Starting phenix.real_space_refine on Tue May 20 03:44:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ssb_40750/05_2025/8ssb_40750.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ssb_40750/05_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_40750/05_2025/8ssb_40750.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ssb_40750/05_2025/8ssb_40750.map" model { file = "/net/cci-nas-00/data/ceres_data/8ssb_40750/05_2025/8ssb_40750.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ssb_40750/05_2025/8ssb_40750.cif" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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-1': 4, 'PCW:plan-2': 1, '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-2': 1, 'PCW:plan-4': 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-1': 4, 'PCW:plan-2': 1, '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-2': 2, 'PCW:plan-4': 1} 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-1': 1, 'PCW:plan-2': 2, '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-2': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 11.27, per 1000 atoms: 0.59 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: 4.36 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 1.73 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: 5.13 Time building geometry restraints manager: 4.93 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 1035 or resid 1101 or (resid 1102 through 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 na \ me 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 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 O \ 3P or name O4P or name P )) or (resid 1104 through 1106 and (name C13 or name C1 \ 4 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or nam \ e C21 or name C22 or name C23)) or resid 1108 through 1109)) selection = (chain 'C' and (resid 394 through 1035 or resid 1101 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 na \ me 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 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 O \ 3P or name O4P or name P )) or resid 1104 through 1108)) } ncs_group { reference = (chain 'B' and (resid 394 through 821 or resid 1101 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 C \ 15 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 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 O31 or name O3P or name O4P or name P )) or (resid 1105 and (name N or nam \ e 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 C21 or name C22 \ or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name C \ 36 or name C37 or name C38 or name C39 or name C4 or name C40 or name C41 or nam \ e 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 )))) selection = (chain 'D' and (resid 394 through 821 or resid 1101 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 C \ 15 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 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 O31 or name O3P or name 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: 4.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.780 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 39.360 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.770 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.018 0.003 TRP B 578 HIS 0.013 0.003 HIS E 27 PHE 0.026 0.003 PHE A 546 TYR 0.033 0.003 TYR F 149 ARG 0.007 0.001 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.29522 ( 834) hydrogen bonds : angle 10.26796 ( 2436) SS BOND : bond 0.00662 ( 6) SS BOND : angle 1.02563 ( 12) covalent geometry : bond 0.00946 (19427) covalent geometry : angle 1.54546 (26060) *********************** 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 : 1.876 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: 0.8633 (ttm) REVERT: A 467 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7561 (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: 0.7774 (mm-30) REVERT: A 713 GLU cc_start: 0.8629 (pp20) cc_final: 0.8380 (pp20) 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: 0.7506 (mtt) REVERT: B 421 TYR cc_start: 0.7901 (m-10) cc_final: 0.7632 (m-10) REVERT: B 460 TRP cc_start: 0.6636 (m-90) cc_final: 0.6428 (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: 0.8626 (tm-30) REVERT: B 714 GLN cc_start: 0.7642 (tp-100) cc_final: 0.7256 (tp40) REVERT: B 760 ASP cc_start: 0.9255 (m-30) cc_final: 0.8811 (t70) REVERT: B 761 LYS cc_start: 0.9498 (tptp) cc_final: 0.9238 (tppt) REVERT: B 764 ASN cc_start: 0.8725 (m-40) cc_final: 0.8189 (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: 0.8853 (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: 0.5923 (ttt90) REVERT: C 1029 MET cc_start: 0.8040 (mmm) cc_final: 0.7677 (mtp) REVERT: D 395 VAL cc_start: 0.8295 (OUTLIER) cc_final: 0.8091 (p) 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: 0.6074 (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: 0.8144 (tp) REVERT: D 702 TYR cc_start: 0.7747 (t80) cc_final: 0.7138 (t80) REVERT: D 714 GLN cc_start: 0.7907 (tp-100) cc_final: 0.7441 (tp40) REVERT: D 760 ASP cc_start: 0.9467 (m-30) cc_final: 0.9041 (t70) REVERT: D 764 ASN cc_start: 0.9106 (m-40) cc_final: 0.8788 (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: 0.6595 (t-90) REVERT: E 59 ARG cc_start: 0.6999 (tmm-80) cc_final: 0.6663 (tmt-80) REVERT: E 75 HIS cc_start: 0.7453 (t70) cc_final: 0.6541 (t70) REVERT: E 94 ASN cc_start: 0.7672 (p0) cc_final: 0.7412 (p0) REVERT: E 95 ILE cc_start: 0.8136 (tp) cc_final: 0.7020 (tt) REVERT: E 99 PHE cc_start: 0.7789 (m-10) cc_final: 0.7534 (m-80) REVERT: E 101 HIS cc_start: 0.7278 (m170) cc_final: 0.6702 (m170) REVERT: F 33 GLU cc_start: 0.7318 (mm-30) cc_final: 0.7047 (tm-30) REVERT: F 78 PHE cc_start: 0.7518 (m-80) cc_final: 0.7218 (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: 0.6461 (pp-130) outliers start: 14 outliers final: 0 residues processed: 659 average time/residue: 0.3255 time to fit residues: 314.7530 Evaluate side-chains 387 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 384 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain D residue 395 VAL 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 192 optimal weight: 0.8980 chunk 172 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 178 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 108 optimal weight: 0.8980 chunk 133 optimal weight: 8.9990 chunk 207 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4219 r_free = 0.4219 target = 0.166602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.114564 restraints weight = 33476.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.114378 restraints weight = 19536.