Starting phenix.real_space_refine on Sun Aug 24 11:23:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ssb_40750/08_2025/8ssb_40750.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ssb_40750/08_2025/8ssb_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_40750/08_2025/8ssb_40750.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ssb_40750/08_2025/8ssb_40750.map" model { file = "/net/cci-nas-00/data/ceres_data/8ssb_40750/08_2025/8ssb_40750.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ssb_40750/08_2025/8ssb_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-2.0-5787/lib/python3.9/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: 176 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: 173 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: 65 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: 50 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: 4.40, per 1000 atoms: 0.23 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: 1.66 Conformation dependent library (CDL) restraints added in 602.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.37 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: 2.32 Time building geometry restraints manager: 2.10 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: 11207 35.54 - 71.09: 379 71.09 - 106.63: 37 106.63 - 142.17: 8 142.17 - 177.72: 2 Dihedral angle restraints: 11633 sinusoidal: 4991 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 11630 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: 4.850 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: 0.040 Extract box with map and model: 0.360 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.830 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 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 : 17.483 177.715 7367 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 aren 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 covalent geometry : bond 0.00946 (19427) covalent geometry : angle 1.54546 (26060) SS BOND : bond 0.00662 ( 6) SS BOND : angle 1.02563 ( 12) hydrogen bonds : bond 0.29522 ( 834) hydrogen bonds : angle 10.26796 ( 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 : 0.624 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: 0.8951 (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: 0.6542 (t70) REVERT: E 94 ASN cc_start: 0.7672 (p0) cc_final: 0.7412 (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: 0.7286 (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: 0.1348 time to fit residues: 131.6557 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 : 0.502 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.167572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.112143 restraints weight = 33433.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.116468 restraints weight = 18811.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.116543 restraints weight = 12559.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.116688 restraints weight = 12697.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.116800 restraints weight = 12602.841| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 19433 Z= 0.164 Angle : 0.825 11.486 26072 Z= 0.425 Chirality : 0.046 0.190 2836 Planarity : 0.006 0.079 3142 Dihedral : 18.357 161.364 3218 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.62 % Allowed : 10.03 % Favored : 89.36 % Rotamer: Outliers : 4.49 % Allowed : 15.58 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 6.25 % 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 aren not related in a simple way. whole: -3.93 (0.15), residues: 2264 helix: -1.81 (0.12), residues: 1354 sheet: -3.81 (0.36), residues: 142 loop : -3.64 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 108 TYR 0.036 0.002 TYR D 450 PHE 0.028 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 covalent geometry : bond 0.00349 (19427) covalent geometry : angle 0.82415 (26060) SS BOND : bond 0.03096 ( 6) SS BOND : angle 2.10620 ( 12) hydrogen bonds : bond 0.04763 ( 834) hydrogen bonds : angle 4.86840 ( 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 567 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 479 time to evaluate : 0.608 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: 0.9135 (OUTLIER) cc_final: 0.8518 (tp) REVERT: A 585 MET cc_start: 0.8353 (mpt) cc_final: 0.7981 (mpt) REVERT: A 619 ASN cc_start: 0.7988 (m110) cc_final: 0.7443 (t0) REVERT: A 670 MET cc_start: 0.9145 (OUTLIER) cc_final: 0.8886 (mtm) REVERT: A 924 MET cc_start: 0.7147 (mmm) cc_final: 0.6826 (mmp) REVERT: A 926 ARG cc_start: 0.7269 (ptm160) cc_final: 0.7014 (ptm160) REVERT: A 938 PHE cc_start: 0.8790 (m-10) cc_final: 0.8564 (m-80) REVERT: A 1016 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8540 (mt) REVERT: B 493 LYS cc_start: 0.8933 (mttp) cc_final: 0.8657 (tttm) REVERT: B 669 LYS cc_start: 0.9148 (pttt) cc_final: 0.8941 (pttt) REVERT: B 713 GLU cc_start: 0.9018 (tm-30) cc_final: 0.8715 (tm-30) REVERT: B 714 GLN cc_start: 0.8034 (tp-100) cc_final: 0.7308 (tp40) REVERT: B 721 MET cc_start: 0.7865 (ppp) cc_final: 0.7566 (ppp) REVERT: B 748 LEU cc_start: 0.9516 (tp) cc_final: 0.9162 (pp) REVERT: B 760 ASP cc_start: 0.9303 (m-30) cc_final: 0.8733 (t0) REVERT: B 763 LYS cc_start: 0.9271 (tppt) cc_final: 0.9071 (tppt) REVERT: B 764 ASN cc_start: 0.8890 (m-40) cc_final: 0.8162 (m-40) REVERT: C 450 TYR cc_start: 0.7095 (m-80) cc_final: 0.6357 (m-80) REVERT: C 518 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8549 (pp) REVERT: C 581 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.8976 (tp) REVERT: C 683 VAL cc_start: 0.8113 (OUTLIER) cc_final: 0.7601 (m) REVERT: C 705 GLU cc_start: 0.7256 (mt-10) cc_final: 0.7031 (mt-10) REVERT: C 713 GLU cc_start: 0.8612 (pp20) cc_final: 0.8179 (pp20) REVERT: C 714 GLN cc_start: 0.8554 (mm-40) cc_final: 0.7851 (mm-40) REVERT: C 891 PHE cc_start: 0.5638 (m-80) cc_final: 0.5335 (m-10) REVERT: C 926 ARG cc_start: 0.6379 (ttm-80) cc_final: 0.5739 (tmt170) REVERT: C 991 ARG cc_start: 0.6850 (mmt-90) cc_final: 0.6343 (mmt90) REVERT: C 1000 ASN cc_start: 0.7909 (m-40) cc_final: 0.7350 (m110) REVERT: D 421 TYR cc_start: 0.8017 (m-10) cc_final: 0.7716 (m-10) REVERT: D 479 LEU cc_start: 0.8772 (tp) cc_final: 0.8557 (tp) REVERT: D 493 LYS cc_start: 0.8712 (mttp) cc_final: 0.8115 (tttm) REVERT: D 533 TYR cc_start: 0.8712 (t80) cc_final: 0.8415 (t80) REVERT: D 702 TYR cc_start: 0.7635 (t80) cc_final: 0.7308 (t80) REVERT: D 714 GLN cc_start: 0.8478 (tp-100) cc_final: 0.7577 (tp40) REVERT: D 760 ASP cc_start: 0.9382 (m-30) cc_final: 0.8972 (t70) REVERT: D 762 LEU cc_start: 0.9333 (mm) cc_final: 0.9112 (mm) REVERT: E 75 HIS cc_start: 0.7507 (t70) cc_final: 0.6001 (t70) REVERT: E 78 PHE cc_start: 0.7857 (m-80) cc_final: 0.7462 (m-80) REVERT: E 87 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7546 (mm-30) REVERT: E 94 ASN cc_start: 0.7700 (p0) cc_final: 0.7343 (p0) REVERT: E 95 ILE cc_start: 0.8526 (tp) cc_final: 0.7791 (tt) REVERT: E 99 PHE cc_start: 0.7988 (m-10) cc_final: 0.7709 (m-80) REVERT: E 101 HIS cc_start: 0.7396 (m170) cc_final: 0.6282 (m170) REVERT: E 104 ARG cc_start: 0.8619 (tpt-90) cc_final: 0.8396 (tpt-90) REVERT: F 78 PHE cc_start: 0.7720 (m-80) cc_final: 0.7477 (m-80) REVERT: F 99 PHE cc_start: 0.7577 (m-10) cc_final: 0.7087 (t80) REVERT: F 104 ARG cc_start: 0.8790 (tpt90) cc_final: 0.8403 (tpt-90) outliers start: 88 outliers final: 30 residues processed: 537 average time/residue: 0.1327 time to fit residues: 107.2325 Evaluate side-chains 413 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 377 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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 B residue 807 MET 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 527 MET 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 68 VAL 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: 9.9990 chunk 30 optimal weight: 8.9990 chunk 89 optimal weight: 0.8980 chunk 176 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 19 optimal weight: 0.2980 chunk 70 optimal weight: 0.5980 chunk 143 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 714 GLN A 726 ASN B 587 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 ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.163645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.108015 restraints weight = 33618.