Starting phenix.real_space_refine on Sat Jul 4 07:58:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ssb_40750/07_2026/8ssb_40750.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ssb_40750/07_2026/8ssb_40750.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ssb_40750/07_2026/8ssb_40750.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ssb_40750/07_2026/8ssb_40750.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8ssb_40750/07_2026/8ssb_40750.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ssb_40750/07_2026/8ssb_40750.cif" model { file = "/net/cci-nas-00/data/ceres_data/8ssb_40750/07_2026/8ssb_40750.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ssb_40750/07_2026/8ssb_40750.cif" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 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: 5 Type Number sf(0) Gaussians P 18 5.49 5 S 132 5.16 5 C 12575 2.51 5 N 2907 2.21 5 O 3416 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19048 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4698 Classifications: {'peptide': 602} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 585} Chain breaks: 4 Chain: "B" Number of atoms: 3177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3177 Classifications: {'peptide': 408} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 394} Chain breaks: 1 Chain: "C" Number of atoms: 4698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4698 Classifications: {'peptide': 602} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 585} Chain breaks: 4 Chain: "D" Number of atoms: 3177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3177 Classifications: {'peptide': 408} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 394} Chain breaks: 1 Chain: "E" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1166 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain breaks: 1 Chain: "F" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1166 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain breaks: 1 Chain: "A" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 250 Unusual residues: {'PCW': 8} Inner-chain residues flagged as termini: ['pdbres="GLU A1108 "'] Classifications: {'peptide': 1, 'undetermined': 8} Modifications used: {'COO': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PCW:plan-2': 1, 'PCW:plan-1': 4, 'PCW:plan-3': 4, 'PCW:plan-4': 4} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 196 Unusual residues: {'PCW': 4, 'SPD': 1} Inner-chain residues flagged as termini: ['pdbres="GLU B1104 "'] Classifications: {'peptide': 1, 'undetermined': 5} Modifications used: {'COO': 1} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'PCW:plan-4': 1, 'PCW:plan-2': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 199 Unusual residues: {'PCW': 7} Inner-chain residues flagged as termini: ['pdbres="GLU C1107 "'] Classifications: {'peptide': 1, 'undetermined': 7} Modifications used: {'COO': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PCW:plan-2': 1, 'PCW:plan-1': 4, 'PCW:plan-3': 4, 'PCW:plan-4': 4} Unresolved non-hydrogen planarities: 49 Chain: "D" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 174 Unusual residues: {'PCW': 4} Classifications: {'peptide': 1, 'undetermined': 4} Modifications used: {'COO': 1} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'PCW:plan-4': 1, 'PCW:plan-2': 2} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {'PCW': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-2': 2, 'PCW:plan-1': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 15 Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'PCW': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1, 'PCW:plan-2': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 3.76, per 1000 atoms: 0.20 Number of scatterers: 19048 At special positions: 0 Unit cell: (117.86, 122.01, 134.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 132 16.00 P 18 15.00 O 3416 8.00 N 2907 7.00 C 12575 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.02 Simple disulfide: pdb=" SG CYS A 890 " - pdb=" SG CYS A 900 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 900 " distance=2.02 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.60 Conformation dependent library (CDL) restraints added in 704.1 milliseconds 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4248 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 18 sheets defined 58.2% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.643A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG A 420 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TYR A 421 " --> pdb=" O ASN A 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 421' Processing helix chain 'A' and resid 423 through 436 Processing helix chain 'A' and resid 464 through 469 removed outlier: 3.545A pdb=" N TYR A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 489 removed outlier: 3.649A pdb=" N GLU A 487 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL A 488 " --> pdb=" O VAL A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 522 through 544 removed outlier: 4.119A pdb=" N VAL A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL A 539 " --> pdb=" O GLY A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 585 Processing helix chain 'A' and resid 597 through 628 removed outlier: 4.270A pdb=" N VAL A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TRP A 606 " --> pdb=" O GLY A 602 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE A 613 " --> pdb=" O THR A 609 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A 624 " --> pdb=" O LEU A 620 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N THR A 625 " --> pdb=" O ALA A 621 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 626 " --> pdb=" O ALA A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 642 removed outlier: 3.722A pdb=" N LYS A 641 " --> pdb=" O GLU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 662 removed outlier: 3.594A pdb=" N GLU A 657 " --> pdb=" O GLY A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 676 Processing helix chain 'A' and resid 685 through 697 removed outlier: 3.635A pdb=" N LYS A 697 " --> pdb=" O VAL A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 713 removed outlier: 4.167A pdb=" N TYR A 711 " --> pdb=" O THR A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 756 removed outlier: 3.521A pdb=" N VAL A 746 " --> pdb=" O LEU A 742 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU A 755 " --> pdb=" O LEU A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 766 removed outlier: 3.547A pdb=" N TRP A 766 " --> pdb=" O LEU A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 781 removed outlier: 4.342A pdb=" N LYS A 781 " --> pdb=" O SER A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 822 removed outlier: 3.824A pdb=" N LEU A 808 " --> pdb=" O GLY A 804 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA A 822 " --> pdb=" O SER A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 858 removed outlier: 3.597A pdb=" N SER A 842 " --> pdb=" O THR A 838 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA A 845 " --> pdb=" O SER A 841 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY A 850 " --> pdb=" O VAL A 846 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 852 " --> pdb=" O GLY A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 929 Processing helix chain 'A' and resid 929 through 951 removed outlier: 3.909A pdb=" N LEU A 933 " --> pdb=" O THR A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 991 removed outlier: 3.711A pdb=" N SER A 962 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE A 965 " --> pdb=" O VAL A 961 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE A 967 " --> pdb=" O GLY A 963 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 975 " --> pdb=" O LEU A 971 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG A 991 " --> pdb=" O GLU A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1032 removed outlier: 3.861A pdb=" N ILE A1012 " --> pdb=" O ALA A1008 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER A1013 " --> pdb=" O PHE A1009 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A1015 " --> pdb=" O ALA A1011 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL A1025 " --> pdb=" O GLY A1021 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 414 Processing helix chain 'B' and resid 416 through 421 removed outlier: 3.504A pdb=" N ARG B 420 " --> pdb=" O GLY B 417 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR B 421 " --> pdb=" O ASN B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 437 removed outlier: 3.583A pdb=" N ALA B 430 " --> pdb=" O VAL B 426 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N HIS B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 468 Processing helix chain 'B' and resid 482 through 489 removed outlier: 3.528A pdb=" N VAL B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.859A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 546 removed outlier: 4.135A pdb=" N VAL B 530 " --> pdb=" O TRP B 526 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL B 539 " --> pdb=" O GLY B 535 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE B 541 " --> pdb=" O SER B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 585 removed outlier: 3.561A pdb=" N PHE B 579 " --> pdb=" O ASN B 575 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU B 581 " --> pdb=" O LEU B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 624 removed outlier: 3.506A pdb=" N TRP B 606 " --> pdb=" O GLY B 602 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA B 618 " --> pdb=" O SER B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 642 Processing helix chain 'B' and resid 653 through 661 removed outlier: 3.963A pdb=" N GLU B 657 " --> pdb=" O GLY B 653 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE B 659 " --> pdb=" O THR B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 676 Processing helix chain 'B' and resid 685 through 697 removed outlier: 3.558A pdb=" N VAL B 690 " --> pdb=" O THR B 686 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL B 693 " --> pdb=" O GLY B 689 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER B 696 " --> pdb=" O ARG B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 713 removed outlier: 3.859A pdb=" N TYR B 711 " --> pdb=" O THR B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 756 removed outlier: 3.566A pdb=" N LEU B 748 " --> pdb=" O THR B 744 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN B 756 " --> pdb=" O LYS B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 767 removed outlier: 3.632A pdb=" N TRP B 767 " --> pdb=" O LYS B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 791 Processing helix chain 'B' and resid 792 through 819 removed outlier: 3.752A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU B 811 " --> pdb=" O MET B 807 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 removed outlier: 3.644A pdb=" N GLU C 419 " --> pdb=" O GLU C 416 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG C 420 " --> pdb=" O GLY C 417 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TYR C 421 " --> pdb=" O ASN C 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 416 through 421' Processing helix chain 'C' and resid 423 through 436 Processing helix chain 'C' and resid 464 