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.114656 restraints weight = 16877.747| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 19433 Z= 0.173 Angle : 0.830 11.605 26072 Z= 0.429 Chirality : 0.046 0.198 2836 Planarity : 0.006 0.079 3142 Dihedral : 18.349 160.931 3219 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.62 % Allowed : 10.16 % Favored : 89.22 % Rotamer: Outliers : 3.93 % Allowed : 16.45 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.95 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.99 (0.15), residues: 2264 helix: -1.86 (0.12), residues: 1356 sheet: -4.26 (0.35), residues: 120 loop : -3.63 (0.19), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 671 HIS 0.013 0.002 HIS E 107 PHE 0.030 0.002 PHE A 901 TYR 0.035 0.002 TYR D 450 ARG 0.007 0.001 ARG C 684 Details of bonding type rmsd hydrogen bonds : bond 0.04945 ( 834) hydrogen bonds : angle 4.90783 ( 2436) SS BOND : bond 0.01422 ( 6) SS BOND : angle 2.21846 ( 12) covalent geometry : bond 0.00373 (19427) covalent geometry : angle 0.82865 (26060) *********************** 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 540 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 463 time to evaluate : 1.865 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 581 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8611 (tp) REVERT: A 585 MET cc_start: 0.8346 (mpt) cc_final: 0.8032 (mpt) REVERT: A 619 ASN cc_start: 0.8212 (m110) cc_final: 0.7374 (t0) REVERT: A 670 MET cc_start: 0.9123 (mtm) cc_final: 0.8905 (mtm) REVERT: A 879 LYS cc_start: 0.8403 (ttpt) cc_final: 0.7895 (mmtm) REVERT: A 1016 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8604 (mt) REVERT: B 400 ILE cc_start: 0.6965 (tt) cc_final: 0.6745 (mp) REVERT: B 463 MET cc_start: 0.7179 (ptp) cc_final: 0.6812 (ptp) REVERT: B 493 LYS cc_start: 0.8957 (mttp) cc_final: 0.8522 (tttm) REVERT: B 669 LYS cc_start: 0.9134 (pttt) cc_final: 0.8918 (pttt) REVERT: B 713 GLU cc_start: 0.8970 (tm-30) cc_final: 0.8683 (tm-30) REVERT: B 714 GLN cc_start: 0.8025 (tp-100) cc_final: 0.7322 (tp40) REVERT: B 721 MET cc_start: 0.7885 (ppp) cc_final: 0.7660 (ppp) REVERT: B 748 LEU cc_start: 0.9524 (tp) cc_final: 0.9117 (pp) REVERT: B 760 ASP cc_start: 0.9250 (m-30) cc_final: 0.8749 (t70) REVERT: B 764 ASN cc_start: 0.8856 (m-40) cc_final: 0.8190 (m-40) REVERT: C 450 TYR cc_start: 0.7120 (m-80) cc_final: 0.6377 (m-80) REVERT: C 518 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8543 (pp) REVERT: C 581 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9043 (tp) REVERT: C 714 GLN cc_start: 0.8557 (mm-40) cc_final: 0.7964 (mm-40) REVERT: C 880 MET cc_start: 0.7915 (tmm) cc_final: 0.7660 (tmm) REVERT: C 891 PHE cc_start: 0.5727 (m-80) cc_final: 0.5417 (m-10) REVERT: C 926 ARG cc_start: 0.6351 (ttm-80) cc_final: 0.5736 (tmt170) REVERT: C 991 ARG cc_start: 0.6834 (mmt-90) cc_final: 0.6344 (mmt90) REVERT: C 1000 ASN cc_start: 0.7972 (m-40) cc_final: 0.7432 (m110) REVERT: D 421 TYR cc_start: 0.7927 (m-10) cc_final: 0.7671 (m-10) REVERT: D 493 LYS cc_start: 0.8718 (mttp) cc_final: 0.8182 (tttm) REVERT: D 533 TYR cc_start: 0.8735 (t80) cc_final: 0.8510 (t80) REVERT: D 702 TYR cc_start: 0.7627 (t80) cc_final: 0.7327 (t80) REVERT: D 714 GLN cc_start: 0.8424 (tp-100) cc_final: 0.7640 (tp40) REVERT: D 760 ASP cc_start: 0.9321 (m-30) cc_final: 0.8933 (t0) REVERT: D 762 LEU cc_start: 0.9291 (mm) cc_final: 0.9083 (mm) REVERT: E 75 HIS cc_start: 0.7553 (t70) cc_final: 0.6179 (t70) REVERT: E 78 PHE cc_start: 0.7837 (m-80) cc_final: 0.7412 (m-80) REVERT: E 87 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7555 (mm-30) REVERT: E 94 ASN cc_start: 0.7723 (p0) cc_final: 0.7376 (p0) REVERT: E 95 ILE cc_start: 0.8528 (tp) cc_final: 0.7741 (tt) REVERT: E 99 PHE cc_start: 0.7965 (m-10) cc_final: 0.7698 (m-80) REVERT: E 101 HIS cc_start: 0.7494 (m170) cc_final: 0.6453 (m170) REVERT: F 78 PHE cc_start: 0.7714 (m-80) cc_final: 0.7427 (m-80) REVERT: F 99 PHE cc_start: 0.7577 (m-10) cc_final: 0.7121 (t80) REVERT: F 104 ARG cc_start: 0.8810 (tpt90) cc_final: 0.8421 (tpt-90) outliers start: 77 outliers final: 28 residues processed: 514 average time/residue: 0.3351 time to fit residues: 261.1055 Evaluate side-chains 408 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 376 time to evaluate : 2.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 443 THR 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 864 LEU Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 504 ILE Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 900 CYS 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 23 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 188 optimal weight: 5.9990 chunk 124 optimal weight: 0.4980 chunk 116 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 196 optimal weight: 0.2980 chunk 213 optimal weight: 0.8980 chunk 147 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 714 GLN B 435 HIS B 587 GLN ** C 883 HIS ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.163843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.111533 restraints weight = 33416.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.112309 restraints weight = 19917.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.111867 restraints weight = 15939.591| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.4604 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= 0.190 Angle : 0.805 12.080 26072 Z= 0.411 Chirality : 0.046 0.185 2836 Planarity : 0.006 0.079 3142 Dihedral : 17.173 149.370 3213 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.44 % Allowed : 11.44 % Favored : 88.12 % Rotamer: Outliers : 4.70 % Allowed : 18.08 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 1.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.17), residues: 2264 helix: -0.76 (0.13), residues: 1336 sheet: -3.84 (0.38), residues: 120 loop : -3.41 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 460 HIS 0.015 0.002 HIS F 101 PHE 0.026 0.002 PHE E 146 TYR 0.036 0.002 TYR B 450 ARG 0.009 0.001 ARG F 108 Details of bonding type rmsd hydrogen bonds : bond 0.04299 ( 834) hydrogen bonds : angle 4.42707 ( 2436) SS BOND : bond 0.00779 ( 6) SS BOND : angle 1.90379 ( 12) covalent geometry : bond 0.00439 (19427) covalent geometry : angle 0.80374 (26060) *********************** 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 514 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 422 time to evaluate : 1.901 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: 0.7388 (m-80) cc_final: 0.6909 (m-10) REVERT: A 581 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.8993 (tp) REVERT: A 705 GLU cc_start: 0.7411 (mt-10) cc_final: 0.6302 (mt-10) REVERT: A 714 GLN cc_start: 0.9105 (OUTLIER) cc_final: 0.8796 (mm-40) REVERT: A 924 MET cc_start: 0.7069 (mmm) cc_final: 0.6381 (mmp) REVERT: A 926 ARG cc_start: 0.7348 (ptm160) cc_final: 0.6974 (ptm160) REVERT: A 1000 ASN cc_start: 0.7889 (m-40) cc_final: 0.7305 (m-40) REVERT: B 419 GLU cc_start: 0.6944 (tp30) cc_final: 0.6594 (tp30) REVERT: B 714 GLN cc_start: 0.8105 (tp-100) cc_final: 0.7419 (tp40) REVERT: B 748 LEU cc_start: 0.9431 (tp) cc_final: 0.8998 (pp) REVERT: B 760 ASP cc_start: 0.9095 (m-30) cc_final: 0.8760 (t70) REVERT: B 762 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.8977 (mm) REVERT: C 450 TYR cc_start: 0.7179 (m-80) cc_final: 0.6461 (m-80) REVERT: C 518 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8923 (pp) REVERT: C 581 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.8929 (tp) REVERT: C 714 GLN cc_start: 0.8684 (mm-40) cc_final: 0.8216 (mm-40) REVERT: C 865 GLU cc_start: 0.7555 (mm-30) cc_final: 0.6820 (mm-30) REVERT: C 890 CYS cc_start: 0.2296 (t) cc_final: 0.1961 (t) REVERT: C 926 ARG cc_start: 0.6512 (ttm-80) cc_final: 0.5817 (tmt170) REVERT: C 991 ARG cc_start: 0.6775 (mmt-90) cc_final: 0.6135 (mmt90) REVERT: C 999 PHE cc_start: 0.6972 (OUTLIER) cc_final: 0.6242 (m-80) REVERT: C 1000 ASN cc_start: 0.8167 (m-40) cc_final: 0.7446 (m-40) REVERT: D 419 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7754 (tp30) REVERT: D 431 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8130 (mp0) REVERT: D 460 TRP cc_start: 0.6251 (m-90) cc_final: 0.5929 (m-90) REVERT: D 493 LYS cc_start: 0.8728 (mttp) cc_final: 0.8137 (mtpp) REVERT: D 714 GLN cc_start: 0.8459 (tp-100) cc_final: 0.7650 (tp40) REVERT: D 760 ASP cc_start: 0.9164 (m-30) cc_final: 0.8794 (t0) REVERT: E 75 HIS cc_start: 0.7645 (t70) cc_final: 0.6779 (t70) REVERT: E 78 PHE cc_start: 0.7794 (m-80) cc_final: 0.7539 (m-80) REVERT: E 87 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7647 (mm-30) REVERT: E 94 ASN cc_start: 0.7735 (p0) cc_final: 0.7431 (p0) REVERT: E 95 ILE cc_start: 0.8563 (tp) cc_final: 0.7807 (tt) REVERT: E 99 PHE cc_start: 0.7948 (m-10) cc_final: 0.7628 (m-80) REVERT: E 101 HIS cc_start: 0.7819 (m170) cc_final: 0.7365 (m-70) REVERT: F 78 PHE cc_start: 0.7783 (m-80) cc_final: 0.7555 (m-80) REVERT: F 99 PHE cc_start: 0.7625 (m-10) cc_final: 0.7172 (t80) REVERT: F 104 ARG cc_start: 0.8655 (tpt90) cc_final: 0.8276 (tpt-90) outliers start: 92 outliers final: 33 residues processed: 476 average time/residue: 0.2942 time to fit residues: 213.6109 Evaluate side-chains 407 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 367 time to evaluate : 1.