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.110546 restraints weight = 19997.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.111137 restraints weight = 14749.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.110957 restraints weight = 13930.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.111309 restraints weight = 13645.314| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 19433 Z= 0.194 Angle : 0.813 12.330 26072 Z= 0.414 Chirality : 0.046 0.208 2836 Planarity : 0.006 0.078 3142 Dihedral : 17.285 151.299 3213 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.40 % Allowed : 11.13 % Favored : 88.47 % Rotamer: Outliers : 4.65 % Allowed : 18.18 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 1.04 % 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 aren not related in a simple way. whole: -2.87 (0.16), residues: 2264 helix: -0.82 (0.13), residues: 1338 sheet: -3.83 (0.38), residues: 120 loop : -3.39 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 108 TYR 0.034 0.002 TYR D 450 PHE 0.027 0.002 PHE F 141 TRP 0.018 0.002 TRP B 460 HIS 0.013 0.002 HIS F 101 Details of bonding type rmsd covalent geometry : bond 0.00450 (19427) covalent geometry : angle 0.81230 (26060) SS BOND : bond 0.00766 ( 6) SS BOND : angle 1.97745 ( 12) hydrogen bonds : bond 0.04401 ( 834) hydrogen bonds : angle 4.41321 ( 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 499 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 408 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 TYR cc_start: 0.7343 (m-80) cc_final: 0.6900 (m-10) REVERT: A 498 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7992 (mp) REVERT: A 581 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.8985 (tp) REVERT: A 670 MET cc_start: 0.9185 (OUTLIER) cc_final: 0.8876 (mtm) REVERT: A 705 GLU cc_start: 0.7518 (mt-10) cc_final: 0.6465 (mt-10) REVERT: A 726 ASN cc_start: 0.7936 (OUTLIER) cc_final: 0.7504 (t0) REVERT: A 924 MET cc_start: 0.7212 (mmm) cc_final: 0.6590 (mmp) REVERT: A 1000 ASN cc_start: 0.7861 (m-40) cc_final: 0.7299 (m-40) REVERT: B 401 LEU cc_start: 0.8902 (pp) cc_final: 0.8369 (tp) REVERT: B 421 TYR cc_start: 0.8252 (m-10) cc_final: 0.7914 (m-10) REVERT: B 493 LYS cc_start: 0.8894 (mttp) cc_final: 0.8683 (tttm) REVERT: B 714 GLN cc_start: 0.8133 (tp-100) cc_final: 0.7423 (tp40) REVERT: B 760 ASP cc_start: 0.9185 (m-30) cc_final: 0.8814 (t0) REVERT: B 763 LYS cc_start: 0.9272 (tppt) cc_final: 0.9055 (tppt) REVERT: C 450 TYR cc_start: 0.7179 (m-80) cc_final: 0.6352 (m-80) REVERT: C 518 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8880 (pp) REVERT: C 674 MET cc_start: 0.7880 (mtp) cc_final: 0.7667 (mtp) REVERT: C 713 GLU cc_start: 0.8546 (pp20) cc_final: 0.8225 (pp20) REVERT: C 865 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7418 (mm-30) REVERT: C 890 CYS cc_start: 0.2120 (t) cc_final: 0.1917 (t) REVERT: C 926 ARG cc_start: 0.6517 (ttm-80) cc_final: 0.5768 (tmt170) REVERT: C 991 ARG cc_start: 0.6718 (mmt-90) cc_final: 0.6343 (mmt90) REVERT: C 1000 ASN cc_start: 0.8115 (m-40) cc_final: 0.7366 (m-40) REVERT: D 431 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8156 (mp0) REVERT: D 460 TRP cc_start: 0.6451 (m-90) cc_final: 0.6058 (m-90) REVERT: D 493 LYS cc_start: 0.8695 (mttp) cc_final: 0.8179 (mtpp) REVERT: D 714 GLN cc_start: 0.8514 (tp-100) cc_final: 0.7636 (tp40) REVERT: D 760 ASP cc_start: 0.9283 (m-30) cc_final: 0.8857 (t70) REVERT: E 75 HIS cc_start: 0.7587 (t70) cc_final: 0.6607 (t70) REVERT: E 78 PHE cc_start: 0.7833 (m-80) cc_final: 0.7593 (m-80) REVERT: E 87 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7653 (mm-30) REVERT: E 95 ILE cc_start: 0.8539 (tp) cc_final: 0.7706 (tt) REVERT: E 99 PHE cc_start: 0.7955 (m-10) cc_final: 0.7622 (m-80) REVERT: E 101 HIS cc_start: 0.7774 (m170) cc_final: 0.6653 (m170) REVERT: F 75 HIS cc_start: 0.7858 (t-90) cc_final: 0.7616 (t-90) REVERT: F 99 PHE cc_start: 0.7560 (m-10) cc_final: 0.7101 (t80) REVERT: F 104 ARG cc_start: 0.8752 (tpt90) cc_final: 0.8295 (tpt-90) outliers start: 91 outliers final: 33 residues processed: 466 average time/residue: 0.1180 time to fit residues: 85.1542 Evaluate side-chains 398 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 359 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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 498 LEU Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 726 ASN Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 889 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 495 PHE Chi-restraints excluded: chain B residue 504 ILE Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 403 SER 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 576 SER 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 D residue 431 GLU Chi-restraints excluded: chain D residue 474 ILE 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 15 VAL Chi-restraints excluded: chain E residue 24 VAL 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 4 THR Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 69 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 140 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 151 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 145 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN B 586 GLN ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 94 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.165287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.111283 restraints weight = 33803.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.113888 restraints weight = 20243.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.113979 restraints weight = 14760.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.114018 restraints weight = 15204.