through 469 removed outlier: 3.544A pdb=" N TYR C 469 " --> pdb=" O GLY C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 489 removed outlier: 3.649A pdb=" N GLU C 487 " --> pdb=" O LEU C 483 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL C 488 " --> pdb=" O VAL C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 519 Processing helix chain 'C' and resid 522 through 544 removed outlier: 4.119A pdb=" N VAL C 530 " --> pdb=" O TRP C 526 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL C 539 " --> pdb=" O GLY C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 585 Processing helix chain 'C' and resid 597 through 628 removed outlier: 4.269A pdb=" N VAL C 601 " --> pdb=" O SER C 597 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TRP C 606 " --> pdb=" O GLY C 602 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE C 613 " --> pdb=" O THR C 609 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU C 624 " --> pdb=" O LEU C 620 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N THR C 625 " --> pdb=" O ALA C 621 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL C 626 " --> pdb=" O ALA C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 642 removed outlier: 3.722A pdb=" N LYS C 641 " --> pdb=" O GLU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 662 removed outlier: 3.593A pdb=" N GLU C 657 " --> pdb=" O GLY C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 666 through 676 Processing helix chain 'C' and resid 685 through 697 removed outlier: 3.634A pdb=" N LYS C 697 " --> pdb=" O VAL C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 713 removed outlier: 4.166A pdb=" N TYR C 711 " --> pdb=" O THR C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 756 removed outlier: 3.521A pdb=" N VAL C 746 " --> pdb=" O LEU C 742 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU C 755 " --> pdb=" O LEU C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 766 removed outlier: 3.547A pdb=" N TRP C 766 " --> pdb=" O LEU C 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 777 through 781 removed outlier: 4.342A pdb=" N LYS C 781 " --> pdb=" O SER C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 793 through 822 removed outlier: 3.824A pdb=" N LEU C 808 " --> pdb=" O GLY C 804 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA C 822 " --> pdb=" O SER C 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 832 through 858 removed outlier: 3.596A pdb=" N SER C 842 " --> pdb=" O THR C 838 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA C 845 " --> pdb=" O SER C 841 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY C 850 " --> pdb=" O VAL C 846 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU C 852 " --> pdb=" O GLY C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 917 through 929 Processing helix chain 'C' and resid 929 through 951 removed outlier: 3.909A pdb=" N LEU C 933 " --> pdb=" O THR C 929 " (cutoff:3.500A) Processing helix chain 'C' and resid 957 through 991 removed outlier: 3.712A pdb=" N SER C 962 " --> pdb=" O LEU C 958 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE C 965 " --> pdb=" O VAL C 961 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE C 967 " --> pdb=" O GLY C 963 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL C 975 " --> pdb=" O LEU C 971 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG C 991 " --> pdb=" O GLU C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1032 removed outlier: 3.861A pdb=" N ILE C1012 " --> pdb=" O ALA C1008 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER C1013 " --> pdb=" O PHE C1009 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU C1015 " --> pdb=" O ALA C1011 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL C1025 " --> pdb=" O GLY C1021 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 414 Processing helix chain 'D' and resid 416 through 421 removed outlier: 3.504A pdb=" N ARG D 420 " --> pdb=" O GLY D 417 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR D 421 " --> pdb=" O ASN D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 437 removed outlier: 3.583A pdb=" N ALA D 430 " --> pdb=" O VAL D 426 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N HIS D 435 " --> pdb=" O GLU D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 468 Processing helix chain 'D' and resid 482 through 489 removed outlier: 3.529A pdb=" N VAL D 488 " --> pdb=" O VAL D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.860A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 546 removed outlier: 4.135A pdb=" N VAL D 530 " --> pdb=" O TRP D 526 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL D 539 " --> pdb=" O GLY D 535 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE D 541 " --> pdb=" O SER D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 585 removed outlier: 3.560A pdb=" N PHE D 579 " --> pdb=" O ASN D 575 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER D 580 " --> pdb=" O SER D 576 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU D 581 " --> pdb=" O LEU D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 624 removed outlier: 3.507A pdb=" N TRP D 606 " --> pdb=" O GLY D 602 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE D 611 " --> pdb=" O PHE D 607 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA D 618 " --> pdb=" O SER D 614 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 642 Processing helix chain 'D' and resid 653 through 661 removed outlier: 3.963A pdb=" N GLU D 657 " --> pdb=" O GLY D 653 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE D 659 " --> pdb=" O THR D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 676 Processing helix chain 'D' and resid 685 through 697 removed outlier: 3.559A pdb=" N VAL D 690 " --> pdb=" O THR D 686 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL D 693 " --> pdb=" O GLY D 689 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER D 696 " --> pdb=" O ARG D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 705 through 713 removed outlier: 3.859A pdb=" N TYR D 711 " --> pdb=" O THR D 707 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 756 removed outlier: 3.566A pdb=" N LEU D 748 " --> pdb=" O THR D 744 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN D 756 " --> pdb=" O LYS D 752 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 767 removed outlier: 3.632A pdb=" N TRP D 767 " --> pdb=" O LYS D 763 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 791 Processing helix chain 'D' and resid 792 through 819 removed outlier: 3.752A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU D 811 " --> pdb=" O MET D 807 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 24 removed outlier: 3.585A pdb=" N THR E 13 " --> pdb=" O CYS E 9 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL E 15 " --> pdb=" O MET E 11 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA E 18 " --> pdb=" O LEU E 14 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER E 19 " --> pdb=" O VAL E 15 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE E 22 " --> pdb=" O ALA E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 36 removed outlier: 3.888A pdb=" N ILE E 28 " --> pdb=" O VAL E 24 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE E 31 " --> pdb=" O HIS E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 67 removed outlier: 4.183A pdb=" N LYS E 66 " --> pdb=" O CYS E 62 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU E 67 " --> pdb=" O LEU E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 86 removed outlier: 4.442A pdb=" N HIS E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N CYS E 79 " --> pdb=" O HIS E 75 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU E 80 " --> pdb=" O GLY E 76 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU E 83 " --> pdb=" O CYS E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 107 removed outlier: 4.296A pdb=" N HIS E 107 " --> pdb=" O TRP E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 111 removed outlier: 3.909A pdb=" N ASP E 111 " --> pdb=" O ARG E 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 108 through 111' Processing helix chain 'E' and resid 126 through 158 removed outlier: 3.574A pdb=" N TRP E 136 " --> pdb=" O GLN E 132 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA E 140 " --> pdb=" O TRP E 136 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU E 143 " --> pdb=" O LEU E 139 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU E 144 " --> pdb=" O ALA E 140 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL E 158 " --> pdb=" O VAL E 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 24 removed outlier: 3.518A pdb=" N THR F 13 " --> pdb=" O CYS F 9 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA F 18 " --> pdb=" O LEU F 14 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER F 19 " --> pdb=" O VAL F 15 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE F 22 " --> pdb=" O ALA F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 36 removed outlier: 3.653A pdb=" N PHE F 31 " --> pdb=" O HIS F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 67 removed outlier: 4.258A pdb=" N LYS F 66 " --> pdb=" O CYS F 62 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU F 67 " --> pdb=" O LEU F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 86 removed outlier: 4.356A pdb=" N HIS F 75 " --> pdb=" O GLU F 71 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE F 78 " --> pdb=" O ILE F 74 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS F 79 " --> pdb=" O HIS F 75 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU F 80 " --> pdb=" O GLY F 76 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU F 83 " --> pdb=" O CYS F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 107 removed outlier: 4.193A pdb=" N HIS F 107 " --> pdb=" O TRP F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 158 removed outlier: 3.583A pdb=" N TYR F 130 " --> pdb=" O ASP F 126 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TRP F 136 " --> pdb=" O GLN F 132 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU F 139 " --> pdb=" O SER F 135 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU F 143 " --> pdb=" O LEU F 139 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR F 156 " --> pdb=" O SER F 152 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL F 158 " --> pdb=" O VAL F 154 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 396 through 399 removed outlier: 6.142A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 480 through 481 removed outlier: 4.407A pdb=" N GLY A 731 " --> pdb=" O ILE A 481 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 500 through 501 Processing sheet with id=AA4, first strand: chain 'A' and resid 503 through 505 removed outlier: 3.647A pdb=" N ILE A 504 " --> pdb=" O MET A 721 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 646 through 647 removed outlier: 6.348A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 862 through 863 removed outlier: 3.696A pdb=" N LYS A1002 " --> pdb=" O TYR A 863 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 888 through 889 removed outlier: 4.014A pdb=" N VAL A 889 " --> pdb=" O PHE A 901 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE A 901 " --> pdb=" O VAL A 889 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 497 through 498 Processing sheet with id=AA9, first strand: chain 'B' and resid 502 through 505 removed outlier: 4.044A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL B 723 " --> pdb=" O ILE B 502 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 396 through 399 removed outlier: 6.141A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 480 through 481 removed outlier: 4.407A pdb=" N GLY C 731 " --> pdb=" O ILE C 481 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 500 through 501 Processing sheet with id=AB4, first strand: chain 'C' and resid 503 through 505 removed outlier: 3.647A pdb=" N ILE C 504 " --> pdb=" O MET C 721 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 646 through 647 removed outlier: 6.347A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 862 through 863 removed outlier: 3.696A pdb=" N LYS C1002 " --> pdb=" O TYR C 863 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 888 through 889 removed outlier: 4.013A pdb=" N VAL C 889 " --> pdb=" O PHE C 901 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE C 901 " --> pdb=" O VAL C 889 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 497 through 498 Processing sheet with id=AB9, first strand: chain 'D' and resid 502 through 505 removed outlier: 4.044A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL D 723 " --> pdb=" O ILE D 502 " (cutoff:3.500A) 834 hydrogen bonds defined for protein. 