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 714 GLN 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 447 ASP 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 B residue 762 LEU 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 581 LEU Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 638 ASP 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 474 ILE Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 637 GLU 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 F residue 4 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 76 optimal weight: 1.9990 chunk 184 optimal weight: 0.0570 chunk 93 optimal weight: 5.9990 chunk 72 optimal weight: 0.5980 chunk 153 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 169 optimal weight: 20.0000 chunk 112 optimal weight: 0.5980 chunk 122 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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 A 714 GLN B 435 HIS ** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 GLN ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 883 HIS D 508 GLN D 575 ASN ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.166123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.110741 restraints weight = 33622.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.114300 restraints weight = 19000.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.114801 restraints weight = 13715.109| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.5124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19433 Z= 0.146 Angle : 0.778 12.783 26072 Z= 0.392 Chirality : 0.045 0.201 2836 Planarity : 0.005 0.071 3142 Dihedral : 16.317 144.100 3213 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.51 % Favored : 89.18 % Rotamer: Outliers : 4.19 % Allowed : 20.74 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.99 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.17), residues: 2264 helix: -0.15 (0.14), residues: 1344 sheet: -3.42 (0.36), residues: 150 loop : -3.35 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 460 HIS 0.015 0.002 HIS F 101 PHE 0.038 0.002 PHE A 943 TYR 0.041 0.002 TYR D 673 ARG 0.004 0.000 ARG F 108 Details of bonding type rmsd hydrogen bonds : bond 0.03768 ( 834) hydrogen bonds : angle 4.16223 ( 2436) SS BOND : bond 0.00788 ( 6) SS BOND : angle 2.82857 ( 12) covalent geometry : bond 0.00325 (19427) covalent geometry : angle 0.77590 (26060) *********************** 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 492 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 410 time to evaluate : 1.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 TYR cc_start: 0.7368 (m-80) cc_final: 0.6651 (m-80) REVERT: A 581 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.8884 (tp) REVERT: A 619 ASN cc_start: 0.8977 (OUTLIER) cc_final: 0.7638 (m-40) REVERT: A 755 GLU cc_start: 0.8929 (mp0) cc_final: 0.8498 (mp0) REVERT: A 926 ARG cc_start: 0.7136 (ptm160) cc_final: 0.6718 (ptm160) REVERT: A 1000 ASN cc_start: 0.7905 (m-40) cc_final: 0.7106 (m-40) REVERT: B 419 GLU cc_start: 0.7070 (tp30) cc_final: 0.6732 (tp30) REVERT: B 714 GLN cc_start: 0.8219 (tp-100) cc_final: 0.7334 (tp40) REVERT: B 748 LEU cc_start: 0.9477 (tp) cc_final: 0.9034 (pp) REVERT: B 760 ASP cc_start: 0.9162 (m-30) cc_final: 0.8569 (t70) REVERT: B 762 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9003 (mm) REVERT: B 764 ASN cc_start: 0.8840 (m-40) cc_final: 0.8359 (m110) REVERT: C 450 TYR cc_start: 0.7172 (m-80) cc_final: 0.6508 (m-80) REVERT: C 518 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8849 (pp) REVERT: C 581 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.8903 (tp) REVERT: C 674 MET cc_start: 0.7739 (mtp) cc_final: 0.7523 (mtp) REVERT: C 688 GLU cc_start: 0.7436 (pt0) cc_final: 0.7219 (tp30) REVERT: C 713 GLU cc_start: 0.8607 (pp20) cc_final: 0.8012 (pp20) REVERT: C 714 GLN cc_start: 0.8684 (mm-40) cc_final: 0.7981 (mm110) REVERT: C 864 LEU cc_start: 0.7122 (mt) cc_final: 0.6682 (mp) REVERT: C 926 ARG cc_start: 0.6752 (ttm-80) cc_final: 0.5822 (tmt170) REVERT: C 1000 ASN cc_start: 0.7918 (m-40) cc_final: 0.7516 (m-40) REVERT: C 1019 SER cc_start: 0.9423 (t) cc_final: 0.9222 (t) REVERT: D 401 LEU cc_start: 0.8775 (pp) cc_final: 0.8412 (tt) REVERT: D 419 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7610 (tp30) REVERT: D 431 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8165 (mp0) REVERT: D 493 LYS cc_start: 0.8592 (mttp) cc_final: 0.8002 (mtpp) REVERT: D 633 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8229 (mp) REVERT: D 714 GLN cc_start: 0.8449 (tp-100) cc_final: 0.7768 (tm-30) REVERT: D 748 LEU cc_start: 0.9493 (tp) cc_final: 0.9001 (pp) REVERT: D 760 ASP cc_start: 0.9271 (m-30) cc_final: 0.8745 (t70) REVERT: D 781 LYS cc_start: 0.5426 (tptt) cc_final: 0.5166 (mtpp) REVERT: D 783 LYS cc_start: 0.6862 (pmtt) cc_final: 0.6452 (ptpp) REVERT: E 75 HIS cc_start: 0.7541 (t70) cc_final: 0.6953 (t70) REVERT: E 87 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7589 (tp30) REVERT: E 95 ILE cc_start: 0.8521 (tp) cc_final: 0.7734 (tt) REVERT: E 99 PHE cc_start: 0.7944 (m-10) cc_final: 0.7601 (m-80) REVERT: E 101 HIS cc_start: 0.7803 (m170) cc_final: 0.7347 (m-70) REVERT: E 134 GLU cc_start: 0.7357 (tm-30) cc_final: 0.6874 (tm-30) REVERT: F 99 PHE cc_start: 0.7600 (m-10) cc_final: 0.7140 (t80) REVERT: F 104 ARG cc_start: 0.8681 (tpt90) cc_final: 0.8404 (tpt-90) REVERT: F 123 MET cc_start: 0.5863 (mmm) cc_final: 0.5658 (mmm) outliers start: 82 outliers final: 44 residues processed: 462 average time/residue: 0.3008 time to fit residues: 213.9023 Evaluate side-chains 411 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 360 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 469 TYR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain A residue 638 ASP 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 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 762 LEU Chi-restraints excluded: chain C residue 398 THR 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 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 581 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 900 CYS 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 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 4 THR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 144 LEU 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 118 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 196 optimal weight: 7.9990 chunk 148 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 71 optimal weight: 0.0060 chunk 30 optimal weight: 4.9990 overall best weight: 0.9202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 HIS A 642 GLN A 874 GLN ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 ASN ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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 = 0.4211 r_free = 0.4211 target = 0.165778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.110243 restraints weight = 33672.