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.114264 restraints weight = 13842.826| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.5111 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= 0.157 Angle : 0.782 12.608 26072 Z= 0.396 Chirality : 0.045 0.219 2836 Planarity : 0.005 0.075 3142 Dihedral : 16.401 144.649 3213 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.64 % Favored : 89.05 % Rotamer: Outliers : 4.39 % Allowed : 20.33 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 6.25 % 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 aren not related in a simple way. whole: -2.31 (0.17), residues: 2264 helix: -0.23 (0.14), residues: 1344 sheet: -3.62 (0.36), residues: 142 loop : -3.43 (0.20), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 108 TYR 0.041 0.002 TYR D 673 PHE 0.037 0.002 PHE A 943 TRP 0.026 0.001 TRP B 460 HIS 0.010 0.002 HIS F 101 Details of bonding type rmsd covalent geometry : bond 0.00354 (19427) covalent geometry : angle 0.77943 (26060) SS BOND : bond 0.00721 ( 6) SS BOND : angle 2.88031 ( 12) hydrogen bonds : bond 0.03820 ( 834) hydrogen bonds : angle 4.16783 ( 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 484 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 398 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 TYR cc_start: 0.7391 (m-80) cc_final: 0.6734 (m-80) REVERT: A 581 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.8962 (tp) REVERT: A 670 MET cc_start: 0.9169 (OUTLIER) cc_final: 0.8846 (mtm) REVERT: A 755 GLU cc_start: 0.8945 (mp0) cc_final: 0.8568 (mp0) REVERT: A 1000 ASN cc_start: 0.7879 (m-40) cc_final: 0.7107 (m-40) REVERT: A 1003 TYR cc_start: 0.8018 (m-80) cc_final: 0.7364 (m-80) REVERT: B 401 LEU cc_start: 0.8809 (pp) cc_final: 0.8460 (tp) REVERT: B 419 GLU cc_start: 0.7280 (tp30) cc_final: 0.6601 (tp30) REVERT: B 421 TYR cc_start: 0.8224 (m-10) cc_final: 0.7865 (m-10) REVERT: B 493 LYS cc_start: 0.8811 (mttp) cc_final: 0.8196 (mtpp) REVERT: B 714 GLN cc_start: 0.8240 (tp-100) cc_final: 0.7362 (tp40) REVERT: B 760 ASP cc_start: 0.9167 (m-30) cc_final: 0.8601 (t70) REVERT: B 764 ASN cc_start: 0.8805 (m-40) cc_final: 0.8335 (m110) REVERT: C 450 TYR cc_start: 0.7204 (m-80) cc_final: 0.6310 (m-80) REVERT: C 518 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8829 (pp) REVERT: C 596 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8297 (tm) REVERT: C 705 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7022 (mt-10) REVERT: C 713 GLU cc_start: 0.8472 (pp20) cc_final: 0.8002 (pp20) REVERT: C 864 LEU cc_start: 0.6627 (OUTLIER) cc_final: 0.6385 (mp) REVERT: C 865 GLU cc_start: 0.7637 (mm-30) cc_final: 0.6864 (mm-30) REVERT: C 926 ARG cc_start: 0.6745 (ttm-80) cc_final: 0.5825 (tmt170) REVERT: C 969 SER cc_start: 0.8864 (p) cc_final: 0.8643 (t) REVERT: C 999 PHE cc_start: 0.6935 (OUTLIER) cc_final: 0.6276 (m-80) REVERT: C 1000 ASN cc_start: 0.7988 (m-40) cc_final: 0.7289 (m-40) REVERT: C 1019 SER cc_start: 0.9451 (t) cc_final: 0.9244 (t) REVERT: D 401 LEU cc_start: 0.8786 (pp) cc_final: 0.8360 (tp) REVERT: D 431 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8166 (mp0) REVERT: D 493 LYS cc_start: 0.8604 (mttp) cc_final: 0.8090 (mtpp) REVERT: D 714 GLN cc_start: 0.8473 (tp-100) cc_final: 0.7702 (tm-30) REVERT: D 760 ASP cc_start: 0.9279 (m-30) cc_final: 0.8740 (t0) REVERT: D 762 LEU cc_start: 0.9260 (mm) cc_final: 0.9040 (mm) REVERT: D 781 LYS cc_start: 0.5430 (tptt) cc_final: 0.5185 (mtpp) REVERT: D 783 LYS cc_start: 0.6883 (pmtt) cc_final: 0.6529 (ptpp) REVERT: E 75 HIS cc_start: 0.7671 (t70) cc_final: 0.7137 (t70) REVERT: E 87 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7598 (tp30) REVERT: E 99 PHE cc_start: 0.7937 (m-10) cc_final: 0.7720 (t80) REVERT: E 101 HIS cc_start: 0.7830 (m170) cc_final: 0.7422 (m-70) REVERT: E 108 ARG cc_start: 0.6459 (mmm160) cc_final: 0.5971 (mmm160) REVERT: E 134 GLU cc_start: 0.7542 (tm-30) cc_final: 0.6973 (tm-30) REVERT: F 65 ARG cc_start: 0.7720 (ptt90) cc_final: 0.7501 (ptt90) REVERT: F 75 HIS cc_start: 0.7858 (t-90) cc_final: 0.7626 (t-90) REVERT: F 99 PHE cc_start: 0.7521 (m-10) cc_final: 0.7097 (t80) REVERT: F 104 ARG cc_start: 0.8664 (tpt90) cc_final: 0.8434 (tpt-90) REVERT: F 123 MET cc_start: 0.5888 (mmm) cc_final: 0.5680 (mmm) REVERT: C 1107 GLU cc_start: 0.4117 (mm-30) cc_final: 0.3611 (mm-30) outliers start: 86 outliers final: 48 residues processed: 451 average time/residue: 0.1254 time to fit residues: 87.2350 Evaluate side-chains 412 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 357 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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 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 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 524 GLU 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 527 MET Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 900 CYS Chi-restraints excluded: chain C residue 999 PHE 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 524 GLU Chi-restraints excluded: chain D residue 573 ILE 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 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 F residue 4 THR Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 69 VAL 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: 0.9980 chunk 3 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 138 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 chunk 155 optimal weight: 0.3980 chunk 163 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN A 874 GLN B 435 HIS ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 883 HIS D 575 ASN ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 GLN ** 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 ** F 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.165510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.109157 restraints weight = 33665.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.112747 restraints weight = 20075.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.113693 restraints weight = 13560.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.113534 restraints weight = 13377.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.113672 restraints weight = 13015.468| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.5492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19433 Z= 0.153 Angle : 0.755 13.043 26072 Z= 0.382 Chirality : 0.045 0.228 2836 Planarity : 0.005 0.067 3142 Dihedral : 15.775 139.398 3213 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.51 % Favored : 89.22 % Rotamer: Outliers : 4.70 % Allowed : 21.91 % Favored : 73.39 % 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 aren not related in a simple way. whole: -1.83 (0.18), residues: 2264 helix: 0.20 (0.14), residues: 1328 sheet: -2.99 (0.39), residues: 136 loop : -3.38 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 108 TYR 0.031 0.002 TYR D 450 PHE 0.031 0.002 PHE A 943 TRP 0.024 0.001 TRP B 460 HIS 0.009 0.001 HIS E 107 Details of bonding type rmsd covalent geometry : bond 0.00349 (19427) covalent geometry : angle 0.75457 (26060) SS BOND : bond 0.00567 ( 6) SS BOND : angle 1.57563 ( 12) hydrogen bonds : bond 0.03656 ( 834) hydrogen bonds : angle 4.06010 ( 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 491 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 399 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 TYR cc_start: 0.7335 (m-80) cc_final: 0.6699 (m-80) REVERT: A 524 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7244 (pt0) REVERT: A 581 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.8881 (tp) REVERT: A 619 ASN cc_start: 0.9137 (OUTLIER) cc_final: 0.7736 (m-40) REVERT: A 670 MET cc_start: 0.9229 (OUTLIER) cc_final: 0.8841 (mtm) REVERT: A 755 GLU cc_start: 0.8941 (mp0) cc_final: 0.8551 (mp0) REVERT: A 1000 ASN cc_start: 0.7884 (m-40) cc_final: 0.7269 (m-40) REVERT: A 1003 TYR cc_start: 0.8059 (m-80) cc_final: 0.7822 (m-80) REVERT: A 1028 PHE cc_start: 0.8111 (t80) cc_final: 0.7883 (t80) REVERT: A 1029 MET cc_start: 0.7994 (mmm) cc_final: 0.7553 (mtt) REVERT: B 419 GLU cc_start: 0.7274 (tp30) cc_final: 0.6652 (tp30) REVERT: B 421 TYR cc_start: 0.8210 (m-10) cc_final: 0.7870 (m-10) REVERT: B 493 LYS cc_start: 0.8577 (mttp) cc_final: 0.8249 (mtpp) REVERT: B 674 MET cc_start: 0.8534 (ttm) cc_final: 0.7884 (tpp) REVERT: B 714 GLN cc_start: 0.8258 (tp-100) cc_final: 0.7441 (tp40) REVERT: B 748 LEU cc_start: 0.9540 (tp) cc_final: 0.9108 (pp) REVERT: B 760 ASP cc_start: 0.9135 (m-30) cc_final: 0.8596 (t70) REVERT: B 763 LYS cc_start: 0.9272 (tppt) cc_final: 0.8996 (tppt) REVERT: B 764 ASN cc_start: 0.8852 (m-40) cc_final: 0.8412 (m110) REVERT: C 450 TYR cc_start: 0.7430 (m-80) cc_final: 0.6422 (m-80) REVERT: C 518 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8916 (pp) REVERT: C 596 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8306 (tm) REVERT: C 713 GLU cc_start: 0.8518 (pp20) cc_final: 0.8044 (pp20) REVERT: C 716 LYS cc_start: 0.8437 (mppt) cc_final: 0.8234 (ttpp) REVERT: C 926 ARG cc_start: 0.6870 (ttm-80) cc_final: 0.5928 (tmt170) REVERT: C 969 SER cc_start: 0.8850 (p) cc_final: 0.8612 (t) REVERT: C 999 PHE cc_start: 0.6837 (OUTLIER) cc_final: 0.6204 (m-80) REVERT: C 1000 ASN cc_start: 0.7973 (m-40) cc_final: 0.7590 (m-40) REVERT: C 1019 SER cc_start: 0.9481 (t) cc_final: 0.9255 (t) REVERT: D 401 LEU cc_start: 0.8811 (pp) cc_final: 0.8480 (tt) REVERT: D 407 MET cc_start: 0.7485 (mpp) cc_final: 0.7096 (mpp) REVERT: D 415 LEU cc_start: 0.8567 (tp) cc_final: 0.7936 (tp) REVERT: D 419 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7728 (tp30) REVERT: D 431 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8131 (mp0) REVERT: D 493 LYS cc_start: 0.8567 (mttp) cc_final: 0.8268 (tttm) REVERT: D 519 ASP cc_start: 0.7889 (OUTLIER) cc_final: 0.7668 (m-30) REVERT: D 673 TYR cc_start: 0.8160 (m-80) cc_final: 0.7696 (m-80) REVERT: D 714 GLN cc_start: 0.8484 (tp-100) cc_final: 0.7829 (tm-30) REVERT: D 748 LEU cc_start: 0.9350 (tp) cc_final: 0.8971 (pp) REVERT: D 760 ASP cc_start: 0.9246 (m-30) cc_final: 0.8648 (t0) REVERT: D 761 LYS cc_start: 0.9384 (mmmt) cc_final: 0.8995 (mmtm) REVERT: D 762 LEU cc_start: 0.9262 (mm) cc_final: 0.9030 (mm) REVERT: E 75 HIS cc_start: 0.7651 (t70) cc_final: 0.7200 (t70) REVERT: E 87 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7625 (tp30) REVERT: E 99 PHE cc_start: 0.7915 (m-10) cc_final: 0.7550 (t80) REVERT: E 101 HIS cc_start: 0.7900 (m170) cc_final: 0.7483 (m-70) REVERT: E 123 MET cc_start: 0.5995 (mmm) cc_final: 0.5129 (mmm) REVERT: E 134 GLU cc_start: 0.7360 (tm-30) cc_final: 0.6897 (tm-30) REVERT: F 87 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7205 (tp30) REVERT: F 99 PHE cc_start: 0.7538 (m-10) cc_final: 0.7021 (t80) REVERT: F 104 ARG cc_start: 0.8682 (tpt90) cc_final: 0.8410 (tpp80) outliers start: 92 outliers final: 54 residues processed: 454 average time/residue: 0.1333 time to fit residues: 93.8541 Evaluate side-chains 430 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 368 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 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 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 406 VAL Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 788 SER 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 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 576 SER Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 744 THR 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 1007 PHE 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 524 GLU Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 573 ILE 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 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 69 VAL Chi-restraints excluded: chain F residue 124 ASN Chi-restraints excluded: chain F residue 153 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 72 optimal weight: 0.9980 chunk 127 optimal weight: 0.7980 chunk 192 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 156 optimal weight: 9.9990 chunk 167 optimal weight: 1.9990 chunk 36 optimal weight: 0.0000 chunk 125 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 222 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN A 874 GLN B 435 HIS B 642 GLN ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 874 GLN D 575 ASN ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.166310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.109595 restraints weight = 33175.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.113241 restraints weight = 18623.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.115486 restraints weight = 13920.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.116403 restraints weight = 12041.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.117290 restraints weight = 11246.260| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.5813 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= 0.150 Angle : 0.782 13.477 26072 Z= 0.395 Chirality : 0.045 0.359 2836 Planarity : 0.005 0.065 3142 Dihedral : 15.360 133.559 3213 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.60 % Favored : 89.27 % Rotamer: Outliers : 4.29 % Allowed : 23.85 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.68 % 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 aren not related in a simple way. whole: -1.50 (0.18), residues: 2264 helix: 0.45 (0.15), residues: 1338 sheet: -2.80 (0.39), residues: 144 loop : -3.28 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 108 TYR 0.027 0.001 TYR B 450 PHE 0.033 0.002 PHE A 943 TRP 0.054 0.002 TRP B 460 HIS 0.017 0.002 HIS F 101 Details of bonding type rmsd covalent geometry : bond 0.00337 (19427) covalent geometry : angle 0.77860 (26060) SS BOND : bond 0.01299 ( 6) SS BOND : angle 3.52771 ( 12) hydrogen bonds : bond 0.03554 ( 834) hydrogen bonds : angle 3.94910 ( 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 488 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 404 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 TYR cc_start: 0.7412 (m-80) cc_final: 0.6723 (m-80) REVERT: A 524 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7324 (pt0) REVERT: A 581 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.8885 (tp) REVERT: A 619 ASN cc_start: 0.9099 (OUTLIER) cc_final: 0.8348 (m-40) REVERT: A 670 MET cc_start: 0.9126 (OUTLIER) cc_final: 0.8759 (mtm) REVERT: A 755 GLU cc_start: 0.8939 (mp0) cc_final: 0.8634 (mp0) REVERT: A 891 PHE cc_start: 0.6122 (m-10) cc_final: 0.5571 (m-10) REVERT: A 988 MET cc_start: 0.8723 (mmp) cc_final: 0.8344 (mmm) REVERT: A 1000 ASN cc_start: 0.7717 (m-40) cc_final: 0.7208 (m-40) REVERT: A 1003 TYR cc_start: 0.8014 (m-80) cc_final: 0.7647 (m-80) REVERT: B 407 MET cc_start: 0.7453 (mpp) cc_final: 0.7090 (mpp) REVERT: B 419 GLU cc_start: 0.6994 (tp30) cc_final: 0.6465 (tp30) REVERT: B 421 TYR cc_start: 0.8204 (m-10) cc_final: 0.7889 (m-10) REVERT: B 491 PHE cc_start: 0.5950 (OUTLIER) cc_final: 0.5732 (t80) REVERT: B 493 LYS cc_start: 0.8605 (mttp) cc_final: 0.8239 (mtpp) REVERT: B 714 GLN cc_start: 0.8258 (tp-100) cc_final: 0.7553 (tp40) REVERT: B 748 LEU cc_start: 0.9515 (tp) cc_final: 0.9060 (pp) REVERT: B 760 ASP cc_start: 0.9046 (m-30) cc_final: 0.8501 (t70) REVERT: B 763 LYS cc_start: 0.9229 (tppt) cc_final: 0.8982 (tppt) REVERT: B 764 ASN cc_start: 0.8783 (m-40) cc_final: 0.8304 (m110) REVERT: C 408 MET cc_start: 0.7102 (tpp) cc_final: 0.6385 (tpp) REVERT: C 450 TYR cc_start: 0.7380 (m-80) cc_final: 0.6552 (m-80) REVERT: C 518 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8924 (pp) REVERT: C 591 ILE cc_start: 0.7213 (OUTLIER) cc_final: 0.6861 (tp) REVERT: C 596 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8356 (tm) REVERT: C 705 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7252 (mt-10) REVERT: C 713 GLU cc_start: 0.8515 (pp20) cc_final: 0.8086 (pp20) REVERT: C 926 ARG cc_start: 0.6680 (ttm-80) cc_final: 0.5949 (tmt170) REVERT: C 1000 ASN cc_start: 0.7882 (m-40) cc_final: 0.7232 (m-40) REVERT: D 407 MET cc_start: 0.7443 (mpp) cc_final: 0.7073 (mpp) REVERT: D 419 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7595 (tp30) REVERT: D 431 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8063 (mp0) REVERT: D 460 TRP cc_start: 0.5870 (m-10) cc_final: 0.4476 (m-10) REVERT: D 493 LYS cc_start: 0.8631 (mttp) cc_final: 0.8059 (mtpp) REVERT: D 519 ASP cc_start: 0.7828 (OUTLIER) cc_final: 0.7603 (m-30) REVERT: D 637 GLU cc_start: 0.8417 (pt0) cc_final: 0.8060 (pm20) REVERT: D 714 GLN cc_start: 0.8398 (tp-100) cc_final: 0.7879 (tm-30) REVERT: D 748 LEU cc_start: 0.9314 (tp) cc_final: 0.8939 (pp) REVERT: D 760 ASP cc_start: 0.9074 (m-30) cc_final: 0.8482 (t0) REVERT: D 761 LYS cc_start: 0.9329 (mmmt) cc_final: 0.9015 (mttm) REVERT: D 764 ASN cc_start: 0.8942 (m-40) cc_final: 0.8445 (m-40) REVERT: D 781 LYS cc_start: 0.5647 (tptt) cc_final: 0.5092 (mtpp) REVERT: D 783 LYS cc_start: 0.6688 (pmtt) cc_final: 0.6319 (ptpp) REVERT: E 75 HIS cc_start: 0.7652 (t70) cc_final: 0.7276 (t70) REVERT: E 99 PHE cc_start: 0.7906 (m-10) cc_final: 0.7630 (t80) REVERT: E 101 HIS cc_start: 0.7919 (m170) cc_final: 0.7527 (m-70) REVERT: E 108 ARG cc_start: 0.6355 (mmm160) cc_final: 0.5826 (mmm160) REVERT: E 134 GLU cc_start: 0.7346 (tm-30) cc_final: 0.6873 (tm-30) REVERT: F 99 PHE cc_start: 0.7547 (m-10) cc_final: 0.7246 (t80) REVERT: C 1107 GLU cc_start: 0.4410 (mm-30) cc_final: 0.4074 (mm-30) outliers start: 84 outliers final: 52 residues processed: 459 average time/residue: 0.1259 time to fit residues: 89.6666 Evaluate side-chains 416 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 355 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 619 ASN Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 670 MET 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 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 474 ILE Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain C residue 403 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 576 SER Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 744 THR 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 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 524 GLU Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 788 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 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 Chi-restraints excluded: chain F residue 153 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 195 optimal weight: 0.8980 chunk 127 optimal weight: 0.8980 chunk 103 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 169 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 175 optimal weight: 4.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN A 874 GLN B 435 HIS ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 756 GLN ** 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 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN 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 = 0.162569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.107491 restraints weight = 33663.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.109888 restraints weight = 19986.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.109556 restraints weight = 15210.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.109934 restraints weight = 15008.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.110150 restraints weight = 14005.553| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.6036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 19433 Z= 0.221 Angle : 0.816 14.589 26072 Z= 0.413 Chirality : 0.048 0.294 2836 Planarity : 0.006 0.070 3142 Dihedral : 15.543 132.255 3213 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.00 % Favored : 88.83 % Rotamer: Outliers : 4.44 % Allowed : 24.57 % Favored : 70.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 7.81 % Twisted General : 0.72 % 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 aren not related in a simple way. whole: -1.57 (0.18), residues: 2264 helix: 0.44 (0.15), residues: 1332 sheet: -3.40 (0.40), residues: 122 loop : -3.26 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 108 TYR 0.032 0.002 TYR B 450 PHE 0.034 0.002 PHE A 943 TRP 0.065 0.002 TRP B 460 HIS 0.015 0.002 HIS F 101 Details of bonding type rmsd covalent geometry : bond 0.00517 (19427) covalent geometry : angle 0.81460 (26060) SS BOND : bond 0.00910 ( 6) SS BOND : angle 2.48515 ( 12) hydrogen bonds : bond 0.03922 ( 834) hydrogen bonds : angle 4.14184 ( 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 446 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 359 time to evaluate : 0.501 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 411 ASN cc_start: 0.8977 (m-40) cc_final: 0.8772 (m110) REVERT: A 450 TYR cc_start: 0.7600 (m-80) cc_final: 0.7269 (m-10) REVERT: A 581 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.8960 (tp) REVERT: A 619 ASN cc_start: 0.9214 (OUTLIER) cc_final: 0.8491 (m-40) REVERT: A 670 MET cc_start: 0.9222 (OUTLIER) cc_final: 0.8828 (mtm) REVERT: A 755 GLU cc_start: 0.8913 (mp0) cc_final: 0.8703 (mp0) REVERT: A 988 MET cc_start: 0.8722 (mmp) cc_final: 0.8372 (mmm) REVERT: A 1000 ASN cc_start: 0.7763 (m-40) cc_final: 0.7255 (m110) REVERT: B 419 GLU cc_start: 0.7226 (tp30) cc_final: 0.6548 (tp30) REVERT: B 421 TYR cc_start: 0.8285 (m-10) cc_final: 0.8012 (m-10) REVERT: B 491 PHE cc_start: 0.6179 (OUTLIER) cc_final: 0.5898 (t80) REVERT: B 493 LYS cc_start: 0.8681 (mttp) cc_final: 0.8267 (mtpp) REVERT: B 714 GLN cc_start: 0.8309 (tp-100) cc_final: 0.7652 (tm-30) REVERT: B 748 LEU cc_start: 0.9514 (tp) cc_final: 0.9064 (pp) REVERT: B 760 ASP cc_start: 0.9132 (m-30) cc_final: 0.8740 (t70) REVERT: C 518 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.9024 (pp) REVERT: C 585 MET cc_start: 0.8673 (mmt) cc_final: 0.8106 (mmt) REVERT: C 713 GLU cc_start: 0.8575 (pp20) cc_final: 0.8034 (pp20) REVERT: C 865 GLU cc_start: 0.6977 (mm-30) cc_final: 0.6750 (mm-30) REVERT: C 926 ARG cc_start: 0.6785 (ttm-80) cc_final: 0.5938 (tmt170) REVERT: C 999 PHE cc_start: 0.6873 (OUTLIER) cc_final: 0.6517 (m-80) REVERT: C 1000 ASN cc_start: 0.7966 (m-40) cc_final: 0.7267 (m-40) REVERT: D 407 MET cc_start: 0.7190 (mpp) cc_final: 0.6959 (mpp) REVERT: D 419 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7578 (tp30) REVERT: D 431 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8052 (mp0) REVERT: D 493 LYS cc_start: 0.8660 (mttp) cc_final: 0.8200 (mtpp) REVERT: D 519 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.7669 (m-30) REVERT: D 714 GLN cc_start: 0.8468 (tp-100) cc_final: 0.7872 (tm-30) REVERT: D 748 LEU cc_start: 0.9339 (tp) cc_final: 0.8927 (pp) REVERT: D 760 ASP cc_start: 0.9171 (m-30) cc_final: 0.8707 (t0) REVERT: D 761 LYS cc_start: 0.9365 (mmmt) cc_final: 0.9044 (mmtm) REVERT: E 75 HIS cc_start: 0.7681 (t70) cc_final: 0.7344 (t70) REVERT: E 99 PHE cc_start: 0.7980 (m-10) cc_final: 0.7583 (t80) REVERT: E 101 HIS cc_start: 0.8039 (m170) cc_final: 0.7518 (m-70) REVERT: E 134 GLU cc_start: 0.7412 (tm-30) cc_final: 0.6930 (tm-30) REVERT: F 99 PHE cc_start: 0.7422 (m-10) cc_final: 0.6999 (t80) outliers start: 87 outliers final: 56 residues processed: 409 average time/residue: 0.1237 time to fit residues: 78.6281 Evaluate side-chains 404 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 340 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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 