2436 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.65 Time building geometry restraints manager: 2.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2884 1.31 - 1.44: 5292 1.44 - 1.57: 11003 1.57 - 1.69: 36 1.69 - 1.82: 212 Bond restraints: 19427 Sorted by residual: bond pdb=" C ASP C 519 " pdb=" N PRO C 520 " ideal model delta sigma weight residual 1.336 1.386 -0.051 1.08e-02 8.57e+03 2.20e+01 bond pdb=" C ASP A 519 " pdb=" N PRO A 520 " ideal model delta sigma weight residual 1.336 1.386 -0.050 1.08e-02 8.57e+03 2.15e+01 bond pdb=" C31 PCW C1102 " pdb=" O2 PCW C1102 " ideal model delta sigma weight residual 1.333 1.424 -0.091 2.00e-02 2.50e+03 2.07e+01 bond pdb=" C VAL F 69 " pdb=" N PRO F 70 " ideal model delta sigma weight residual 1.335 1.394 -0.059 1.30e-02 5.92e+03 2.06e+01 bond pdb=" C VAL E 69 " pdb=" N PRO E 70 " ideal model delta sigma weight residual 1.335 1.394 -0.059 1.30e-02 5.92e+03 2.03e+01 ... (remaining 19422 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 24810 3.09 - 6.18: 933 6.18 - 9.27: 255 9.27 - 12.37: 48 12.37 - 15.46: 14 Bond angle restraints: 26060 Sorted by residual: angle pdb=" C ASN A 411 " pdb=" N HIS A 412 " pdb=" CA HIS A 412 " ideal model delta sigma weight residual 121.54 134.09 -12.55 1.91e+00 2.74e-01 4.32e+01 angle pdb=" C ASN C 411 " pdb=" N HIS C 412 " pdb=" CA HIS C 412 " ideal model delta sigma weight residual 121.54 134.05 -12.51 1.91e+00 2.74e-01 4.29e+01 angle pdb=" C ASP C 454 " pdb=" N ALA C 455 " pdb=" CA ALA C 455 " ideal model delta sigma weight residual 120.79 129.69 -8.90 1.39e+00 5.18e-01 4.10e+01 angle pdb=" C ASP A 454 " pdb=" N ALA A 455 " pdb=" CA ALA A 455 " ideal model delta sigma weight residual 120.79 129.69 -8.90 1.39e+00 5.18e-01 4.10e+01 angle pdb=" C ILE C 591 " pdb=" N SER C 592 " pdb=" CA SER C 592 " ideal model delta sigma weight residual 121.80 137.26 -15.46 2.44e+00 1.68e-01 4.01e+01 ... (remaining 26055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.54: 11136 35.54 - 71.09: 285 71.09 - 106.63: 22 106.63 - 142.17: 8 142.17 - 177.72: 2 Dihedral angle restraints: 11453 sinusoidal: 4811 harmonic: 6642 Sorted by residual: dihedral pdb=" CA SER A 403 " pdb=" C SER A 403 " pdb=" N PRO A 404 " pdb=" CA PRO A 404 " ideal model delta harmonic sigma weight residual 180.00 -119.87 -60.13 0 5.00e+00 4.00e-02 1.45e+02 dihedral pdb=" CA SER C 403 " pdb=" C SER C 403 " pdb=" N PRO C 404 " pdb=" CA PRO C 404 " ideal model delta harmonic sigma weight residual 180.00 -119.88 -60.12 0 5.00e+00 4.00e-02 1.45e+02 dihedral pdb=" CA LYS C 458 " pdb=" C LYS C 458 " pdb=" N ILE C 459 " pdb=" CA ILE C 459 " ideal model delta harmonic sigma weight residual -180.00 -125.97 -54.03 0 5.00e+00 4.00e-02 1.17e+02 ... (remaining 11450 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2198 0.064 - 0.128: 522 0.128 - 0.192: 88 0.192 - 0.256: 20 0.256 - 0.320: 8 Chirality restraints: 2836 Sorted by residual: chirality pdb=" C2 PCW B1101 " pdb=" C1 PCW B1101 " pdb=" C3 PCW B1101 " pdb=" O2 PCW B1101 " both_signs ideal model delta sigma weight residual False -2.32 -2.64 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CB ILE D 459 " pdb=" CA ILE D 459 " pdb=" CG1 ILE D 459 " pdb=" CG2 ILE D 459 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CB ILE B 459 " pdb=" CA ILE B 459 " pdb=" CG1 ILE B 459 " pdb=" CG2 ILE B 459 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.45e+00 ... (remaining 2833 not shown) Planarity restraints: 3142 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 716 " -0.067 5.00e-02 4.00e+02 1.01e-01 1.62e+01 pdb=" N PRO B 717 " 0.174 5.00e-02 4.00e+02 pdb=" CA PRO B 717 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 717 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 716 " 0.067 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO D 717 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO D 717 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO D 717 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 403 " 0.052 5.00e-02 4.00e+02 7.74e-02 9.57e+00 pdb=" N PRO A 404 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO A 404 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 404 " 0.042 5.00e-02 4.00e+02 ... (remaining 3139 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4708 2.79 - 3.31: 17672 3.31 - 3.84: 31682 3.84 - 4.37: 37273 4.37 - 4.90: 60640 Nonbonded interactions: 151975 Sorted by model distance: nonbonded pdb=" OG SER A 729 " pdb=" OG SER D 729 " model vdw 2.258 3.040 nonbonded pdb=" O ASP B 490 " pdb=" OG1 THR B 736 " model vdw 2.268 3.040 nonbonded pdb=" O ASP D 490 " pdb=" OG1 THR D 736 " model vdw 2.268 3.040 nonbonded pdb=" OE1 GLU C 705 " pdb=" OH TYR C 732 " model vdw 2.278 3.040 nonbonded pdb=" OE1 GLU A 705 " pdb=" OH TYR A 732 " model vdw 2.278 3.040 ... (remaining 151970 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 394 through 1101 or (resid 1102 through 1103 and (name N o \ r name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C1 \ 6 or name C17 or name C18 or name C19 or name C2 or name C20 or name C3 or name \ C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or n \ ame C38 or name C39 or name C4 or name C40 or name C41 or name C42 or name C43 o \ r name C44 or name C45 or name C5 or name C6 or name C7 or name C8 or name O11 o \ r name O1P or name O2 or name O2P or name O3 or name O31 or name O3P or name O4P \ or name P )) or (resid 1104 through 1106 and (name C13 or name C14 or name C15 \ or name C16 or name C17 or name C18 or name C19 or name C20 or name C21 or name \ C22 or name C23)) or resid 1108 through 1109)) selection = (chain 'C' and (resid 394 through 1102 or (resid 1103 and (name N or name C1 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 \ or name C18 or name C19 or name C2 or name C20 or name C3 or name C31 or name C \ 32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or na \ me C39 or name C4 or name C40 or name C41 or name C42 or name C43 or name C44 or \ name C45 or name C5 or name C6 or name C7 or name C8 or name O11 or name O1P or \ name O2 or name O2P or name O3 or name O31 or name O3P or name O4P or name P )) \ or resid 1104 through 1108)) } ncs_group { reference = (chain 'B' and (resid 394 through 1102 or (resid 1103 and (name N or name C1 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 \ or name C18 or name C19 or name C2 or name C3 or name C31 or name C32 or name C \ 33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or na \ me C4 or name C40 or name C41 or name C5 or name C6 or name C7 or name C8 or nam \ e O11 or name O1P or name O2 or name O2P or name O3 or name O31 or name O3P or n \ ame O4P or name P )) or (resid 1105 and (name N or name C1 or name C11 or name C \ 12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or na \ me C19 or name C2 or name C20 or name C21 or name C22 or name C3 or name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 \ or name C39 or name C4 or name C40 or name C41 or name C5 or name C6 or name C7 \ or name C8 or name O11 or name O1P or name O2 or name O2P or name O3 or name O3 \ 1 or name O3P or name O4P or name P )))) selection = (chain 'D' and (resid 394 through 1102 or (resid 1103 and (name N or name C1 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 \ or name C18 or name C19 or name C2 or name C3 or name C31 or name C32 or name C \ 33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or na \ me C4 or name C40 or name C41 or name C5 or name C6 or name C7 or name C8 or nam \ e O11 or name O1P or name O2 or name O2P or name O3 or name O31 or name O3P or n \ ame O4P or name P )) or resid 1104)) } ncs_group { reference = (chain 'E' and (resid 2 through 159 or (resid 202 and (name C13 or name C14 or n \ ame C15 or name C16 or name C17 or name C18 or name C19 or name C20)))) selection = (chain 'F' and (resid 2 through 159 or (resid 202 and (name C13 or name C14 or n \ ame C15 or name C16 or name C17 or name C18 or name C19 or name C20)))) } 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: 6.870 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 15.230 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.094 19433 Z= 0.459 Angle : 1.545 15.457 26072 Z= 0.805 Chirality : 0.060 0.320 2836 Planarity : 0.008 0.101 3142 Dihedral : 16.063 177.715 7187 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 1.24 % Allowed : 11.40 % Favored : 87.37 % Rotamer: Outliers : 0.72 % Allowed : 6.49 % Favored : 92.