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.112628 restraints weight = 20628.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.113416 restraints weight = 14840.140| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.5507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19433 Z= 0.156 Angle : 0.751 13.398 26072 Z= 0.381 Chirality : 0.045 0.185 2836 Planarity : 0.005 0.066 3142 Dihedral : 15.769 138.460 3213 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.42 % Favored : 89.31 % Rotamer: Outliers : 5.11 % Allowed : 22.11 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.86 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.18), residues: 2264 helix: 0.18 (0.14), residues: 1342 sheet: -2.82 (0.40), residues: 132 loop : -3.39 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 460 HIS 0.017 0.002 HIS F 101 PHE 0.032 0.002 PHE A 943 TYR 0.027 0.002 TYR D 450 ARG 0.008 0.000 ARG E 108 Details of bonding type rmsd hydrogen bonds : bond 0.03701 ( 834) hydrogen bonds : angle 4.06053 ( 2436) SS BOND : bond 0.00548 ( 6) SS BOND : angle 1.36114 ( 12) covalent geometry : bond 0.00358 (19427) covalent geometry : angle 0.75110 (26060) *********************** 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 493 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 393 time to evaluate : 2.074 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: 0.7400 (m-80) cc_final: 0.6730 (m-80) REVERT: A 581 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9005 (tp) REVERT: A 619 ASN cc_start: 0.9097 (OUTLIER) cc_final: 0.7760 (m-40) REVERT: A 688 GLU cc_start: 0.7631 (pt0) cc_final: 0.7386 (tp30) REVERT: A 755 GLU cc_start: 0.8928 (mp0) cc_final: 0.8532 (mp0) REVERT: A 926 ARG cc_start: 0.7038 (ptm160) cc_final: 0.6799 (ptm160) REVERT: A 1000 ASN cc_start: 0.7870 (m-40) cc_final: 0.7257 (m-40) REVERT: B 401 LEU cc_start: 0.8994 (tp) cc_final: 0.8688 (pt) REVERT: B 407 MET cc_start: 0.7316 (mpp) cc_final: 0.6720 (mpp) REVERT: B 419 GLU cc_start: 0.6978 (tp30) cc_final: 0.6711 (tp30) REVERT: B 714 GLN cc_start: 0.8252 (tp-100) cc_final: 0.7474 (tp40) REVERT: B 760 ASP cc_start: 0.9133 (m-30) cc_final: 0.8586 (t70) REVERT: B 762 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8897 (mm) REVERT: B 764 ASN cc_start: 0.8863 (m-40) cc_final: 0.8361 (m110) REVERT: C 450 TYR cc_start: 0.7498 (m-80) cc_final: 0.6760 (m-80) REVERT: C 518 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8934 (pp) REVERT: C 581 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.8900 (tp) REVERT: C 596 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8303 (tm) REVERT: C 688 GLU cc_start: 0.7645 (pt0) cc_final: 0.7289 (tp30) REVERT: C 713 GLU cc_start: 0.8653 (pp20) cc_final: 0.8141 (pp20) REVERT: C 714 GLN cc_start: 0.8772 (mm-40) cc_final: 0.8185 (mm110) REVERT: C 926 ARG cc_start: 0.6886 (ttm-80) cc_final: 0.5918 (tmt170) REVERT: C 999 PHE cc_start: 0.6742 (OUTLIER) cc_final: 0.6261 (m-80) REVERT: C 1000 ASN cc_start: 0.7911 (m-40) cc_final: 0.7596 (m-40) REVERT: C 1019 SER cc_start: 0.9469 (t) cc_final: 0.9269 (t) REVERT: D 401 LEU cc_start: 0.8822 (pp) cc_final: 0.8487 (tt) REVERT: D 419 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7636 (tp30) REVERT: D 431 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8136 (mp0) REVERT: D 493 LYS cc_start: 0.8602 (mttp) cc_final: 0.8126 (mtpp) REVERT: D 519 ASP cc_start: 0.7903 (OUTLIER) cc_final: 0.7668 (m-30) REVERT: D 637 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8101 (pm20) REVERT: D 673 TYR cc_start: 0.8180 (m-80) cc_final: 0.7723 (m-80) REVERT: D 714 GLN cc_start: 0.8445 (tp-100) cc_final: 0.7613 (tp40) REVERT: D 748 LEU cc_start: 0.9467 (tp) cc_final: 0.9000 (pp) REVERT: D 760 ASP cc_start: 0.9262 (m-30) cc_final: 0.8610 (t0) REVERT: D 764 ASN cc_start: 0.9006 (m-40) cc_final: 0.8462 (m-40) REVERT: E 11 MET cc_start: 0.8643 (mtp) cc_final: 0.8440 (mtp) REVERT: E 75 HIS cc_start: 0.7481 (t70) cc_final: 0.7085 (t70) REVERT: E 87 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7609 (tp30) REVERT: E 95 ILE cc_start: 0.8516 (tp) cc_final: 0.7648 (tt) REVERT: E 99 PHE cc_start: 0.7945 (m-10) cc_final: 0.7554 (m-80) REVERT: E 101 HIS cc_start: 0.7929 (m170) cc_final: 0.7452 (m-70) REVERT: E 123 MET cc_start: 0.6069 (mmm) cc_final: 0.5807 (mmm) REVERT: E 134 GLU cc_start: 0.7408 (tm-30) cc_final: 0.6912 (tm-30) REVERT: F 87 GLU cc_start: 0.7522 (mm-30) cc_final: 0.7315 (tp30) REVERT: F 99 PHE cc_start: 0.7613 (m-10) cc_final: 0.7064 (t80) REVERT: F 104 ARG cc_start: 0.8710 (tpt90) cc_final: 0.8466 (tpp80) outliers start: 100 outliers final: 58 residues processed: 453 average time/residue: 0.2945 time to fit residues: 206.5463 Evaluate side-chains 425 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 357 time to evaluate : 2.144 ------------------------------------------------------------------------------- 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 638 ASP Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1005 TRP Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 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 525 ILE 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 581 LEU Chi-restraints excluded: chain C residue 591 ILE 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 546 PHE Chi-restraints excluded: chain D residue 637 GLU Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 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 68 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 129 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 171 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 146 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 86 optimal weight: 0.0370 chunk 75 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 162 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** 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** ** D 756 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.167698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.115328 restraints weight = 33682.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.116389 restraints weight = 19075.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.116127 restraints weight = 15000.469| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.5852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19433 Z= 0.141 Angle : 0.770 13.625 26072 Z= 0.387 Chirality : 0.044 0.253 2836 Planarity : 0.005 0.063 3142 Dihedral : 15.239 132.187 3213 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.22 % Allowed : 10.38 % Favored : 89.40 % Rotamer: Outliers : 4.34 % Allowed : 23.60 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.81 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.18), residues: 2264 helix: 0.48 (0.15), residues: 1334 sheet: -2.60 (0.38), residues: 154 loop : -3.35 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP B 460 HIS 0.018 0.002 HIS F 101 PHE 0.034 0.002 PHE A 943 TYR 0.028 0.001 TYR B 450 ARG 0.008 0.000 ARG E 108 Details of bonding type rmsd hydrogen bonds : bond 0.03507 ( 834) hydrogen bonds : angle 3.94978 ( 2436) SS BOND : bond 0.00544 ( 6) SS BOND : angle 3.47090 ( 12) covalent geometry : bond 0.00315 (19427) covalent geometry : angle 0.76670 (26060) *********************** 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 472 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 387 time to evaluate : 2.