619 ASN Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 670 MET 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 A residue 1027 LEU Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 474 ILE 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 403 SER 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 1007 PHE Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 408 MET 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 519 ASP 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 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 65 ARG Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 124 ASN Chi-restraints excluded: chain F residue 153 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 142 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 130 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 210 optimal weight: 5.9990 chunk 115 optimal weight: 0.4980 chunk 6 optimal weight: 6.9990 chunk 198 optimal weight: 0.5980 chunk 7 optimal weight: 0.3980 chunk 189 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 950 HIS D 575 ASN ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.166472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.111200 restraints weight = 33519.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.114733 restraints weight = 19383.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.115080 restraints weight = 13061.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.115042 restraints weight = 13428.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.115138 restraints weight = 12993.054| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.6309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19433 Z= 0.149 Angle : 0.796 16.170 26072 Z= 0.394 Chirality : 0.046 0.268 2836 Planarity : 0.005 0.068 3142 Dihedral : 14.892 127.163 3213 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.42 % Favored : 89.53 % Rotamer: Outliers : 3.88 % Allowed : 25.28 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 7.81 % 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 aren not related in a simple way. whole: -1.35 (0.18), residues: 2264 helix: 0.63 (0.15), residues: 1330 sheet: -2.82 (0.42), residues: 126 loop : -3.28 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 108 TYR 0.045 0.002 TYR B 673 PHE 0.033 0.002 PHE A 943 TRP 0.044 0.001 TRP B 460 HIS 0.013 0.001 HIS F 101 Details of bonding type rmsd covalent geometry : bond 0.00340 (19427) covalent geometry : angle 0.79315 (26060) SS BOND : bond 0.00515 ( 6) SS BOND : angle 3.24219 ( 12) hydrogen bonds : bond 0.03578 ( 834) hydrogen bonds : angle 3.98681 ( 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 448 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 372 time to evaluate : 0.751 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: 0.7484 (m-80) cc_final: 0.7138 (m-10) REVERT: A 524 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7472 (pt0) REVERT: A 581 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8758 (tp) REVERT: A 619 ASN cc_start: 0.9141 (OUTLIER) cc_final: 0.8358 (m-40) REVERT: A 638 ASP cc_start: 0.8420 (OUTLIER) cc_final: 0.8124 (t0) REVERT: A 670 MET cc_start: 0.9191 (OUTLIER) cc_final: 0.8764 (mtm) REVERT: A 985 ASN cc_start: 0.8351 (m-40) cc_final: 0.7933 (m110) REVERT: A 988 MET cc_start: 0.8733 (mmp) cc_final: 0.8379 (mmm) REVERT: A 1000 ASN cc_start: 0.7613 (m-40) cc_final: 0.7074 (m110) REVERT: B 407 MET cc_start: 0.7744 (mpp) cc_final: 0.7362 (mpp) REVERT: B 419 GLU cc_start: 0.7253 (tp30) cc_final: 0.6627 (tp30) REVERT: B 421 TYR cc_start: 0.8295 (m-10) cc_final: 0.8028 (m-10) REVERT: B 487 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7788 (pp20) REVERT: B 491 PHE cc_start: 0.6049 (OUTLIER) cc_final: 0.5823 (t80) REVERT: B 493 LYS cc_start: 0.8618 (mttp) cc_final: 0.8225 (mtpp) REVERT: B 709 ASN cc_start: 0.8675 (t0) cc_final: 0.8440 (t0) REVERT: B 714 GLN cc_start: 0.8290 (tp-100) cc_final: 0.7600 (tm-30) REVERT: B 748 LEU cc_start: 0.9524 (tp) cc_final: 0.9083 (pp) REVERT: B 760 ASP cc_start: 0.9130 (m-30) cc_final: 0.8476 (t70) REVERT: B 764 ASN cc_start: 0.8786 (m-40) cc_final: 0.8172 (m110) REVERT: C 408 MET cc_start: 0.7694 (tpp) cc_final: 0.7018 (tpp) REVERT: C 449 LYS cc_start: 0.8906 (mptp) cc_final: 0.8655 (mppt) REVERT: C 518 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8889 (pp) REVERT: C 591 ILE cc_start: 0.7256 (OUTLIER) cc_final: 0.6804 (tp) REVERT: C 713 GLU cc_start: 0.8564 (pp20) cc_final: 0.8122 (pp20) REVERT: C 926 ARG cc_start: 0.6676 (ttm-80) cc_final: 0.5984 (ptt90) REVERT: C 1000 ASN cc_start: 0.7817 (m-40) cc_final: 0.7071 (m-40) REVERT: D 407 MET cc_start: 0.7045 (mpp) cc_final: 0.6576 (mpp) REVERT: D 419 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7456 (tp30) REVERT: D 431 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8010 (mp0) REVERT: D 493 LYS cc_start: 0.8546 (mttp) cc_final: 0.8131 (mtpp) REVERT: D 637 GLU cc_start: 0.8519 (pt0) cc_final: 0.8050 (pm20) REVERT: D 714 GLN cc_start: 0.8438 (tp-100) cc_final: 0.7797 (tm-30) REVERT: D 760 ASP cc_start: 0.9109 (m-30) cc_final: 0.8519 (t70) REVERT: D 764 ASN cc_start: 0.9005 (m-40) cc_final: 0.8393 (m110) REVERT: E 75 HIS cc_start: 0.7591 (t70) cc_final: 0.7047 (t70) REVERT: E 99 PHE cc_start: 0.7979 (m-10) cc_final: 0.7614 (t80) REVERT: E 101 HIS cc_start: 0.7990 (m170) cc_final: 0.7319 (m-70) REVERT: E 108 ARG cc_start: 0.6389 (mmm160) cc_final: 0.5811 (mmm160) REVERT: E 123 MET cc_start: 0.5793 (mmm) cc_final: 0.5411 (mmm) REVERT: F 87 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7310 (tt0) REVERT: F 99 PHE cc_start: 0.7276 (m-10) cc_final: 0.6869 (t80) REVERT: F 151 TYR cc_start: 0.6776 (OUTLIER) cc_final: 0.6370 (t80) outliers start: 76 outliers final: 52 residues processed: 414 average time/residue: 0.1295 time to fit residues: 83.4658 Evaluate side-chains 402 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 341 time to evaluate : 0.664 ------------------------------------------------------------------------------- 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 469 TYR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 670 MET 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 474 ILE Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 700 TYR Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 403 SER 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 591 ILE Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 744 THR 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 986 ASP Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 395 VAL 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 546 PHE Chi-restraints excluded: chain D residue 573 ILE 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 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 24 VAL Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 65 ARG 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 151 TYR Chi-restraints excluded: chain F residue 153 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 61 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 71 optimal weight: 4.9990 chunk 146 optimal weight: 0.7980 chunk 145 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 169 optimal weight: 0.5980 chunk 64 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 136 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 ASN ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 950 HIS ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 747 ASN E 94 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 = 0.4290 r_free = 0.4290 target = 0.170625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.115120 restraints weight = 33166.