 (t80) cc_final: 0.7082 (t80) REVERT: D 704 LEU cc_start: 0.9282 (tp) cc_final: 0.8883 (tp) REVERT: D 767 TRP cc_start: 0.8375 (m-90) cc_final: 0.7438 (m-90) REVERT: E 64 ARG cc_start: 0.6318 (ptm-80) cc_final: 0.3923 (ptp-170) REVERT: E 78 GLN cc_start: 0.8222 (mm-40) cc_final: 0.7255 (mm-40) REVERT: F 190 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8543 (mm-30) REVERT: F 205 LYS cc_start: 0.8841 (tttt) cc_final: 0.8376 (tptp) REVERT: G 97 LEU cc_start: 0.7974 (tt) cc_final: 0.7316 (mt) REVERT: G 116 MET cc_start: 0.3546 (ttt) cc_final: 0.3277 (ttt) REVERT: G 190 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8582 (mm-30) REVERT: H 23 MET cc_start: 0.8222 (ttt) cc_final: 0.7446 (tpt) REVERT: H 127 TYR cc_start: 0.6667 (m-80) cc_final: 0.6234 (m-80) REVERT: H 148 ASN cc_start: 0.9022 (m110) cc_final: 0.8733 (m110) REVERT: H 177 TRP cc_start: 0.7400 (p90) cc_final: 0.6900 (p90) REVERT: H 205 LYS cc_start: 0.9025 (mttp) cc_final: 0.8632 (mmtp) outliers start: 0 outliers final: 0 residues processed: 318 average time/residue: 0.2592 time to fit residues: 130.2781 Evaluate side-chains 269 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 2.102 ------------------------------------------------------------------------------- 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: 4.9990 chunk 151 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 95 optimal weight: 0.0040 chunk 172 optimal weight: 0.7980 chunk 186 optimal weight: 2.9990 chunk 174 optimal weight: 0.0050 chunk 164 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 overall best weight: 0.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 756 GLN E 131 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.144885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.103380 restraints weight = 54410.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.101739 restraints weight = 41907.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.101410 restraints weight = 37870.174| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.6276 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= 0.112 Angle : 0.591 7.838 25226 Z= 0.305 Chirality : 0.042 0.216 2826 Planarity : 0.003 0.049 3102 Dihedral : 4.297 58.377 2522 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.48 % Favored : 96.26 % 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: 1224 sheet: -0.90 (0.39), residues: 154 loop : -0.76 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP E 177 HIS 0.014 0.001 HIS B 435 PHE 0.023 0.001 PHE E 179 TYR 0.015 0.001 TYR D 816 ARG 0.004 0.000 ARG D 545 Details of bonding type rmsd hydrogen bonds : bond 0.04011 ( 975) hydrogen bonds : angle 4.38898 ( 2796) SS BOND : bond 0.00237 ( 12) SS BOND : angle 0.68814 ( 24) covalent geometry : bond 0.00234 (18686) covalent geometry : angle 0.59085 (25202) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5928.84 seconds wall clock time: 104 minutes 53.28 seconds (6293.28 seconds total)