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 TYR cc_start: 0.7349 (m-80) cc_final: 0.6807 (m-80) REVERT: A 524 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7287 (pt0) REVERT: A 581 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.8862 (tp) REVERT: A 619 ASN cc_start: 0.9006 (OUTLIER) cc_final: 0.8408 (m-40) REVERT: A 688 GLU cc_start: 0.7583 (pt0) cc_final: 0.7323 (tp30) REVERT: A 755 GLU cc_start: 0.8870 (mp0) cc_final: 0.8557 (mp0) REVERT: A 891 PHE cc_start: 0.6062 (m-10) cc_final: 0.5378 (m-10) REVERT: A 926 ARG cc_start: 0.7059 (ptm160) cc_final: 0.6843 (ptm160) REVERT: A 988 MET cc_start: 0.8749 (mmp) cc_final: 0.8399 (mmm) REVERT: A 998 TYR cc_start: 0.7942 (p90) cc_final: 0.7409 (p90) REVERT: A 1000 ASN cc_start: 0.7659 (m-40) cc_final: 0.7269 (m110) REVERT: B 401 LEU cc_start: 0.8828 (tp) cc_final: 0.8480 (pt) REVERT: B 407 MET cc_start: 0.7486 (mpp) cc_final: 0.7197 (mmm) REVERT: B 491 PHE cc_start: 0.5929 (OUTLIER) cc_final: 0.5606 (t80) REVERT: B 674 MET cc_start: 0.8496 (ttm) cc_final: 0.7819 (tpp) REVERT: B 714 GLN cc_start: 0.8257 (tp-100) cc_final: 0.7483 (tp40) REVERT: B 760 ASP cc_start: 0.9092 (m-30) cc_final: 0.8522 (t70) REVERT: B 762 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8823 (mm) REVERT: B 764 ASN cc_start: 0.8858 (m-40) cc_final: 0.8344 (m110) REVERT: C 408 MET cc_start: 0.7007 (tpp) cc_final: 0.6503 (tpp) REVERT: C 450 TYR cc_start: 0.7490 (m-80) cc_final: 0.6764 (m-80) REVERT: C 518 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8879 (pp) REVERT: C 581 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.8876 (tp) REVERT: C 596 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8334 (tm) REVERT: C 713 GLU cc_start: 0.8665 (pp20) cc_final: 0.8294 (pp20) REVERT: C 714 GLN cc_start: 0.8727 (mm-40) cc_final: 0.8249 (mm110) REVERT: C 926 ARG cc_start: 0.6704 (ttm-80) cc_final: 0.5855 (tmt170) REVERT: C 1000 ASN cc_start: 0.7856 (m-40) cc_final: 0.7172 (m-40) REVERT: D 419 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7549 (tp30) REVERT: D 421 TYR cc_start: 0.8081 (m-10) cc_final: 0.7859 (m-10) REVERT: D 431 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8090 (mp0) REVERT: D 460 TRP cc_start: 0.5859 (m-10) cc_final: 0.4504 (m-10) REVERT: D 493 LYS cc_start: 0.8598 (mttp) cc_final: 0.8370 (tttm) REVERT: D 519 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7642 (m-30) REVERT: D 714 GLN cc_start: 0.8377 (tp-100) cc_final: 0.7635 (tp40) REVERT: D 748 LEU cc_start: 0.9454 (tp) cc_final: 0.9029 (pp) REVERT: D 760 ASP cc_start: 0.9188 (m-30) cc_final: 0.8588 (t0) REVERT: D 764 ASN cc_start: 0.8972 (m-40) cc_final: 0.8421 (m-40) REVERT: E 75 HIS cc_start: 0.7549 (t70) cc_final: 0.7154 (t70) REVERT: E 99 PHE cc_start: 0.7926 (m-10) cc_final: 0.7675 (t80) REVERT: E 101 HIS cc_start: 0.7965 (m170) cc_final: 0.7500 (m-70) REVERT: E 108 ARG cc_start: 0.6293 (mmm160) cc_final: 0.5639 (mmm160) REVERT: E 123 MET cc_start: 0.6285 (mmm) cc_final: 0.5711 (mmm) REVERT: F 64 LEU cc_start: 0.7402 (mt) cc_final: 0.7073 (pp) REVERT: F 99 PHE cc_start: 0.7629 (m-10) cc_final: 0.7128 (t80) REVERT: F 114 GLU cc_start: 0.6838 (tm-30) cc_final: 0.6499 (tm-30) REVERT: F 147 PHE cc_start: 0.8602 (m-80) cc_final: 0.8396 (m-80) outliers start: 85 outliers final: 57 residues processed: 438 average time/residue: 0.2899 time to fit residues: 196.8205 Evaluate side-chains 418 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 352 time to evaluate : 1.894 ------------------------------------------------------------------------------- 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 683 VAL 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 431 GLU Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 682 PHE Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 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 581 LEU Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 683 VAL 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 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 504 ILE 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 788 SER Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 68 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 65 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 chunk 139 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 215 optimal weight: 0.0370 chunk 181 optimal weight: 0.0970 chunk 208 optimal weight: 0.8980 chunk 219 optimal weight: 0.0470 chunk 134 optimal weight: 0.3980 chunk 109 optimal weight: 0.0050 chunk 187 optimal weight: 10.0000 overall best weight: 0.1168 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 GLN ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 726 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.171251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.118783 restraints weight = 33396.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.121772 restraints weight = 18552.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.121409 restraints weight = 13375.967| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.6265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 19433 Z= 0.134 Angle : 0.768 22.696 26072 Z= 0.381 Chirality : 0.044 0.248 2836 Planarity : 0.005 0.061 3142 Dihedral : 14.463 122.687 3213 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.34 % Favored : 89.58 % Rotamer: Outliers : 3.78 % Allowed : 24.72 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.59 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.18), residues: 2264 helix: 0.76 (0.15), residues: 1310 sheet: -2.94 (0.35), residues: 172 loop : -3.26 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.001 TRP B 460 HIS 0.016 0.001 HIS F 101 PHE 0.033 0.002 PHE A 943 TYR 0.030 0.001 TYR D 450 ARG 0.009 0.000 ARG B 675 Details of bonding type rmsd hydrogen bonds : bond 0.03399 ( 834) hydrogen bonds : angle 3.83420 ( 2436) SS BOND : bond 0.00803 ( 6) SS BOND : angle 2.38223 ( 12) covalent geometry : bond 0.00288 (19427) covalent geometry : angle 0.76651 (26060) *********************** 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 481 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 407 time to evaluate : 2.346 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: 0.8869 (m-40) cc_final: 0.8598 (t0) REVERT: A 450 TYR cc_start: 0.7116 (m-80) cc_final: 0.6875 (m-80) REVERT: A 581 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8773 (tp) REVERT: A 638 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7924 (t0) REVERT: A 926 ARG cc_start: 0.6977 (ptm160) cc_final: 0.6765 (ptm160) REVERT: A 988 MET cc_start: 0.8692 (mmp) cc_final: 0.8317 (mmm) REVERT: A 1000 ASN cc_start: 0.7599 (m-40) cc_final: 0.7020 (m-40) REVERT: B 407 MET cc_start: 0.7531 (mpp) cc_final: 0.7056 (mpp) REVERT: B 682 PHE cc_start: 0.7315 (OUTLIER) cc_final: 0.7105 (m-80) REVERT: B 714 GLN cc_start: 0.8264 (tp-100) cc_final: 0.7467 (tp40) REVERT: B 760 ASP cc_start: 0.9050 (m-30) cc_final: 0.8430 (t70) REVERT: B 764 ASN cc_start: 0.8772 (m-40) cc_final: 0.8295 (m110) REVERT: C 408 MET cc_start: 0.6535 (tpp) cc_final: 0.6162 (tpp) REVERT: C 450 TYR cc_start: 0.7098 (m-80) cc_final: 0.6604 (m-80) REVERT: C 518 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8821 (pp) REVERT: C 581 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8780 (tp) REVERT: C 713 GLU cc_start: 0.8691 (pp20) cc_final: 0.8274 (pp20) REVERT: C 714 GLN cc_start: 0.8680 (mm-40) cc_final: 0.8171 (mm110) REVERT: C 926 ARG cc_start: 0.6529 (ttm-80) cc_final: 0.5452 (tmt170) REVERT: C 1000 ASN cc_start: 0.7667 (m-40) cc_final: 0.7140 (m-40) REVERT: D 419 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7565 (tp30) REVERT: D 421 TYR cc_start: 0.8048 (m-10) cc_final: 0.7813 (m-10) REVERT: D 431 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8078 (mp0) REVERT: D 519 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.7639 (m-30) REVERT: D 637 GLU cc_start: 0.8400 (pt0) cc_final: 0.7978 (pm20) REVERT: D 682 PHE cc_start: 0.7203 (OUTLIER) cc_final: 0.6850 (m-80) REVERT: D 714 GLN cc_start: 0.8335 (tp-100) cc_final: 0.7596 (tp40) REVERT: D 760 ASP cc_start: 0.9069 (m-30) cc_final: 0.8589 (t0) REVERT: D 772 GLU cc_start: 0.6581 (mm-30) cc_final: 0.6340 (mm-30) REVERT: E 75 HIS cc_start: 0.7619 (t70) cc_final: 0.7223 (t70) REVERT: E 99 PHE cc_start: 0.7925 (m-10) cc_final: 0.7579 (t80) REVERT: E 101 HIS cc_start: 0.7927 (m170) cc_final: 0.7701 (m-70) REVERT: E 106 PHE cc_start: 0.7585 (p90) cc_final: 0.7144 (t80) REVERT: E 108 ARG cc_start: 0.6279 (mmm160) cc_final: 0.5784 (mmm160) REVERT: E 123 MET cc_start: 0.5973 (mmm) cc_final: 0.5496 (mmm) REVERT: F 64 LEU cc_start: 0.7282 (mt) cc_final: 0.7070 (pp) REVERT: F 65 ARG cc_start: 0.7900 (ptt90) cc_final: 0.7647 (ptt90) REVERT: F 99 PHE cc_start: 0.7531 (m-10) cc_final: 0.7127 (t80) REVERT: F 123 MET cc_start: 0.5615 (mmm) cc_final: 0.5293 (mmm) outliers start: 74 outliers final: 46 residues processed: 452 average time/residue: 0.2931 time to fit residues: 204.3975 Evaluate side-chains 398 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 344 time to evaluate : 2.123 ------------------------------------------------------------------------------- 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 581 LEU Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 683 VAL 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 1007 PHE Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 682 PHE Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 456 ASP 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 576 SER Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 683 VAL 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 1007 PHE 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 504 ILE 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 682 PHE 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 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 68 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 15 optimal weight: 0.0270 chunk 29 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 223 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 187 optimal weight: 0.8980 chunk 69 optimal weight: 7.9990 chunk 146 optimal weight: 7.9990 chunk 193 optimal weight: 3.9990 overall best weight: 1.3844 ------------------------------------------------------------------------------- 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 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 ASN ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 756 GLN ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 726 ASN ** D 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 HIS E 75 HIS ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.169507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.114176 restraints weight = 33209.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.117467 restraints weight = 18648.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.118985 restraints weight = 13016.850| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.6351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 19433 Z= 0.194 Angle : 0.830 17.115 26072 Z= 0.412 Chirality : 0.047 0.296 2836 Planarity : 0.005 0.060 3142 Dihedral : 14.740 125.610 3213 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.51 % Favored : 89.36 % Rotamer: Outliers : 4.24 % Allowed : 26.20 % Favored : 69.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 4.69 % Twisted General : 0.41 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.18), residues: 2264 helix: 0.68 (0.15), residues: 1308 sheet: -3.02 (0.39), residues: 142 loop : -3.21 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 767 HIS 0.011 0.002 HIS F 101 PHE 0.031 0.002 PHE E 146 TYR 0.029 0.002 TYR D 450 ARG 0.005 0.000 ARG E 108 Details of bonding type rmsd hydrogen bonds : bond 0.03875 ( 834) hydrogen bonds : angle 4.06132 ( 2436) SS BOND : bond 0.01145 ( 6) SS BOND : angle 3.03953 ( 12) covalent geometry : bond 0.00454 (19427) covalent geometry : angle 0.82728 (26060) *********************** 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 442 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 359 time to evaluate : 2.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 ASN cc_start: 0.9001 (m-40) cc_final: 0.8634 (t0) REVERT: A 450 TYR cc_start: 0.7474 (m-80) cc_final: 0.7223 (m-10) REVERT: A 581 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.8997 (tp) REVERT: A 943 PHE cc_start: 0.8482 (t80) cc_final: 0.8276 (t80) REVERT: A 988 MET cc_start: 0.8714 (mmp) cc_final: 0.8371 (mmm) REVERT: A 1000 ASN cc_start: 0.7559 (m-40) cc_final: 0.7016 (m-40) REVERT: B 407 MET cc_start: 0.7534 (mpp) cc_final: 0.7171 (mpp) REVERT: B 597 SER cc_start: 0.8838 (p) cc_final: 0.8606 (p) REVERT: B 710 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7991 (mp0) REVERT: B 714 GLN cc_start: 0.8207 (tp-100) cc_final: 0.7519 (tp40) REVERT: B 748 LEU cc_start: 0.9420 (tp) cc_final: 0.9002 (pp) REVERT: B 760 ASP cc_start: 0.9025 (m-30) cc_final: 0.8480 (t70) REVERT: B 764 ASN cc_start: 0.8826 (m-40) cc_final: 0.8167 (m110) REVERT: B 772 GLU cc_start: 0.5326 (mm-30) cc_final: 0.5044 (mt-10) REVERT: C 408 MET cc_start: 0.6991 (tpp) cc_final: 0.6631 (tpp) REVERT: C 450 TYR cc_start: 0.7353 (m-80) cc_final: 0.6584 (m-80) REVERT: C 518 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.9023 (pp) REVERT: C 581 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.8872 (tp) REVERT: C 585 MET cc_start: 0.8160 (mpt) cc_final: 0.7660 (mpt) REVERT: C 713 GLU cc_start: 0.8753 (pp20) cc_final: 0.8261 (pp20) REVERT: C 714 GLN cc_start: 0.8746 (mm-40) cc_final: 0.8176 (mm110) REVERT: C 926 ARG cc_start: 0.6555 (ttm-80) cc_final: 0.5482 (tmt170) REVERT: C 1000 ASN cc_start: 0.7781 (m-40) cc_final: 0.7241 (m-40) REVERT: D 419 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7502 (tp30) REVERT: D 431 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8062 (mp0) REVERT: D 519 ASP cc_start: 0.7837 (OUTLIER) cc_final: 0.7606 (m-30) REVERT: D 682 PHE cc_start: 0.7456 (OUTLIER) cc_final: 0.7133 (m-80) REVERT: D 714 GLN cc_start: 0.8446 (tp-100) cc_final: 0.7791 (tm-30) REVERT: D 760 ASP cc_start: 0.8999 (m-30) cc_final: 0.8460 (t0) REVERT: D 764 ASN cc_start: 0.8915 (m-40) cc_final: 0.8368 (m-40) REVERT: E 75 HIS cc_start: 0.7382 (t-90) cc_final: 0.7145 (t70) REVERT: E 99 PHE cc_start: 0.7862 (m-10) cc_final: 0.7460 (t80) REVERT: E 106 PHE cc_start: 0.7568 (p90) cc_final: 0.7188 (t80) REVERT: E 108 ARG cc_start: 0.6348 (mmm160) cc_final: 0.6005 (mmm160) REVERT: E 123 MET cc_start: 0.5943 (mmm) cc_final: 0.5466 (mmm) REVERT: F 64 LEU cc_start: 0.7358 (mt) cc_final: 0.7102 (pp) REVERT: F 77 LEU cc_start: 0.6533 (OUTLIER) cc_final: 0.6288 (tp) REVERT: F 87 GLU cc_start: 0.7237 (tp30) cc_final: 0.6963 (tt0) REVERT: F 99 PHE cc_start: 0.7304 (m-10) cc_final: 0.6905 (t80) outliers start: 83 outliers final: 60 residues processed: 409 average time/residue: 0.2861 time to fit residues: 182.0758 Evaluate side-chains 406 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 339 time to evaluate : 1.911 ------------------------------------------------------------------------------- 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 498 LEU Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 456 ASP 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 525 ILE Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain C residue 900 CYS Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain C residue 1019 SER 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 504 ILE 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 682 PHE Chi-restraints excluded: chain D residue 747 ASN 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 118 ASP 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 68 VAL Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 118 ASP Chi-restraints excluded: chain F residue 124 ASN 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 194 optimal weight: 0.0470 chunk 195 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 111 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 119 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 177 optimal weight: 0.6980 chunk 79 optimal weight: 0.6980 chunk 48 optimal weight: 10.0000 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN A 985 ASN ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 HIS ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 747 ASN ** D 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.172858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.121417 restraints weight = 33281.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.123009 restraints weight = 17702.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.123480 restraints weight = 12784.049| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.6601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 19433 Z= 0.147 Angle : 0.804 14.305 26072 Z= 0.399 Chirality : 0.046 0.291 2836 Planarity : 0.005 0.060 3142 Dihedral : 14.259 122.636 3213 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.16 % Favored : 89.80 % Rotamer: Outliers : 3.42 % Allowed : 26.51 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.18), residues: 2264 helix: 0.81 (0.15), residues: 1308 sheet: -2.94 (0.39), residues: 146 loop : -3.16 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 887 HIS 0.018 0.002 HIS E 101 PHE 0.032 0.002 PHE F 106 TYR 0.044 0.002 TYR B 673 ARG 0.005 0.000 ARG F 65 Details of bonding type rmsd hydrogen bonds : bond 0.03593 ( 834) hydrogen bonds : angle 3.95747 ( 2436) SS BOND : bond 0.00769 ( 6) SS BOND : angle 2.68551 ( 12) covalent geometry : bond 0.00331 (19427) covalent geometry : angle 0.80245 (26060) *********************** 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 431 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 364 time to evaluate : 1.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 ASN cc_start: 0.8969 (m-40) cc_final: 0.8717 (t0) REVERT: A 450 TYR cc_start: 0.7362 (m-80) cc_final: 0.7134 (m-80) REVERT: A 581 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.8877 (tp) REVERT: A 926 ARG cc_start: 0.6915 (ptm160) cc_final: 0.6383 (ptm160) REVERT: A 988 MET cc_start: 0.8691 (mmp) cc_final: 0.8384 (mmm) REVERT: A 1000 ASN cc_start: 0.7442 (m-40) cc_final: 0.6985 (m110) REVERT: B 407 MET cc_start: 0.7672 (mpp) cc_final: 0.7438 (mpp) REVERT: B 431 GLU cc_start: 0.8394 (mp0) cc_final: 0.8190 (mp0) REVERT: B 597 SER cc_start: 0.8745 (p) cc_final: 0.8484 (p) REVERT: B 629 MET cc_start: 0.8431 (tpp) cc_final: 0.7867 (mtt) REVERT: B 714 GLN cc_start: 0.8201 (tp-100) cc_final: 0.7442 (tm-30) REVERT: B 748 LEU cc_start: 0.9415 (tp) cc_final: 0.9002 (pp) REVERT: B 760 ASP cc_start: 0.8957 (m-30) cc_final: 0.8388 (t70) REVERT: B 764 ASN cc_start: 0.8773 (m-40) cc_final: 0.8126 (m-40) REVERT: C 408 MET cc_start: 0.6770 (tpp) cc_final: 0.6383 (tpp) REVERT: C 450 TYR cc_start: 0.7194 (m-80) cc_final: 0.6465 (m-80) REVERT: C 518 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8780 (pp) REVERT: C 581 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.8851 (tp) REVERT: C 713 GLU cc_start: 0.8698 (pp20) cc_final: 0.8282 (pp20) REVERT: C 714 GLN cc_start: 0.8671 (mm-40) cc_final: 0.8145 (mm110) REVERT: C 926 ARG cc_start: 0.6383 (ttm-80) cc_final: 0.5377 (tmt170) REVERT: C 1000 ASN cc_start: 0.7652 (m-40) cc_final: 0.7170 (m-40) REVERT: D 401 LEU cc_start: 0.8812 (pt) cc_final: 0.8141 (tt) REVERT: D 419 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7363 (tp30) REVERT: D 431 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8046 (mp0) REVERT: D 508 GLN cc_start: 0.7964 (mm-40) cc_final: 0.7574 (mm110) REVERT: D 519 ASP cc_start: 0.7795 (OUTLIER) cc_final: 0.7584 (m-30) REVERT: D 682 PHE cc_start: 0.7275 (OUTLIER) cc_final: 0.7068 (m-80) REVERT: D 714 GLN cc_start: 0.8401 (tp-100) cc_final: 0.7763 (tm-30) REVERT: D 748 LEU cc_start: 0.9179 (pp) cc_final: 0.8813 (mm) REVERT: D 760 ASP cc_start: 0.8972 (m-30) cc_final: 0.8546 (t70) REVERT: D 761 LYS cc_start: 0.9296 (mmmt) cc_final: 0.9009 (mmtm) REVERT: D 772 GLU cc_start: 0.6749 (mm-30) cc_final: 0.6163 (mm-30) REVERT: E 99 PHE cc_start: 0.7855 (m-10) cc_final: 0.7423 (t80) REVERT: E 106 PHE cc_start: 0.7286 (p90) cc_final: 0.7064 (t80) REVERT: E 108 ARG cc_start: 0.6261 (mmm160) cc_final: 0.5782 (mmm160) REVERT: E 123 MET cc_start: 0.5755 (mmm) cc_final: 0.5372 (mmm) REVERT: F 77 LEU cc_start: 0.6690 (OUTLIER) cc_final: 0.6446 (tp) REVERT: F 99 PHE cc_start: 0.7211 (m-10) cc_final: 0.6827 (t80) REVERT: F 123 MET cc_start: 0.5490 (mmm) cc_final: 0.5178 (mmm) outliers start: 67 outliers final: 45 residues processed: 405 average time/residue: 0.2938 time to fit residues: 184.4056 Evaluate side-chains 394 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 342 time to evaluate : 1.946 ------------------------------------------------------------------------------- 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 581 LEU Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 456 ASP 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 576 SER Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 662 SER Chi-restraints excluded: chain C residue 682 PHE Chi-restraints excluded: chain C residue 683 VAL 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 408 MET Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 504 ILE 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 682 PHE Chi-restraints excluded: chain D residue 747 ASN 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 151 TYR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 95 ILE 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 160 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 178 optimal weight: 0.9980 chunk 165 optimal weight: 0.5980 chunk 175 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 104 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 194 optimal weight: 0.0270 chunk 141 optimal weight: 8.9990 overall best weight: 1.1242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 950 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.170228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.116460 restraints weight = 33269.