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 9.38 % Twisted General : 1.35 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.92 (0.12), residues: 2264 helix: -3.81 (0.08), residues: 1320 sheet: -4.58 (0.35), residues: 102 loop : -3.75 (0.18), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 599 TYR 0.033 0.003 TYR F 149 PHE 0.026 0.003 PHE A 546 TRP 0.018 0.003 TRP B 578 HIS 0.013 0.003 HIS E 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00946 / 0.46 (19427) covalent geometry : angle 1.54546 / 0.81 (26060) SS BOND : bond 0.00662 / 0.33 ( 6) SS BOND : angle 1.02563 / 0.55 ( 12) hydrogen bonds : bond 0.29522 / 19.50 ( 834) hydrogen bonds : angle 10.26796 / 7.08 ( 2436) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 650 time to evaluate : 0.689 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: 0.9021 (ttp) cc_final: 0.8632 (ttm) REVERT: A 467 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7560 (tp) REVERT: A 585 MET cc_start: 0.8384 (mpt) cc_final: 0.7829 (mpt) REVERT: A 657 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7778 (mm-30) REVERT: A 713 GLU cc_start: 0.8629 (pp20) cc_final: 0.8377 (pp20) REVERT: A 726 ASN cc_start: 0.8570 (m-40) cc_final: 0.8361 (m-40) REVERT: A 879 LYS cc_start: 0.8521 (ttpt) cc_final: 0.8098 (mmtm) REVERT: A 938 PHE cc_start: 0.8754 (m-10) cc_final: 0.8501 (m-80) REVERT: A 943 PHE cc_start: 0.9008 (t80) cc_final: 0.8570 (t80) REVERT: A 968 LEU cc_start: 0.8985 (mt) cc_final: 0.8766 (mt) REVERT: A 1003 TYR cc_start: 0.8063 (m-80) cc_final: 0.7341 (m-80) REVERT: A 1005 TRP cc_start: 0.5466 (m100) cc_final: 0.5156 (m-90) REVERT: A 1028 PHE cc_start: 0.8162 (t80) cc_final: 0.7945 (t80) REVERT: A 1029 MET cc_start: 0.7793 (mmm) cc_final: 0.7505 (mtt) REVERT: B 421 TYR cc_start: 0.7901 (m-10) cc_final: 0.7633 (m-10) REVERT: B 460 TRP cc_start: 0.6636 (m-90) cc_final: 0.6427 (m-10) REVERT: B 626 VAL cc_start: 0.9301 (t) cc_final: 0.9038 (m) REVERT: B 713 GLU cc_start: 0.8980 (tm-30) cc_final: 0.8625 (tm-30) REVERT: B 714 GLN cc_start: 0.7642 (tp-100) cc_final: 0.7255 (tp40) REVERT: B 760 ASP cc_start: 0.9255 (m-30) cc_final: 0.8798 (t0) REVERT: B 761 LYS cc_start: 0.9498 (tptp) cc_final: 0.9232 (tppt) REVERT: B 764 ASN cc_start: 0.8725 (m-40) cc_final: 0.8153 (m110) REVERT: C 461 ASN cc_start: 0.8081 (t0) cc_final: 0.7807 (p0) REVERT: C 463 MET cc_start: 0.9121 (ttp) cc_final: 0.8852 (ttm) REVERT: C 657 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7726 (mm-30) REVERT: C 695 LYS cc_start: 0.9067 (mttp) cc_final: 0.8638 (mmtt) REVERT: C 714 GLN cc_start: 0.8594 (mm-40) cc_final: 0.8330 (mm-40) REVERT: C 879 LYS cc_start: 0.8123 (ttpt) cc_final: 0.7410 (mmtm) REVERT: C 926 ARG cc_start: 0.6446 (ttm-80) cc_final: 0.5924 (ttt90) REVERT: C 1029 MET cc_start: 0.8040 (mmm) cc_final: 0.7677 (mtp) REVERT: D 410 LYS cc_start: 0.9028 (ptmm) cc_final: 0.8761 (mmmt) REVERT: D 412 HIS cc_start: 0.6282 (t70) cc_final: 0.6061 (t70) REVERT: D 533 TYR cc_start: 0.8605 (t80) cc_final: 0.8297 (t80) REVERT: D 635 SER cc_start: 0.8950 (t) cc_final: 0.8734 (p) REVERT: D 650 LEU cc_start: 0.8388 (tp) cc_final: 0.8145 (tp) REVERT: D 702 TYR cc_start: 0.7747 (t80) cc_final: 0.7136 (t80) REVERT: D 714 GLN cc_start: 0.7907 (tp-100) cc_final: 0.7439 (tp40) REVERT: D 760 ASP cc_start: 0.9467 (m-30) cc_final: 0.9031 (t0) REVERT: D 764 ASN cc_start: 0.9106 (m-40) cc_final: 0.8764 (m110) REVERT: D 783 LYS cc_start: 0.7335 (pmtt) cc_final: 0.6880 (ptpp) REVERT: E 27 HIS cc_start: 0.6832 (t-90) cc_final: 0.6593 (t-90) REVERT: E 59 ARG cc_start: 0.6999 (tmm-80) cc_final: 0.6662 (tmt-80) REVERT: E 75 HIS cc_start: 0.7453 (t70) cc_final: 0.6541 (t70) REVERT: E 94 ASN cc_start: 0.7672 (p0) cc_final: 0.7411 (p0) REVERT: E 95 ILE cc_start: 0.8136 (tp) cc_final: 0.7021 (tt) REVERT: E 99 PHE cc_start: 0.7789 (m-10) cc_final: 0.7532 (m-80) REVERT: E 101 HIS cc_start: 0.7278 (m170) cc_final: 0.6687 (m170) REVERT: F 33 GLU cc_start: 0.7318 (mm-30) cc_final: 0.7039 (tm-30) REVERT: F 78 PHE cc_start: 0.7518 (m-80) cc_final: 0.7215 (m-80) REVERT: F 99 PHE cc_start: 0.7524 (m-10) cc_final: 0.7285 (m-80) REVERT: F 116 MET cc_start: 0.6719 (OUTLIER) cc_final: 0.6466 (pp-130) outliers start: 14 outliers final: 0 residues processed: 659 average time/residue: 0.1363 time to fit residues: 134.3958 Evaluate side-chains 387 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 385 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain F residue 116 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.6980 chunk 98 optimal weight: 0.5980 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.0170 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 overall best weight: 0.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 ASN A 920 ASN B 411 ASN B 412 HIS B 435 HIS B 461 ASN C 587 GLN C 726 ASN C 747 ASN C 920 ASN C 950 HIS D 411 ASN D 435 HIS D 461 ASN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.167752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.112198 restraints weight = 33435.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.116097 restraints weight = 19345.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.116408 restraints weight = 13344.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.116892 restraints weight = 13075.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.117046 restraints weight = 12516.950| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19433 Z= 0.161 Angle : 0.822 11.444 26072 Z= 0.423 Chirality : 0.045 0.191 2836 Planarity : 0.006 0.079 3142 Dihedral : 16.290 161.009 3038 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.62 % Allowed : 10.11 % Favored : 89.27 % Rotamer: Outliers : 4.44 % Allowed : 15.83 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.95 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.92 (0.15), residues: 2264 helix: -1.80 (0.12), residues: 1354 sheet: -3.82 (0.35), residues: 142 loop : -3.63 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 684 TYR 0.034 0.002 TYR D 450 PHE 0.032 0.002 PHE A 901 TRP 0.017 0.002 TRP B 671 HIS 0.013 0.002 HIS B 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (19427) covalent geometry : angle 0.82089 / 0.42 (26060) SS BOND : bond 0.00931 / 0.45 ( 6) SS BOND : angle 1.84131 / 1.18 ( 12) hydrogen bonds : bond 0.04699 / 3.08 ( 834) hydrogen bonds : angle 4.84708 / 3.41 ( 2436) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 479 time to evaluate : 0.668 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: A 581 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8538 (tp) REVERT: A 585 MET cc_start: 0.8350 (mpt) cc_final: 0.7984 (mpt) REVERT: A 670 MET cc_start: 0.9116 (OUTLIER) cc_final: 0.8877 (mtm) REVERT: A 924 MET cc_start: 0.7150 (mmm) cc_final: 0.6826 (mmp) REVERT: A 926 ARG cc_start: 0.7314 (ptm160) cc_final: 0.7097 (ptm160) REVERT: A 938 PHE cc_start: 0.8798 (m-10) cc_final: 0.8572 (m-80) REVERT: A 1016 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8572 (mt) REVERT: B 400 ILE cc_start: 0.6898 (tt) cc_final: 0.6616 (mp) REVERT: B 493 LYS cc_start: 0.8906 (mttp) cc_final: 0.8678 (tttm) REVERT: B 669 LYS cc_start: 0.9117 (pttt) cc_final: 0.8896 (pttt) REVERT: B 713 GLU cc_start: 0.8989 (tm-30) cc_final: 0.8712 (tm-30) REVERT: B 714 GLN cc_start: 0.8041 (tp-100) cc_final: 0.7332 (tp40) REVERT: B 721 MET cc_start: 0.7863 (ppp) cc_final: 0.7607 (ppp) REVERT: B 748 LEU cc_start: 0.9498 (tp) cc_final: 0.9154 (pp) REVERT: B 760 ASP cc_start: 0.9234 (m-30) cc_final: 0.8692 (t0) REVERT: B 764 ASN cc_start: 0.8864 (m-40) cc_final: 0.8158 (m-40) REVERT: C 450 TYR cc_start: 0.7105 (m-80) cc_final: 0.6333 (m-80) REVERT: C 518 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8539 (pp) REVERT: C 581 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.8948 (tp) REVERT: C 683 VAL cc_start: 0.8077 (OUTLIER) cc_final: 0.7573 (m) REVERT: C 705 GLU cc_start: 0.7267 (mt-10) cc_final: 0.7018 (mt-10) REVERT: C 713 GLU cc_start: 0.8602 (pp20) cc_final: 0.8186 (pp20) REVERT: C 714 GLN cc_start: 0.8526 (mm-40) cc_final: 0.7837 (mm-40) REVERT: C 891 PHE cc_start: 0.5603 (m-80) cc_final: 0.5248 (m-10) REVERT: C 926 ARG cc_start: 0.6355 (ttm-80) cc_final: 0.5718 (tmt170) REVERT: C 991 ARG cc_start: 0.6861 (mmt-90) cc_final: 0.6350 (mmt90) REVERT: C 1000 ASN cc_start: 0.7956 (m-40) cc_final: 0.7358 (m110) REVERT: D 493 LYS cc_start: 0.8671 (mttp) cc_final: 0.8135 (tttm) REVERT: D 533 TYR cc_start: 0.8718 (t80) cc_final: 0.8494 (t80) REVERT: D 702 TYR cc_start: 0.7616 (t80) cc_final: 0.7308 (t80) REVERT: D 714 GLN cc_start: 0.8494 (tp-100) cc_final: 0.7601 (tp40) REVERT: D 760 ASP cc_start: 0.9317 (m-30) cc_final: 0.8942 (t70) REVERT: D 762 LEU cc_start: 0.9285 (mm) cc_final: 0.9062 (mm) REVERT: E 75 HIS cc_start: 0.7537 (t70) cc_final: 0.6082 (t70) REVERT: E 78 PHE cc_start: 0.7866 (m-80) cc_final: 0.7432 (m-80) REVERT: E 87 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7538 (mm-30) REVERT: E 94 ASN cc_start: 0.7695 (p0) cc_final: 0.7360 (p0) REVERT: E 95 ILE cc_start: 0.8553 (tp) cc_final: 0.7781 (tt) REVERT: E 99 PHE cc_start: 0.7980 (m-10) cc_final: 0.7712 (m-80) REVERT: E 101 HIS cc_start: 0.7345 (m170) cc_final: 0.6243 (m170) REVERT: E 104 ARG cc_start: 0.8658 (tpt-90) cc_final: 0.8447 (tpt-90) REVERT: F 78 PHE cc_start: 0.7667 (m-80) cc_final: 0.7413 (m-80) REVERT: F 99 PHE cc_start: 0.7631 (m-10) cc_final: 0.7146 (t80) REVERT: F 101 HIS cc_start: 0.6944 (m-70) cc_final: 0.6326 (m-70) REVERT: F 104 ARG cc_start: 0.8785 (tpt90) cc_final: 0.8409 (tpt-90) outliers start: 87 outliers final: 27 residues processed: 537 average time/residue: 0.1296 time to fit residues: 105.7164 Evaluate side-chains 415 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 382 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 504 ILE Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 900 CYS Chi-restraints excluded: chain C residue 925 ILE Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 69 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 17 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 chunk 30 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 176 optimal weight: 2.9990 chunk 81 optimal weight: 0.0050 chunk 14 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 19 optimal weight: 0.3980 chunk 70 optimal weight: 0.5980 chunk 143 optimal weight: 5.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 435 HIS A 619 ASN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 714 GLN ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 950 HIS ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 ASN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.167616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.112237 restraints weight = 33625.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.115435 restraints weight = 19824.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.117173 restraints weight = 13721.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.117060 restraints weight = 13077.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.117160 restraints weight = 12603.997| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19433 Z= 0.143 Angle : 0.779 12.379 26072 Z= 0.395 Chirality : 0.045 0.219 2836 Planarity : 0.006 0.074 3142 Dihedral : 15.114 152.344 3033 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.82 % Favored : 88.87 % Rotamer: Outliers : 4.03 % Allowed : 18.23 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.95 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.76 (0.17), residues: 2264 helix: -0.73 (0.13), residues: 1336 sheet: -3.56 (0.36), residues: 148 loop : -3.37 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 108 TYR 0.030 0.002 TYR D 450 PHE 0.024 0.002 PHE F 141 TRP 0.016 0.001 TRP B 460 HIS 0.011 0.002 HIS E 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (19427) covalent geometry : angle 0.77675 / 0.39 (26060) SS BOND : bond 0.01882 / 0.90 ( 6) SS BOND : angle 2.73538 / 1.69 ( 12) hydrogen bonds : bond 0.04038 / 2.63 ( 834) hydrogen bonds : angle 4.29071 / 3.01 ( 2436) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 438 time to evaluate : 0.804 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 450 TYR cc_start: 0.7197 (m-80) cc_final: 0.6650 (m-80) REVERT: A 581 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8716 (tp) REVERT: A 585 MET cc_start: 0.8374 (mpt) cc_final: 0.8060 (mpt) REVERT: A 670 MET cc_start: 0.9157 (OUTLIER) cc_final: 0.8852 (mtm) REVERT: A 705 GLU cc_start: 0.7508 (mt-10) cc_final: 0.6568 (mt-10) REVERT: A 755 GLU cc_start: 0.8922 (mp0) cc_final: 0.8551 (mp0) REVERT: A 924 MET cc_start: 0.7146 (mmm) cc_final: 0.6521 (mmp) REVERT: A 1000 ASN cc_start: 0.7808 (m-40) cc_final: 0.7303 (m-40) REVERT: B 401 LEU cc_start: 0.8867 (pp) cc_final: 0.8455 (tp) REVERT: B 421 TYR cc_start: 0.8233 (m-10) cc_final: 0.7875 (m-10) REVERT: B 493 LYS cc_start: 0.8823 (mttp) cc_final: 0.8566 (tttm) REVERT: B 714 GLN cc_start: 0.8058 (tp-100) cc_final: 0.7394 (tp40) REVERT: B 760 ASP cc_start: 0.9157 (m-30) cc_final: 0.8613 (t70) REVERT: B 764 ASN cc_start: 0.8827 (m-40) cc_final: 0.8188 (m110) REVERT: C 450 TYR cc_start: 0.6992 (m-80) cc_final: 0.6196 (m-80) REVERT: C 483 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8738 (mp) REVERT: C 518 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8684 (pp) REVERT: C 581 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8950 (tp) REVERT: C 585 MET cc_start: 0.8287 (mmt) cc_final: 0.7705 (mmt) REVERT: C 713 GLU cc_start: 0.8542 (pp20) cc_final: 0.8076 (pp20) REVERT: C 714 GLN cc_start: 0.8471 (mm-40) cc_final: 0.7803 (mm-40) REVERT: C 865 GLU cc_start: 0.7554 (mm-30) cc_final: 0.6789 (mm-30) REVERT: C 926 ARG cc_start: 0.6453 (ttm-80) cc_final: 0.5689 (tmt170) REVERT: C 936 LEU cc_start: 0.8729 (tp) cc_final: 0.8456 (mt) REVERT: C 966 PHE cc_start: 0.8482 (m-80) cc_final: 0.8264 (m-80) REVERT: C 991 ARG cc_start: 0.6645 (mmt-90) cc_final: 0.6291 (mmt90) REVERT: C 1000 ASN cc_start: 0.8027 (m-40) cc_final: 0.7247 (m-40) REVERT: D 419 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7802 (tp30) REVERT: D 493 LYS cc_start: 0.8645 (mttp) cc_final: 0.8029 (mtpp) REVERT: D 714 GLN cc_start: 0.8481 (tp-100) cc_final: 0.7599 (tp40) REVERT: D 760 ASP cc_start: 0.9226 (m-30) cc_final: 0.8842 (t70) REVERT: D 783 LYS cc_start: 0.6636 (pmtt) cc_final: 0.6356 (ptpp) REVERT: E 75 HIS cc_start: 0.7550 (t70) cc_final: 0.6250 (t70) REVERT: E 87 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7533 (tp30) REVERT: E 94 ASN cc_start: 0.7640 (p0) cc_final: 0.7313 (p0) REVERT: E 95 ILE cc_start: 0.8506 (tp) cc_final: 0.7773 (tt) REVERT: E 99 PHE cc_start: 0.7946 (m-10) cc_final: 0.7655 (m-80) REVERT: E 101 HIS cc_start: 0.7591 (m170) cc_final: 0.6510 (m170) REVERT: F 99 PHE cc_start: 0.7353 (m-10) cc_final: 0.6976 (t80) REVERT: F 101 HIS cc_start: 0.6871 (m-70) cc_final: 0.6653 (m-70) REVERT: F 104 ARG cc_start: 0.8673 (tpt90) cc_final: 0.8316 (tpt-90) REVERT: F 123 MET cc_start: 0.5982 (mmm) cc_final: 0.5764 (mmm) outliers start: 79 outliers final: 34 residues processed: 488 average time/residue: 0.1288 time to fit residues: 96.5850 Evaluate side-chains 418 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 379 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain C residue 900 CYS Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 747 ASN Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 124 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 140 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 151 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 642 GLN ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 642 GLN D 508 GLN D 575 ASN ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.162436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.104889 restraints weight = 33724.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.107721 restraints weight = 21058.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.108450 restraints weight = 15361.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.108473 restraints weight = 14724.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.108938 restraints weight = 14265.540| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.5144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 19433 Z= 0.226 Angle : 0.816 12.415 26072 Z= 0.415 Chirality : 0.047 0.215 2836 Planarity : 0.006 0.078 3142 Dihedral : 14.951 147.347 3033 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.40 % Allowed : 11.09 % Favored : 88.52 % Rotamer: Outliers : 4.49 % Allowed : 20.79 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 7.81 % Twisted General : 0.99 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.17), residues: 2264 helix: -0.31 (0.14), residues: 1350 sheet: -3.82 (0.38), residues: 112 loop : -3.53 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 108 TYR 0.031 0.002 TYR D 450 PHE 0.035 0.002 PHE A 943 TRP 0.031 0.002 TRP B 460 HIS 0.009 0.001 HIS E 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.23 (19427) covalent geometry : angle 0.81534 / 0.41 (26060) SS BOND : bond 0.01790 / 0.86 ( 6) SS BOND : angle 2.06343 / 1.23 ( 12) hydrogen bonds : bond 0.04195 / 2.75 ( 834) hydrogen bonds : angle 4.33557 / 3.02 ( 2436) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 381 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 TYR cc_start: 0.7545 (m-80) cc_final: 0.6883 (m-80) REVERT: A 463 MET cc_start: 0.8373 (ttm) cc_final: 0.7998 (ttt) REVERT: A 581 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9043 (tp) REVERT: A 619 ASN cc_start: 0.8990 (OUTLIER) cc_final: 0.7495 (t0) REVERT: A 670 MET cc_start: 0.9169 (OUTLIER) cc_final: 0.8855 (mtm) REVERT: A 755 GLU cc_start: 0.8937 (mp0) cc_final: 0.8558 (mp0) REVERT: A 1000 ASN cc_start: 0.8030 (m-40) cc_final: 0.7286 (m-40) REVERT: A 1003 TYR cc_start: 0.8202 (m-80) cc_final: 0.7563 (m-80) REVERT: B 401 LEU cc_start: 0.8970 (pp) cc_final: 0.8601 (tp) REVERT: B 419 GLU cc_start: 0.7145 (tp30) cc_final: 0.6604 (tp30) REVERT: B 493 LYS cc_start: 0.8788 (mttp) cc_final: 0.8571 (tttm) REVERT: B 629 MET cc_start: 0.8618 (tpp) cc_final: 0.8051 (mtt) REVERT: B 637 GLU cc_start: 0.8383 (pt0) cc_final: 0.8125 (pm20) REVERT: B 714 GLN cc_start: 0.8314 (tp-100) cc_final: 0.7454 (tp40) REVERT: B 760 ASP cc_start: 0.9174 (m-30) cc_final: 0.8850 (t70) REVERT: B 762 LEU cc_start: 0.9293 (mm) cc_final: 0.8976 (mm) REVERT: C 450 TYR cc_start: 0.7444 (m-80) cc_final: 0.6550 (m-80) REVERT: C 518 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8958 (pp) REVERT: C 524 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7487 (pt0) REVERT: C 713 GLU cc_start: 0.8453 (pp20) cc_final: 0.7939 (pp20) REVERT: C 748 LEU cc_start: 0.8955 (pp) cc_final: 0.8645 (mt) REVERT: C 864 LEU cc_start: 0.7253 (mt) cc_final: 0.6668 (mt) REVERT: C 865 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6942 (mm-30) REVERT: C 880 MET cc_start: 0.7894 (tmm) cc_final: 0.7621 (tmm) REVERT: C 926 ARG cc_start: 0.6834 (ttm-80) cc_final: 0.5882 (tmt170) REVERT: C 999 PHE cc_start: 0.6946 (OUTLIER) cc_final: 0.6555 (m-10) REVERT: C 1000 ASN cc_start: 0.8080 (m-40) cc_final: 0.7437 (m-40) REVERT: C 1019 SER cc_start: 0.9496 (t) cc_final: 0.9273 (t) REVERT: D 419 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7602 (tp30) REVERT: D 421 TYR cc_start: 0.8125 (m-10) cc_final: 0.7897 (m-10) REVERT: D 431 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8200 (mp0) REVERT: D 493 LYS cc_start: 0.8642 (mttp) cc_final: 0.8168 (mtpp) REVERT: D 714 GLN cc_start: 0.8500 (tp-100) cc_final: 0.7715 (tm-30) REVERT: D 748 LEU cc_start: 0.9515 (tp) cc_final: 0.9080 (pp) REVERT: D 760 ASP cc_start: 0.9278 (m-30) cc_final: 0.8782 (t0) REVERT: E 14 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8488 (mp) REVERT: E 27 HIS cc_start: 0.7181 (t-90) cc_final: 0.6863 (t-90) REVERT: E 75 HIS cc_start: 0.7597 (t70) cc_final: 0.7131 (t70) REVERT: E 78 PHE cc_start: 0.7856 (m-80) cc_final: 0.7653 (m-80) REVERT: E 95 ILE cc_start: 0.8521 (tp) cc_final: 0.7711 (tt) REVERT: E 99 PHE cc_start: 0.7952 (m-10) cc_final: 0.7611 (m-80) REVERT: E 101 HIS cc_start: 0.7943 (m170) cc_final: 0.7494 (m-70) REVERT: E 108 ARG cc_start: 0.6343 (mmm160) cc_final: 0.5864 (mmm160) REVERT: E 134 GLU cc_start: 0.7589 (tm-30) cc_final: 0.6977 (tm-30) REVERT: F 99 PHE cc_start: 0.7511 (m-10) cc_final: 0.7057 (t80) REVERT: F 101 HIS cc_start: 0.7214 (m-70) cc_final: 0.6773 (m-70) REVERT: F 104 ARG cc_start: 0.8715 (tpt90) cc_final: 0.8463 (tpt-90) REVERT: F 123 MET cc_start: 0.5952 (mmm) cc_final: 0.5729 (mmm) outliers start: 88 outliers final: 49 residues processed: 440 average time/residue: 0.1218 time to fit residues: 83.7459 Evaluate side-chains 401 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 344 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 469 TYR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1005 TRP Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 469 TYR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain C residue 900 CYS Chi-restraints excluded: chain C residue 999 PHE Chi-restraints excluded: chain C residue 1005 TRP Chi-restraints excluded: chain C residue 1016 LEU Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 495 PHE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 747 ASN Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 124 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 193 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 37 optimal weight: 0.0030 chunk 54 optimal weight: 0.6980 chunk 138 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 85 optimal weight: 0.8980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 642 GLN A 874 GLN ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 874 GLN C 883 HIS D 575 ASN ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.166486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.112447 restraints weight = 33573.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.115609 restraints weight = 20104.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.115080 restraints weight = 14078.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.115324 restraints weight = 14089.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.115500 restraints weight = 13482.956| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.5561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19433 Z= 0.145 Angle : 0.764 13.307 26072 Z= 0.385 Chirality : 0.044 0.222 2836 Planarity : 0.005 0.068 3142 Dihedral : 14.250 146.303 3033 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.47 % Favored : 89.27 % Rotamer: Outliers : 4.19 % Allowed : 22.98 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.86 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.18), residues: 2264 helix: 0.14 (0.14), residues: 1350 sheet: -3.20 (0.39), residues: 122 loop : -3.39 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 108 TYR 0.029 0.002 TYR D 450 PHE 0.031 0.002 PHE A 943 TRP 0.051 0.001 TRP B 460 HIS 0.009 0.001 HIS E 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (19427) covalent geometry : angle 0.76068 / 0.38 (26060) SS BOND : bond 0.01543 / 0.74 ( 6) SS BOND : angle 3.36231 / 2.05 ( 12) hydrogen bonds : bond 0.03614 / 2.37 ( 834) hydrogen bonds : angle 4.01327 / 2.82 ( 2436) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 401 time to evaluate : 0.484 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: A 450 TYR cc_start: 0.7397 (m-80) cc_final: 0.6650 (m-80) REVERT: A 463 MET cc_start: 0.8258 (ttm) cc_final: 0.7898 (ttm) REVERT: A 581 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.8969 (tp) REVERT: A 670 MET cc_start: 0.9181 (OUTLIER) cc_final: 0.8816 (mtm) REVERT: A 721 MET cc_start: 0.8391 (ptm) cc_final: 0.8164 (ptp) REVERT: A 755 GLU cc_start: 0.8926 (mp0) cc_final: 0.8557 (mp0) REVERT: A 1000 ASN cc_start: 0.7884 (m-40) cc_final: 0.7209 (m-40) REVERT: A 1003 TYR cc_start: 0.8259 (m-80) cc_final: 0.7789 (m-80) REVERT: B 419 GLU cc_start: 0.6884 (tp30) cc_final: 0.6527 (tp30) REVERT: B 493 LYS cc_start: 0.8708 (mttp) cc_final: 0.8196 (mtpp) REVERT: B 638 ASP cc_start: 0.8942 (p0) cc_final: 0.8711 (p0) REVERT: B 