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.119629 restraints weight = 17594.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.120432 restraints weight = 12048.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.120236 restraints weight = 10882.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.120582 restraints weight = 11444.232| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.6468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 19433 Z= 0.159 Angle : 0.810 14.819 26072 Z= 0.403 Chirality : 0.046 0.286 2836 Planarity : 0.005 0.066 3142 Dihedral : 14.684 125.130 3213 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.87 % Favored : 89.09 % Rotamer: Outliers : 3.52 % Allowed : 26.81 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 6.25 % 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 aren not related in a simple way. whole: -1.38 (0.18), residues: 2264 helix: 0.65 (0.15), residues: 1326 sheet: -3.19 (0.38), residues: 148 loop : -3.26 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 108 TYR 0.042 0.002 TYR D 450 PHE 0.032 0.002 PHE A1028 TRP 0.067 0.002 TRP B 460 HIS 0.013 0.001 HIS F 101 Details of bonding type rmsd covalent geometry : bond 0.00366 (19427) covalent geometry : angle 0.80758 (26060) SS BOND : bond 0.00632 ( 6) SS BOND : angle 2.94146 ( 12) hydrogen bonds : bond 0.03630 ( 834) hydrogen bonds : angle 3.99011 ( 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 424 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 355 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 TYR cc_start: 0.7518 (m-80) cc_final: 0.7242 (m-10) REVERT: A 524 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7457 (pt0) REVERT: A 581 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8723 (tp) REVERT: A 619 ASN cc_start: 0.9108 (OUTLIER) cc_final: 0.8349 (m-40) REVERT: A 638 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.8069 (t0) REVERT: A 670 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8673 (mtm) REVERT: A 943 PHE cc_start: 0.8539 (t80) cc_final: 0.8336 (t80) REVERT: A 985 ASN cc_start: 0.8360 (m-40) cc_final: 0.7927 (m110) REVERT: A 988 MET cc_start: 0.8714 (mmp) cc_final: 0.8397 (mmm) REVERT: A 1000 ASN cc_start: 0.7567 (m-40) cc_final: 0.7064 (m110) REVERT: B 419 GLU cc_start: 0.7102 (tp30) cc_final: 0.6567 (tp30) REVERT: B 487 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7741 (pp20) REVERT: B 491 PHE cc_start: 0.5909 (OUTLIER) cc_final: 0.5690 (t80) REVERT: B 493 LYS cc_start: 0.8630 (mttp) cc_final: 0.8255 (mtpp) REVERT: B 714 GLN cc_start: 0.8247 (tp-100) cc_final: 0.7594 (tm-30) REVERT: B 748 LEU cc_start: 0.9500 (tp) cc_final: 0.9074 (pp) REVERT: B 760 ASP cc_start: 0.9022 (m-30) cc_final: 0.8631 (t70) REVERT: B 767 TRP cc_start: 0.7762 (m-90) cc_final: 0.7428 (m-90) REVERT: C 449 LYS cc_start: 0.8864 (mptp) cc_final: 0.8654 (mppt) REVERT: C 518 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8958 (pp) REVERT: C 585 MET cc_start: 0.8635 (mmt) cc_final: 0.8078 (mmt) REVERT: C 591 ILE cc_start: 0.6999 (OUTLIER) cc_final: 0.6523 (tp) REVERT: C 713 GLU cc_start: 0.8579 (pp20) cc_final: 0.8106 (pp20) REVERT: C 781 LYS cc_start: 0.7986 (mppt) cc_final: 0.7403 (pttp) REVERT: C 926 ARG cc_start: 0.6677 (ttm-80) cc_final: 0.5884 (tmt170) REVERT: C 1000 ASN cc_start: 0.7743 (m-40) cc_final: 0.7140 (m-40) REVERT: D 407 MET cc_start: 0.6914 (mpp) cc_final: 0.6576 (mpp) REVERT: D 419 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7866 (tp30) REVERT: D 431 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7983 (mp0) REVERT: D 493 LYS cc_start: 0.8591 (mttp) cc_final: 0.8184 (mtpp) REVERT: D 637 GLU cc_start: 0.8510 (pt0) cc_final: 0.8045 (pm20) REVERT: D 714 GLN cc_start: 0.8415 (tp-100) cc_final: 0.7664 (tm-30) REVERT: D 748 LEU cc_start: 0.9142 (pp) cc_final: 0.8840 (mm) REVERT: D 760 ASP cc_start: 0.9019 (m-30) cc_final: 0.8483 (t70) REVERT: D 764 ASN cc_start: 0.8969 (m-40) cc_final: 0.8422 (m-40) REVERT: E 75 HIS cc_start: 0.7615 (t70) cc_final: 0.7127 (t70) REVERT: E 99 PHE cc_start: 0.7974 (m-10) cc_final: 0.7617 (t80) REVERT: E 101 HIS cc_start: 0.7936 (m170) cc_final: 0.7300 (m-70) REVERT: E 106 PHE cc_start: 0.7597 (p90) cc_final: 0.7169 (t80) REVERT: E 108 ARG cc_start: 0.6403 (mmm160) cc_final: 0.5711 (mmm160) REVERT: E 123 MET cc_start: 0.5802 (mmm) cc_final: 0.5442 (mmm) REVERT: F 87 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7349 (tt0) REVERT: F 99 PHE cc_start: 0.7140 (m-10) cc_final: 0.6735 (t80) REVERT: F 151 TYR cc_start: 0.6787 (OUTLIER) cc_final: 0.6345 (t80) outliers start: 69 outliers final: 54 residues processed: 393 average time/residue: 0.1292 time to fit residues: 79.3611 Evaluate side-chains 401 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 338 time to evaluate : 0.719 ------------------------------------------------------------------------------- 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 619 ASN Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 670 MET 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 467 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 700 TYR Chi-restraints excluded: chain B residue 747 ASN Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 403 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 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 591 ILE 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 900 CYS Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 986 ASP Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 395 VAL 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 546 PHE Chi-restraints excluded: chain D residue 573 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 14 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 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 65 ARG 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 151 TYR Chi-restraints excluded: chain F residue 153 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 91 optimal weight: 0.0970 chunk 165 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 127 optimal weight: 0.7980 chunk 168 optimal weight: 4.9990 chunk 46 optimal weight: 8.9990 chunk 222 optimal weight: 2.9990 chunk 226 optimal weight: 1.9990 chunk 155 optimal weight: 7.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN B 411 ASN ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 ASN ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 950 HIS D 575 ASN ** 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** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.170597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.117533 restraints weight = 33352.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.119662 restraints weight = 19767.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.121006 restraints weight = 13527.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.121214 restraints weight = 12071.