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.118888 restraints weight = 18910.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.119942 restraints weight = 12955.806| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.6689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 19433 Z= 0.178 Angle : 0.827 15.159 26072 Z= 0.411 Chirality : 0.048 0.385 2836 Planarity : 0.005 0.064 3142 Dihedral : 14.212 124.119 3213 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.69 % Favored : 89.27 % Rotamer: Outliers : 3.27 % Allowed : 27.02 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.18), residues: 2264 helix: 0.80 (0.15), residues: 1300 sheet: -2.48 (0.39), residues: 150 loop : -3.17 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP C 887 HIS 0.012 0.001 HIS F 101 PHE 0.031 0.002 PHE A1028 TYR 0.042 0.002 TYR F 100 ARG 0.007 0.000 ARG B 684 Details of bonding type rmsd hydrogen bonds : bond 0.03796 ( 834) hydrogen bonds : angle 4.04703 ( 2436) SS BOND : bond 0.00670 ( 6) SS BOND : angle 2.53801 ( 12) covalent geometry : bond 0.00415 (19427) covalent geometry : angle 0.82566 (26060) ********************** 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 415 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 351 time to evaluate : 2.118 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: 0.9023 (m-40) cc_final: 0.8777 (t0) REVERT: A 581 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.8899 (tp) REVERT: A 619 ASN cc_start: 0.9006 (OUTLIER) cc_final: 0.7777 (m-40) REVERT: A 721 MET cc_start: 0.9036 (pmm) cc_final: 0.8725 (pmm) REVERT: A 926 ARG cc_start: 0.6854 (ptm160) cc_final: 0.6322 (ptm160) REVERT: A 943 PHE cc_start: 0.8441 (t80) cc_final: 0.8160 (t80) REVERT: A 988 MET cc_start: 0.8686 (mmp) cc_final: 0.8397 (mmm) REVERT: A 1000 ASN cc_start: 0.7543 (m-40) cc_final: 0.7054 (m110) REVERT: B 407 MET cc_start: 0.7585 (mpp) cc_final: 0.7328 (mpp) REVERT: B 431 GLU cc_start: 0.8424 (mp0) cc_final: 0.8201 (mp0) REVERT: B 597 SER cc_start: 0.8837 (p) cc_final: 0.8598 (p) REVERT: B 629 MET cc_start: 0.8371 (tpp) cc_final: 0.7872 (mtt) REVERT: B 704 LEU cc_start: 0.9011 (pt) cc_final: 0.7379 (pt) REVERT: B 714 GLN cc_start: 0.8294 (tp-100) cc_final: 0.7624 (tm-30) REVERT: B 748 LEU cc_start: 0.9433 (tp) cc_final: 0.9017 (pp) REVERT: B 760 ASP cc_start: 0.9007 (m-30) cc_final: 0.8408 (t0) REVERT: B 764 ASN cc_start: 0.8870 (m-40) cc_final: 0.8143 (m110) REVERT: B 772 GLU cc_start: 0.5704 (mm-30) cc_final: 0.4922 (mt-10) REVERT: C 518 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8908 (pp) REVERT: C 581 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.8761 (tp) REVERT: C 585 MET cc_start: 0.8241 (mpt) cc_final: 0.7671 (mpt) REVERT: C 713 GLU cc_start: 0.8728 (pp20) cc_final: 0.8241 (pp20) REVERT: C 714 GLN cc_start: 0.8724 (mm-40) cc_final: 0.8157 (mm110) REVERT: C 723 VAL cc_start: 0.9477 (t) cc_final: 0.9242 (p) REVERT: C 926 ARG cc_start: 0.6520 (ttm-80) cc_final: 0.5563 (tmt170) REVERT: C 988 MET cc_start: 0.8612 (mmm) cc_final: 0.8291 (mmm) REVERT: C 1000 ASN cc_start: 0.7713 (m-40) cc_final: 0.7236 (m-40) REVERT: D 419 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7366 (tp30) REVERT: D 422 GLU cc_start: 0.6847 (pp20) cc_final: 0.6540 (pm20) REVERT: D 431 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8049 (mp0) REVERT: D 508 GLN cc_start: 0.7813 (mm-40) cc_final: 0.7529 (mm110) REVERT: D 714 GLN cc_start: 0.8476 (tp-100) cc_final: 0.7681 (tm-30) REVERT: D 748 LEU cc_start: 0.9185 (pp) cc_final: 0.8714 (mp) REVERT: D 760 ASP cc_start: 0.9008 (m-30) cc_final: 0.8495 (t0) REVERT: D 761 LYS cc_start: 0.9324 (mmmt) cc_final: 0.9065 (mmtt) REVERT: D 764 ASN cc_start: 0.8954 (m-40) cc_final: 0.8452 (m-40) REVERT: D 772 GLU cc_start: 0.6913 (mm-30) cc_final: 0.6573 (mm-30) REVERT: E 99 PHE cc_start: 0.7799 (m-10) cc_final: 0.7245 (t80) REVERT: E 108 ARG cc_start: 0.6418 (mmm160) cc_final: 0.6127 (mmm160) REVERT: E 123 MET cc_start: 0.5836 (mmm) cc_final: 0.5459 (mmm) REVERT: F 77 LEU cc_start: 0.6539 (OUTLIER) cc_final: 0.6284 (tp) REVERT: F 99 PHE cc_start: 0.7060 (m-10) cc_final: 0.6594 (t80) REVERT: F 123 MET cc_start: 0.5605 (mmm) cc_final: 0.5279 (mmm) outliers start: 64 outliers final: 46 residues processed: 390 average time/residue: 0.2840 time to fit residues: 173.1754 Evaluate side-chains 384 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 332 time to evaluate : 1.893 ------------------------------------------------------------------------------- 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 581 LEU Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 662 SER Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 456 ASP 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 525 ILE Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 682 PHE Chi-restraints excluded: chain C residue 683 VAL 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 408 MET Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 504 ILE Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 546 PHE 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 151 TYR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 120 VAL 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 181 optimal weight: 0.9980 chunk 191 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 156 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 198 optimal weight: 0.3980 chunk 177 optimal weight: 0.0870 chunk 126 optimal weight: 0.6980 chunk 139 optimal weight: 0.9990 chunk 166 optimal weight: 6.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 950 HIS D 575 ASN ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.178574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.132167 restraints weight = 34213.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.133912 restraints weight = 17140.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.134231 restraints weight = 12580.797| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.6927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 19433 Z= 0.150 Angle : 0.818 15.431 26072 Z= 0.404 Chirality : 0.046 0.304 2836 Planarity : 0.005 0.060 3142 Dihedral : 13.659 121.181 3213 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer: Outliers : 2.96 % Allowed : 27.58 % Favored : 69.46 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.18), residues: 2264 helix: 0.95 (0.15), residues: 1294 sheet: -2.95 (0.36), residues: 162 loop : -3.16 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 887 HIS 0.012 0.002 HIS F 101 PHE 0.044 0.002 PHE F 106 TYR 0.039 0.002 TYR B 702 ARG 0.008 0.000 ARG D 420 Details of bonding type rmsd hydrogen bonds : bond 0.03586 ( 834) hydrogen bonds : angle 3.93599 ( 2436) SS BOND : bond 0.00549 ( 6) SS BOND : angle 2.33998 ( 12) covalent geometry : bond 0.00337 (19427) covalent geometry : angle 0.81638 (26060) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6956.10 seconds wall clock time: 123 minutes 1.24 seconds (7381.24 seconds total)