714 GLN cc_start: 0.8253 (tp-100) cc_final: 0.7426 (tp40) REVERT: B 748 LEU cc_start: 0.9476 (tp) cc_final: 0.9154 (pp) REVERT: B 760 ASP cc_start: 0.9118 (m-30) cc_final: 0.8597 (t70) REVERT: B 762 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8887 (mm) REVERT: B 764 ASN cc_start: 0.8846 (m-40) cc_final: 0.8364 (m110) REVERT: C 450 TYR cc_start: 0.7315 (m-80) cc_final: 0.6504 (m-80) REVERT: C 518 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8854 (pp) REVERT: C 705 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7047 (mt-10) REVERT: C 713 GLU cc_start: 0.8470 (pp20) cc_final: 0.8039 (pp20) REVERT: C 748 LEU cc_start: 0.8913 (pp) cc_final: 0.8616 (mt) REVERT: C 880 MET cc_start: 0.7753 (tmm) cc_final: 0.5644 (tmm) REVERT: C 926 ARG cc_start: 0.6812 (ttm-80) cc_final: 0.5866 (tmt170) REVERT: C 1000 ASN cc_start: 0.7817 (m-40) cc_final: 0.7498 (m-40) REVERT: C 1019 SER cc_start: 0.9473 (t) cc_final: 0.9270 (t) REVERT: D 419 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7651 (tp30) REVERT: D 421 TYR cc_start: 0.8070 (m-10) cc_final: 0.7800 (m-10) REVERT: D 431 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8121 (mp0) REVERT: D 493 LYS cc_start: 0.8567 (mttp) cc_final: 0.8339 (tttm) REVERT: D 519 ASP cc_start: 0.7833 (OUTLIER) cc_final: 0.7603 (m-30) REVERT: D 714 GLN cc_start: 0.8466 (tp-100) cc_final: 0.7726 (tm-30) REVERT: D 748 LEU cc_start: 0.9490 (tp) cc_final: 0.9088 (pp) REVERT: D 760 ASP cc_start: 0.9224 (m-30) cc_final: 0.8618 (t0) REVERT: D 764 ASN cc_start: 0.9024 (m-40) cc_final: 0.8558 (m-40) REVERT: D 783 LYS cc_start: 0.6940 (pmtt) cc_final: 0.6578 (ptpp) REVERT: E 27 HIS cc_start: 0.7224 (t-90) cc_final: 0.6895 (t70) REVERT: E 75 HIS cc_start: 0.7580 (t70) cc_final: 0.7137 (t70) REVERT: E 87 GLU cc_start: 0.7463 (tp30) cc_final: 0.7141 (tp30) REVERT: E 99 PHE cc_start: 0.7934 (m-10) cc_final: 0.7713 (t80) REVERT: E 101 HIS cc_start: 0.7880 (m170) cc_final: 0.7453 (m-70) REVERT: E 123 MET cc_start: 0.6044 (mmm) cc_final: 0.5168 (mmm) REVERT: E 134 GLU cc_start: 0.7346 (tm-30) cc_final: 0.6839 (tm-30) REVERT: F 99 PHE cc_start: 0.7510 (m-10) cc_final: 0.7050 (t80) REVERT: F 101 HIS cc_start: 0.7188 (m-70) cc_final: 0.6593 (m-70) REVERT: C 1107 GLU cc_start: 0.4452 (mm-30) cc_final: 0.4011 (mm-30) outliers start: 82 outliers final: 50 residues processed: 453 average time/residue: 0.1223 time to fit residues: 86.3096 Evaluate side-chains 407 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 351 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 469 TYR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 688 GLU Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1005 TRP Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 469 TYR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain C residue 900 CYS Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain C residue 1016 LEU Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 519 ASP Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 747 ASN Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 151 TYR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 124 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 72 optimal weight: 2.9990 chunk 127 optimal weight: 0.0050 chunk 192 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 156 optimal weight: 9.9990 chunk 167 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 222 optimal weight: 10.0000 chunk 15 optimal weight: 0.7980 overall best weight: 2.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 642 GLN ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 ASN ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN ** F 101 HIS ** 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 = 0.4157 r_free = 0.4157 target = 0.161029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.103881 restraints weight = 33327.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.106702 restraints weight = 21673.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.107438 restraints weight = 14547.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.107347 restraints weight = 14835.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.107502 restraints weight = 14042.427| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 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 : 0.006 0.053 19433 Z= 0.256 Angle : 0.845 13.960 26072 Z= 0.426 Chirality : 0.048 0.285 2836 Planarity : 0.006 0.072 3142 Dihedral : 14.476 143.655 3033 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.35 % Favored : 88.38 % Rotamer: Outliers : 4.60 % Allowed : 23.85 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 7.81 % Twisted General : 0.81 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.18), residues: 2264 helix: 0.18 (0.14), residues: 1350 sheet: -3.06 (0.38), residues: 136 loop : -3.53 (0.20), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 675 TYR 0.044 0.002 TYR B 673 PHE 0.033 0.002 PHE E 146 TRP 0.065 0.002 TRP B 460 HIS 0.010 0.002 HIS E 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00600 / 0.26 (19427) covalent geometry : angle 0.84422 / 0.43 (26060) SS BOND : bond 0.00841 / 0.41 ( 6) SS BOND : angle 1.91986 / 1.16 ( 12) hydrogen bonds : bond 0.04117 / 2.72 ( 834) hydrogen bonds : angle 4.24360 / 2.96 ( 2436) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 375 time to evaluate : 0.696 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: A 463 MET cc_start: 0.8384 (ttm) cc_final: 0.8080 (ttm) REVERT: A 581 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.8876 (tp) REVERT: A 619 ASN cc_start: 0.8968 (OUTLIER) cc_final: 0.7907 (t0) REVERT: A 670 MET cc_start: 0.9193 (OUTLIER) cc_final: 0.8852 (mtm) REVERT: A 755 GLU cc_start: 0.8921 (mp0) cc_final: 0.8678 (mp0) REVERT: A 865 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7305 (mm-30) REVERT: A 988 MET cc_start: 0.8774 (mmp) cc_final: 0.8480 (mmm) REVERT: A 1000 ASN cc_start: 0.7854 (m-40) cc_final: 0.7184 (m-40) REVERT: A 1029 MET cc_start: 0.7905 (mmm) cc_final: 0.7666 (mmm) REVERT: B 407 MET cc_start: 0.7198 (mpp) cc_final: 0.6708 (mpp) REVERT: B 419 GLU cc_start: 0.7044 (tp30) cc_final: 0.6535 (tp30) REVERT: B 491 PHE cc_start: 0.6340 (OUTLIER) cc_final: 0.5987 (t80) REVERT: B 493 LYS cc_start: 0.8810 (mttp) cc_final: 0.8322 (mtpp) REVERT: B 714 GLN cc_start: 0.8328 (tp-100) cc_final: 0.7631 (tm-30) REVERT: B 760 ASP cc_start: 0.9140 (m-30) cc_final: 0.8781 (t70) REVERT: B 762 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8898 (mm) REVERT: C 518 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9045 (pp) REVERT: C 713 GLU cc_start: 0.8504 (pp20) cc_final: 0.8001 (pp20) REVERT: C 716 LYS cc_start: 0.8557 (mmtm) cc_final: 0.8140 (ptmm) REVERT: C 748 LEU cc_start: 0.8966 (pp) cc_final: 0.8673 (mt) REVERT: C 926 ARG cc_start: 0.6866 (ttm-80) cc_final: 0.5915 (tmt170) REVERT: C 988 MET cc_start: 0.8623 (mmm) cc_final: 0.8403 (mmm) REVERT: C 999 PHE cc_start: 0.6965 (OUTLIER) cc_final: 0.6414 (m-80) REVERT: C 1000 ASN cc_start: 0.7980 (m-40) cc_final: 0.7610 (m-40) REVERT: D 419 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7647 (tp30) REVERT: D 431 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8115 (mp0) REVERT: D 493 LYS cc_start: 0.8662 (mttp) cc_final: 0.8276 (mtpp) REVERT: D 714 GLN cc_start: 0.8494 (tp-100) cc_final: 0.7736 (tp40) REVERT: D 748 LEU cc_start: 0.9360 (tp) cc_final: 0.9032 (pp) REVERT: D 760 ASP cc_start: 0.9212 (m-30) cc_final: 0.8718 (t0) REVERT: E 27 HIS cc_start: 0.7371 (t-90) cc_final: 0.7081 (t70) REVERT: E 75 HIS cc_start: 0.7719 (t70) cc_final: 0.7406 (t70) REVERT: E 87 GLU cc_start: 0.7627 (tp30) cc_final: 0.7321 (tp30) REVERT: E 99 PHE cc_start: 0.7966 (m-10) cc_final: 0.7593 (t80) REVERT: E 101 HIS cc_start: 0.8090 (m170) cc_final: 0.7563 (m-70) REVERT: E 134 GLU cc_start: 0.7387 (tm-30) cc_final: 0.6871 (tm-30) REVERT: F 99 PHE cc_start: 0.7512 (m-10) cc_final: 0.7090 (t80) REVERT: F 101 HIS cc_start: 0.7490 (m-70) cc_final: 0.6520 (m-70) outliers start: 90 outliers final: 58 residues processed: 430 average time/residue: 0.1198 time to fit residues: 81.0535 Evaluate side-chains 404 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 338 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 469 TYR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 688 GLU Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1005 TRP Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 469 TYR Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 900 CYS Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 999 PHE Chi-restraints excluded: chain C residue 1005 TRP Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain C residue 1016 LEU Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 495 PHE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 747 ASN Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 151 TYR Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 124 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 195 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 151 optimal weight: 0.7980 chunk 170 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 642 GLN ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 985 ASN ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.166957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.114026 restraints weight = 33386.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.116920 restraints weight = 18491.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.116195 restraints weight = 13149.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.117073 restraints weight = 13694.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.117073 restraints weight = 13100.936| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.6040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19433 Z= 0.189 Angle : 0.800 14.131 26072 Z= 0.402 Chirality : 0.046 0.219 2836 Planarity : 0.005 0.074 3142 Dihedral : 14.118 142.752 3033 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.04 % Favored : 88.78 % Rotamer: Outliers : 4.14 % Allowed : 24.46 % Favored : 71.