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.121335 restraints weight = 11678.754| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.6500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.303 19433 Z= 0.257 Angle : 1.054 59.200 26072 Z= 0.591 Chirality : 0.049 0.546 2836 Planarity : 0.006 0.066 3142 Dihedral : 14.683 125.109 3213 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.87 % Favored : 89.09 % Rotamer: Outliers : 3.58 % Allowed : 27.07 % Favored : 69.36 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 6.25 % 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 aren not related in a simple way. whole: -1.38 (0.18), residues: 2264 helix: 0.64 (0.15), residues: 1326 sheet: -3.17 (0.38), residues: 148 loop : -3.25 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG F 108 TYR 0.053 0.002 TYR D 450 PHE 0.040 0.002 PHE B 438 TRP 0.064 0.003 TRP D 460 HIS 0.012 0.001 HIS F 101 Details of bonding type rmsd covalent geometry : bond 0.00598 (19427) covalent geometry : angle 1.05271 (26060) SS BOND : bond 0.00661 ( 6) SS BOND : angle 2.75128 ( 12) hydrogen bonds : bond 0.03692 ( 834) hydrogen bonds : angle 3.99563 ( 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 411 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 341 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 TYR cc_start: 0.7525 (m-80) cc_final: 0.7243 (m-10) REVERT: A 524 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7444 (pt0) REVERT: A 581 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8725 (tp) REVERT: A 619 ASN cc_start: 0.9116 (OUTLIER) cc_final: 0.8368 (m-40) REVERT: A 638 ASP cc_start: 0.8375 (OUTLIER) cc_final: 0.8085 (t0) REVERT: A 670 MET cc_start: 0.9106 (OUTLIER) cc_final: 0.8687 (mtm) REVERT: A 943 PHE cc_start: 0.8573 (t80) cc_final: 0.8361 (t80) REVERT: A 985 ASN cc_start: 0.8358 (m-40) cc_final: 0.7918 (m110) REVERT: A 988 MET cc_start: 0.8709 (mmp) cc_final: 0.8398 (mmm) REVERT: A 1000 ASN cc_start: 0.7580 (m-40) cc_final: 0.7063 (m110) REVERT: B 419 GLU cc_start: 0.7209 (tp30) cc_final: 0.6724 (tp30) REVERT: B 487 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7788 (pp20) REVERT: B 491 PHE cc_start: 0.5961 (OUTLIER) cc_final: 0.5732 (t80) REVERT: B 493 LYS cc_start: 0.8614 (mttp) cc_final: 0.8216 (mtpp) REVERT: B 709 ASN cc_start: 0.8737 (t0) cc_final: 0.8498 (t0) REVERT: B 714 GLN cc_start: 0.8269 (tp-100) cc_final: 0.7589 (tm-30) REVERT: B 748 LEU cc_start: 0.9410 (tp) cc_final: 0.9002 (pp) REVERT: B 760 ASP cc_start: 0.9074 (m-30) cc_final: 0.8449 (t70) REVERT: B 764 ASN cc_start: 0.8796 (m-40) cc_final: 0.8178 (m110) REVERT: B 767 TRP cc_start: 0.7778 (m-90) cc_final: 0.7423 (m-90) REVERT: C 449 LYS cc_start: 0.8871 (mptp) cc_final: 0.8635 (mppt) REVERT: C 518 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8947 (pp) REVERT: C 585 MET cc_start: 0.8678 (mmt) cc_final: 0.8127 (mmt) REVERT: C 591 ILE cc_start: 0.7055 (OUTLIER) cc_final: 0.6581 (tp) REVERT: C 713 GLU cc_start: 0.8571 (pp20) cc_final: 0.8102 (pp20) REVERT: C 781 LYS cc_start: 0.7965 (mppt) cc_final: 0.7404 (pttp) REVERT: C 926 ARG cc_start: 0.6685 (ttm-80) cc_final: 0.5873 (tmt170) REVERT: C 1000 ASN cc_start: 0.7764 (m-40) cc_final: 0.7139 (m-40) REVERT: D 407 MET cc_start: 0.6891 (mpp) cc_final: 0.6554 (mpp) REVERT: D 419 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7907 (tp30) REVERT: D 431 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7984 (mp0) REVERT: D 493 LYS cc_start: 0.8579 (mttp) cc_final: 0.8143 (mtpp) REVERT: D 637 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8059 (pm20) REVERT: D 714 GLN cc_start: 0.8434 (tp-100) cc_final: 0.7673 (tm-30) REVERT: D 748 LEU cc_start: 0.9048 (pp) cc_final: 0.8819 (mm) REVERT: D 760 ASP cc_start: 0.9092 (m-30) cc_final: 0.8506 (t70) REVERT: D 764 ASN cc_start: 0.8968 (m-40) cc_final: 0.8448 (m-40) REVERT: E 75 HIS cc_start: 0.7595 (t70) cc_final: 0.7116 (t70) REVERT: E 99 PHE cc_start: 0.7997 (m-10) cc_final: 0.7610 (t80) REVERT: E 101 HIS cc_start: 0.7942 (m170) cc_final: 0.7285 (m-70) REVERT: E 106 PHE cc_start: 0.7631 (p90) cc_final: 0.7234 (t80) REVERT: E 108 ARG cc_start: 0.6302 (mmm160) cc_final: 0.5713 (mmm160) REVERT: E 123 MET cc_start: 0.5768 (mmm) cc_final: 0.5411 (mmm) REVERT: F 87 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7344 (tt0) REVERT: F 99 PHE cc_start: 0.7152 (m-10) cc_final: 0.6715 (t80) REVERT: F 151 TYR cc_start: 0.6760 (OUTLIER) cc_final: 0.6340 (t80) outliers start: 70 outliers final: 54 residues processed: 378 average time/residue: 0.1370 time to fit residues: 81.0295 Evaluate side-chains 403 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 339 time to evaluate : 0.757 ------------------------------------------------------------------------------- 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 619 ASN Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 723 VAL 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 A residue 1027 LEU Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 700 TYR Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 469 TYR Chi-restraints excluded: chain C residue 474 ILE 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 591 ILE Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 900 CYS Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 986 ASP Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 395 VAL 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 546 PHE Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 637 GLU Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 14 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 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 65 ARG 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 151 TYR Chi-restraints excluded: chain F residue 153 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 188 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 168 optimal weight: 0.4980 chunk 13 optimal weight: 0.8980 chunk 117 optimal weight: 0.9980 chunk 145 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 950 HIS D 575 ASN ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 747 ASN ** 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 = 0.4290 r_free = 0.4290 target = 0.170550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.117447 restraints weight = 33235.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.120782 restraints weight = 19725.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.120964 restraints weight = 12487.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.121183 restraints weight = 12346.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.121570 restraints weight = 11949.282| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.6507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.303 19433 Z= 0.257 Angle : 1.054 59.200 26072 Z= 0.591 Chirality : 0.049 0.546 2836 Planarity : 0.006 0.066 3142 Dihedral : 14.683 125.109 3213 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 19.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.87 % Favored : 89.09 % Rotamer: Outliers : 3.32 % Allowed : 27.22 % Favored : 69.46 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 6.25 % 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 aren not related in a simple way. whole: -1.38 (0.18), residues: 2264 helix: 0.64 (0.15), residues: 1326 sheet: -3.17 (0.38), residues: 148 loop : -3.25 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG F 108 TYR 0.053 0.002 TYR D 450 PHE 0.040 0.002 PHE B 438 TRP 0.064 0.003 TRP D 460 HIS 0.012 0.001 HIS F 101 Details of bonding type rmsd covalent geometry : bond 0.00598 (19427) covalent geometry : angle 1.05271 (26060) SS BOND : bond 0.00661 ( 6) SS BOND : angle 2.75128 ( 12) hydrogen bonds : bond 0.03692 ( 834) hydrogen bonds : angle 3.99563 ( 2436) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3705.50 seconds wall clock time: 64 minutes 56.47 seconds (3896.47 seconds total)