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.77 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.18), residues: 2264 helix: 0.30 (0.14), residues: 1362 sheet: -3.65 (0.37), residues: 132 loop : -3.50 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 108 TYR 0.034 0.002 TYR D 673 PHE 0.031 0.002 PHE A 943 TRP 0.068 0.002 TRP B 460 HIS 0.009 0.001 HIS E 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 (19427) covalent geometry : angle 0.79749 / 0.40 (26060) SS BOND : bond 0.01173 / 0.56 ( 6) SS BOND : angle 2.82637 / 1.59 ( 12) hydrogen bonds : bond 0.03825 / 2.52 ( 834) hydrogen bonds : angle 4.07353 / 2.85 ( 2436) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 372 time to evaluate : 0.651 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: A 450 TYR cc_start: 0.7537 (m-80) cc_final: 0.7299 (m-80) REVERT: A 463 MET cc_start: 0.8133 (ttm) cc_final: 0.7855 (ttt) REVERT: A 581 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.8786 (tp) REVERT: A 585 MET cc_start: 0.8257 (mpt) cc_final: 0.7688 (mpt) REVERT: A 619 ASN cc_start: 0.8826 (OUTLIER) cc_final: 0.7926 (t0) REVERT: A 670 MET cc_start: 0.9056 (OUTLIER) cc_final: 0.8730 (mtm) REVERT: A 865 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7203 (mm-30) REVERT: A 988 MET cc_start: 0.8729 (mmp) cc_final: 0.8399 (mmm) REVERT: A 1000 ASN cc_start: 0.7711 (m-40) cc_final: 0.7147 (m110) REVERT: A 1029 MET cc_start: 0.7808 (mmm) cc_final: 0.7567 (mmm) REVERT: B 407 MET cc_start: 0.7458 (mpp) cc_final: 0.7045 (mpp) REVERT: B 419 GLU cc_start: 0.6977 (tp30) cc_final: 0.6447 (tp30) REVERT: B 491 PHE cc_start: 0.6055 (OUTLIER) cc_final: 0.5729 (t80) REVERT: B 493 LYS cc_start: 0.8725 (mttp) cc_final: 0.8290 (mtpp) REVERT: B 629 MET cc_start: 0.8369 (tpp) cc_final: 0.7971 (mtt) REVERT: B 714 GLN cc_start: 0.8286 (tp-100) cc_final: 0.7649 (tm-30) REVERT: B 748 LEU cc_start: 0.9473 (tp) cc_final: 0.9108 (pp) REVERT: B 760 ASP cc_start: 0.9027 (m-30) cc_final: 0.8677 (t70) REVERT: C 518 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8954 (pp) REVERT: C 713 GLU cc_start: 0.8508 (pp20) cc_final: 0.8037 (pp20) REVERT: C 716 LYS cc_start: 0.8412 (mmtm) cc_final: 0.8048 (ttpp) REVERT: C 748 LEU cc_start: 0.8878 (pp) cc_final: 0.8605 (mt) REVERT: C 926 ARG cc_start: 0.6550 (ttm-80) cc_final: 0.5882 (tmt170) REVERT: C 988 MET cc_start: 0.8617 (mmm) cc_final: 0.8386 (mmm) REVERT: C 1000 ASN cc_start: 0.7863 (m-40) cc_final: 0.7536 (m-40) REVERT: D 419 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7444 (tp30) REVERT: D 421 TYR cc_start: 0.8187 (m-10) cc_final: 0.7865 (m-10) REVERT: D 431 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8103 (mp0) REVERT: D 493 LYS cc_start: 0.8669 (mttp) cc_final: 0.8191 (mtpp) REVERT: D 519 ASP cc_start: 0.7900 (OUTLIER) cc_final: 0.7661 (m-30) REVERT: D 714 GLN cc_start: 0.8435 (tp-100) cc_final: 0.7815 (tm-30) REVERT: D 748 LEU cc_start: 0.9483 (tp) cc_final: 0.9055 (pp) REVERT: D 760 ASP cc_start: 0.9093 (m-30) cc_final: 0.8602 (t70) REVERT: D 781 LYS cc_start: 0.5099 (tptt) cc_final: 0.4384 (mmtp) REVERT: E 75 HIS cc_start: 0.7672 (t70) cc_final: 0.7372 (t70) REVERT: E 87 GLU cc_start: 0.7633 (tp30) cc_final: 0.7341 (tp30) REVERT: E 99 PHE cc_start: 0.7891 (m-10) cc_final: 0.7576 (t80) REVERT: E 101 HIS cc_start: 0.8074 (m170) cc_final: 0.7545 (m-70) REVERT: E 123 MET cc_start: 0.5921 (mmm) cc_final: 0.5014 (mmm) REVERT: F 64 LEU cc_start: 0.7813 (mt) cc_final: 0.7391 (pp) REVERT: F 99 PHE cc_start: 0.7487 (m-10) cc_final: 0.7153 (t80) REVERT: F 101 HIS cc_start: 0.7505 (m-70) cc_final: 0.6193 (m-70) outliers start: 81 outliers final: 53 residues processed: 422 average time/residue: 0.1130 time to fit residues: 75.1017 Evaluate side-chains 400 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 340 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 469 TYR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 688 GLU Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1005 TRP Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 469 TYR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 900 CYS Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain C residue 1016 LEU Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 495 PHE Chi-restraints excluded: chain D residue 519 ASP Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 747 ASN Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 151 TYR Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 124 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 142 optimal weight: 0.7980 chunk 52 optimal weight: 9.9990 chunk 130 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 210 optimal weight: 0.3980 chunk 115 optimal weight: 0.5980 chunk 6 optimal weight: 0.0040 chunk 198 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 189 optimal weight: 1.9990 chunk 105 optimal weight: 0.2980 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 642 GLN ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 411 ASN ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 HIS ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.171014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.118644 restraints weight = 33212.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.121420 restraints weight = 18974.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.121553 restraints weight = 13468.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.122164 restraints weight = 12548.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.122373 restraints weight = 11975.440| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.6371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19433 Z= 0.144 Angle : 0.795 16.545 26072 Z= 0.394 Chirality : 0.045 0.230 2836 Planarity : 0.005 0.070 3142 Dihedral : 13.482 140.807 3033 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.69 % Favored : 89.27 % Rotamer: Outliers : 3.17 % Allowed : 26.00 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.54 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.18), residues: 2264 helix: 0.61 (0.15), residues: 1332 sheet: -3.72 (0.33), residues: 168 loop : -3.33 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 675 TYR 0.042 0.002 TYR F 100 PHE 0.032 0.002 PHE A 943 TRP 0.024 0.001 TRP C 887 HIS 0.009 0.002 HIS E 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (19427) covalent geometry : angle 0.79219 / 0.39 (26060) SS BOND : bond 0.01555 / 0.74 ( 6) SS BOND : angle 3.35860 / 2.07 ( 12) hydrogen bonds : bond 0.03509 / 2.31 ( 834) hydrogen bonds : angle 3.95043 / 2.78 ( 2436) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 387 time to evaluate : 0.610 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: A 450 TYR cc_start: 0.7257 (m-80) cc_final: 0.6886 (m-80) REVERT: A 463 MET cc_start: 0.7950 (ttm) cc_final: 0.7687 (ttt) REVERT: A 524 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7335 (pt0) REVERT: A 581 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8770 (tp) REVERT: A 670 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8634 (mtm) REVERT: A 891 PHE cc_start: 0.6399 (m-10) cc_final: 0.5942 (m-10) REVERT: A 988 MET cc_start: 0.8733 (mmp) cc_final: 0.8448 (mmm) REVERT: A 1000 ASN cc_start: 0.7585 (m-40) cc_final: 0.7111 (m110) REVERT: A 1029 MET cc_start: 0.7805 (mmm) cc_final: 0.7567 (mmm) REVERT: B 407 MET cc_start: 0.7396 (mpp) cc_final: 0.7088 (mpp) REVERT: B 422 GLU cc_start: 0.6863 (pp20) cc_final: 0.6450 (pm20) REVERT: B 491 PHE cc_start: 0.5834 (OUTLIER) cc_final: 0.5613 (t80) REVERT: B 493 LYS cc_start: 0.8646 (mttp) cc_final: 0.8274 (mtpp) REVERT: B 714 GLN cc_start: 0.8223 (tp-100) cc_final: 0.7559 (tm-30) REVERT: B 760 ASP cc_start: 0.9000 (m-30) cc_final: 0.8440 (t70) REVERT: B 764 ASN cc_start: 0.8767 (m-40) cc_final: 0.8152 (m110) REVERT: C 408 MET cc_start: 0.7102 (tpp) cc_final: 0.6288 (tpp) REVERT: C 450 TYR cc_start: 0.7595 (m-80) cc_final: 0.7016 (m-80) REVERT: C 518 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8859 (pp) REVERT: C 591 ILE cc_start: 0.7081 (OUTLIER) cc_final: 0.6642 (tp) REVERT: C 713 GLU cc_start: 0.8481 (pp20) cc_final: 0.8260 (pp20) REVERT: C 716 LYS cc_start: 0.8358 (mmtm) cc_final: 0.7948 (ttpp) REVERT: C 748 LEU cc_start: 0.8858 (pp) cc_final: 0.8587 (mt) REVERT: C 926 ARG cc_start: 0.6419 (ttm-80) cc_final: 0.5840 (tmt170) REVERT: C 988 MET cc_start: 0.8637 (mmm) cc_final: 0.8412 (mmm) REVERT: C 998 TYR cc_start: 0.8313 (p90) cc_final: 0.7894 (p90) REVERT: C 1000 ASN cc_start: 0.7701 (m-40) cc_final: 0.7331 (m-40) REVERT: D 408 MET cc_start: 0.6419 (tpp) cc_final: 0.6189 (tpt) REVERT: D 419 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7362 (tp30) REVERT: D 431 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8076 (mp0) REVERT: D 493 LYS cc_start: 0.8573 (mttp) cc_final: 0.8071 (mtpp) REVERT: D 633 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8177 (mt) REVERT: D 714 GLN cc_start: 0.8363 (tp-100) cc_final: 0.7653 (tp40) REVERT: D 748 LEU cc_start: 0.9510 (tp) cc_final: 0.9067 (pp) REVERT: D 760 ASP cc_start: 0.8986 (m-30) cc_final: 0.8546 (t70) REVERT: D 783 LYS cc_start: 0.6880 (pmtt) cc_final: 0.6415 (ptpp) REVERT: E 75 HIS cc_start: 0.7651 (t70) cc_final: 0.7313 (t70) REVERT: E 87 GLU cc_start: 0.7609 (tp30) cc_final: 0.7283 (tp30) REVERT: E 99 PHE cc_start: 0.7956 (m-10) cc_final: 0.7642 (t80) REVERT: E 101 HIS cc_start: 0.7965 (m170) cc_final: 0.7469 (m-70) REVERT: E 123 MET cc_start: 0.6037 (mmm) cc_final: 0.5486 (mmm) REVERT: F 64 LEU cc_start: 0.7591 (mt) cc_final: 0.7238 (pp) REVERT: F 99 PHE cc_start: 0.7228 (m-10) cc_final: 0.6972 (t80) REVERT: F 101 HIS cc_start: 0.6904 (m-70) cc_final: 0.6092 (m-70) outliers start: 62 outliers final: 43 residues processed: 424 average time/residue: 0.1218 time to fit residues: 80.8959 Evaluate side-chains 397 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 347 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 469 TYR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 688 GLU Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1005 TRP Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain C residue 469 TYR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain C residue 900 CYS Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain C residue 1016 LEU Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 495 PHE Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 747 ASN Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 118 ASP Chi-restraints excluded: chain F residue 124 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 61 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 146 optimal weight: 0.9990 chunk 145 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 169 optimal weight: 20.0000 chunk 64 optimal weight: 3.9990 chunk 26 optimal weight: 0.0050 chunk 136 optimal weight: 0.1980 overall best weight: 1.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 747 ASN ** D 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.170270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.116222 restraints weight = 32958.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.120094 restraints weight = 19020.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.121432 restraints weight = 12117.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.121394 restraints weight = 12343.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.121592 restraints weight = 11452.868| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.6469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 19433 Z= 0.199 Angle : 0.834 14.474 26072 Z= 0.416 Chirality : 0.049 0.391 2836 Planarity : 0.006 0.070 3142 Dihedral : 13.565 138.565 3033 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.09 % Favored : 88.78 % Rotamer: Outliers : 3.32 % Allowed : 26.61 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.59 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.18), residues: 2264 helix: 0.68 (0.15), residues: 1306 sheet: -3.50 (0.33), residues: 182 loop : -3.23 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 453 TYR 0.040 0.002 TYR D 673 PHE 0.034 0.002 PHE A1028 TRP 0.023 0.002 TRP D 460 HIS 0.010 0.001 HIS E 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.20 (19427) covalent geometry : angle 0.83253 / 0.42 (26060) SS BOND : bond 0.00786 / 0.38 ( 6) SS BOND : angle 2.66432 / 1.62 ( 12) hydrogen bonds : bond 0.03779 / 2.48 ( 834) hydrogen bonds : angle 4.12024 / 2.88 ( 2436) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 355 time to evaluate : 0.629 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: A 450 TYR cc_start: 0.7439 (m-80) cc_final: 0.7168 (m-80) REVERT: A 463 MET cc_start: 0.7987 (ttm) cc_final: 0.7602 (ttt) REVERT: A 581 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.8703 (tp) REVERT: A 585 MET cc_start: 0.8228 (mpt) cc_final: 0.7588 (mpt) REVERT: A 619 ASN cc_start: 0.8931 (OUTLIER) cc_final: 0.8298 (t0) REVERT: A 670 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.8744 (mtm) REVERT: A 721 MET cc_start: 0.8974 (pmm) cc_final: 0.8676 (pmm) REVERT: A 865 GLU cc_start: 0.7472 (mm-30) cc_final: 0.7250 (mm-30) REVERT: A 988 MET cc_start: 0.8708 (mmp) cc_final: 0.8369 (mmm) REVERT: A 1000 ASN cc_start: 0.7544 (m-40) cc_final: 0.7127 (m110) REVERT: B 407 MET cc_start: 0.7451 (mpp) cc_final: 0.7087 (mpp) REVERT: B 491 PHE cc_start: 0.5951 (OUTLIER) cc_final: 0.5704 (t80) REVERT: B 493 LYS cc_start: 0.8692 (mttp) cc_final: 0.8363 (mtpp) REVERT: B 629 MET cc_start: 0.8162 (tpp) cc_final: 0.7745 (mtt) REVERT: B 714 GLN cc_start: 0.8216 (tp-100) cc_final: 0.7694 (tm-30) REVERT: B 760 ASP cc_start: 0.8975 (m-30) cc_final: 0.8634 (t70) REVERT: B 772 GLU cc_start: 0.5327 (mm-30) cc_final: 0.4654 (mt-10) REVERT: C 408 MET cc_start: 0.7585 (tpp) cc_final: 0.7062 (tpp) REVERT: C 518 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8988 (pp) REVERT: C 716 LYS cc_start: 0.8275 (mmtm) cc_final: 0.7817 (ttpp) REVERT: C 748 LEU cc_start: 0.8868 (pp) cc_final: 0.8593 (mm) REVERT: C 781 LYS cc_start: 0.8029 (mppt) cc_final: 0.7428 (pttp) REVERT: C 926 ARG cc_start: 0.6454 (ttm-80) cc_final: 0.5905 (tmt170) REVERT: C 988 MET cc_start: 0.8644 (mmm) cc_final: 0.8431 (mmm) REVERT: C 1000 ASN cc_start: 0.7733 (m-40) cc_final: 0.7525 (m-40) REVERT: D 408 MET cc_start: 0.6089 (tpp) cc_final: 0.5566 (tpt) REVERT: D 431 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.8043 (mp0) REVERT: D 493 LYS cc_start: 0.8669 (mttp) cc_final: 0.8298 (mtpp) REVERT: D 633 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8141 (mt) REVERT: D 714 GLN cc_start: 0.8372 (tp-100) cc_final: 0.7707 (tm-30) REVERT: D 748 LEU cc_start: 0.9506 (tp) cc_final: 0.9078 (pp) REVERT: D 760 ASP cc_start: 0.8893 (m-30) cc_final: 0.8440 (t0) REVERT: D 764 ASN cc_start: 0.8899 (m-40) cc_final: 0.8338 (m-40) REVERT: E 75 HIS cc_start: 0.7627 (t70) cc_final: 0.7360 (t70) REVERT: E 87 GLU cc_start: 0.7567 (tp30) cc_final: 0.7271 (tp30) REVERT: E 99 PHE cc_start: 0.7920 (m-10) cc_final: 0.7626 (t80) REVERT: E 101 HIS cc_start: 0.8137 (m170) cc_final: 0.7540 (m-70) REVERT: E 123 MET cc_start: 0.6045 (mmm) cc_final: 0.5500 (mmm) REVERT: F 64 LEU cc_start: 0.7677 (mt) cc_final: 0.7292 (pp) REVERT: F 99 PHE cc_start: 0.6940 (m-10) cc_final: 0.6735 (t80) REVERT: F 101 HIS cc_start: 0.7179 (m-70) cc_final: 0.6020 (m-70) REVERT: F 151 TYR cc_start: 0.6934 (OUTLIER) cc_final: 0.6352 (t80) outliers start: 65 outliers final: 48 residues processed: 393 average time/residue: 0.1189 time to fit residues: 73.5178 Evaluate side-chains 390 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 334 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 469 TYR Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 688 GLU Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1005 TRP Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 469 TYR Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 900 CYS Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain C residue 1016 LEU Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 495 PHE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 747 ASN Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 151 TYR Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 118 ASP Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 124 ASN Chi-restraints excluded: chain F residue 151 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 91 optimal weight: 6.9990 chunk 165 optimal weight: 0.5980 chunk 101 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 127 optimal weight: 0.6980 chunk 168 optimal weight: 0.7980 chunk 46 optimal weight: 10.0000 chunk 222 optimal weight: 5.9990 chunk 226 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 747 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN ** F 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.171734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.117301 restraints weight = 33126.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.121479 restraints weight = 17155.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.124242 restraints weight = 12470.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.125246 restraints weight = 10589.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.126032 restraints weight = 9860.224| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.6617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 19433 Z= 0.171 Angle : 0.839 15.338 26072 Z= 0.417 Chirality : 0.047 0.232 2836 Planarity : 0.005 0.070 3142 Dihedral : 13.358 137.775 3033 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.95 % Favored : 89.00 % Rotamer: Outliers : 3.01 % Allowed : 27.27 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.54 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.18), residues: 2264 helix: 0.72 (0.15), residues: 1304 sheet: -3.09 (0.37), residues: 162 loop : -3.28 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 104 TYR 0.039 0.002 TYR B 450 PHE 0.034 0.002 PHE A1028 TRP 0.016 0.001 TRP C 887 HIS 0.009 0.001 HIS E 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (19427) covalent geometry : angle 0.83613 / 0.42 (26060) SS BOND : bond 0.00649 / 0.31 ( 6) SS BOND : angle 3.43285 / 2.00 ( 12) hydrogen bonds : bond 0.03670 / 2.42 ( 834) hydrogen bonds : angle 4.09184 / 2.87 ( 2436) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 348 time to evaluate : 0.471 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: A 450 TYR cc_start: 0.7338 (m-80) cc_final: 0.7135 (m-80) REVERT: A 463 MET cc_start: 0.7756 (ttm) cc_final: 0.7534 (ttt) REVERT: A 524 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7445 (pt0) REVERT: A 581 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.8725 (tp) REVERT: A 585 MET cc_start: 0.8137 (mpt) cc_final: 0.7576 (mpt) REVERT: A 721 MET cc_start: 0.8974 (pmm) cc_final: 0.8708 (pmm) REVERT: A 988 MET cc_start: 0.8652 (mmp) cc_final: 0.8357 (mmm) REVERT: A 1000 ASN cc_start: 0.7479 (m-40) cc_final: 0.7060 (m110) REVERT: B 407 MET cc_start: 0.7408 (mpp) cc_final: 0.7081 (mpp) REVERT: B 493 LYS cc_start: 0.8666 (mttp) cc_final: 0.8327 (mtpp) REVERT: B 714 GLN cc_start: 0.8198 (tp-100) cc_final: 0.7660 (tm-30) REVERT: B 760 ASP cc_start: 0.8900 (m-30) cc_final: 0.8605 (t70) REVERT: B 772 GLU cc_start: 0.5277 (mm-30) cc_final: 0.4702 (mt-10) REVERT: C 518 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8927 (pp) REVERT: C 591 ILE cc_start: 0.6730 (OUTLIER) cc_final: 0.6331 (tp) REVERT: C 713 GLU cc_start: 0.8725 (pp20) cc_final: 0.8169 (pp20) REVERT: C 716 LYS cc_start: 0.8040 (mmtm) cc_final: 0.7702 (ttpp) REVERT: C 748 LEU cc_start: 0.8824 (pp) cc_final: 0.8572 (mm) REVERT: C 781 LYS cc_start: 0.8078 (mppt) cc_final: 0.7434 (pttp) REVERT: C 926 ARG cc_start: 0.6306 (ttm-80) cc_final: 0.5872 (tmt170) REVERT: C 988 MET cc_start: 0.8524 (mmm) cc_final: 0.8321 (mmm) REVERT: C 1000 ASN cc_start: 0.7745 (m-40) cc_final: 0.7516 (m-40) REVERT: D 408 MET cc_start: 0.5878 (tpp) cc_final: 0.5410 (tpt) REVERT: D 431 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8068 (mp0) REVERT: D 438 PHE cc_start: 0.6458 (t80) cc_final: 0.5942 (t80) REVERT: D 493 LYS cc_start: 0.8650 (mttp) cc_final: 0.8226 (mtpp) REVERT: D 633 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8125 (mt) REVERT: D 714 GLN cc_start: 0.8332 (tp-100) cc_final: 0.7705 (tm-30) REVERT: D 748 LEU cc_start: 0.9517 (tp) cc_final: 0.9091 (pp) REVERT: D 760 ASP cc_start: 0.8845 (m-30) cc_final: 0.8358 (t70) REVERT: D 764 ASN cc_start: 0.8796 (m-40) cc_final: 0.8328 (m-40) REVERT: D 783 LYS cc_start: 0.6788 (pmtt) cc_final: 0.6371 (ptpp) REVERT: E 75 HIS cc_start: 0.7600 (t70) cc_final: 0.7307 (t70) REVERT: E 87 GLU cc_start: 0.7571 (tp30) cc_final: 0.7335 (tp30) REVERT: E 101 HIS cc_start: 0.8082 (m170) cc_final: 0.7511 (m-70) REVERT: E 123 MET cc_start: 0.6155 (mmm) cc_final: 0.5629 (mmm) REVERT: F 64 LEU cc_start: 0.7663 (mt) cc_final: 0.7313 (pp) REVERT: F 101 HIS cc_start: 0.7137 (m-70) cc_final: 0.6050 (m-70) REVERT: F 151 TYR cc_start: 0.6958 (OUTLIER) cc_final: 0.6516 (t80) outliers start: 59 outliers final: 44 residues processed: 385 average time/residue: 0.1112 time to fit residues: 67.5435 Evaluate side-chains 383 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 333 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 469 TYR Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 688 GLU Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 469 TYR Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain C residue 900 CYS Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain C residue 1016 LEU Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 495 PHE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 151 TYR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 118 ASP Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 124 ASN Chi-restraints excluded: chain F residue 151 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 188 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 157 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 168 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 117 optimal weight: 0.3980 chunk 145 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 747 ASN ** D 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN ** F 75 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 = 0.4322 r_free = 0.4322 target = 0.173526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.121047 restraints weight = 34248.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.125558 restraints weight = 19643.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.126388 restraints weight = 12738.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.126189 restraints weight = 13737.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.126255 restraints weight = 12340.547| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.6804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 19433 Z= 0.160 Angle : 0.837 15.442 26072 Z= 0.414 Chirality : 0.047 0.251 2836 Planarity : 0.005 0.069 3142 Dihedral : 13.073 135.434 3033 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.87 % Favored : 89.09 % Rotamer: Outliers : 2.91 % Allowed : 27.58 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 4.69 % Twisted General : 0.50 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.18), residues: 2264 helix: 0.79 (0.15), residues: 1302 sheet: -3.23 (0.37), residues: 148 loop : -3.24 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 715 TYR 0.038 0.002 TYR D 673 PHE 0.032 0.002 PHE A1028 TRP 0.053 0.002 TRP D 460 HIS 0.009 0.001 HIS E 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (19427) covalent geometry : angle 0.83416 / 0.41 (26060) SS BOND : bond 0.00536 / 0.26 ( 6) SS BOND : angle 3.07795 / 1.78 ( 12) hydrogen bonds : bond 0.03583 / 2.37 ( 834) hydrogen bonds : angle 4.04833 / 2.83 ( 2436) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3450.63 seconds wall clock time: 60 minutes 29.56 seconds (3629.56 seconds total)