Starting phenix.real_space_refine on Tue Jun 17 04:00:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ssb_40750/06_2025/8ssb_40750.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ssb_40750/06_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_40750/06_2025/8ssb_40750.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ssb_40750/06_2025/8ssb_40750.map" model { file = "/net/cci-nas-00/data/ceres_data/8ssb_40750/06_2025/8ssb_40750.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ssb_40750/06_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 11.75, per 1000 atoms: 0.62 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: 4.55 Conformation dependent library (CDL) restraints added in 2.3 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: 1.70 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: 5.27 Time building geometry restraints manager: 5.41 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: 83.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 41.590 Find NCS groups from input model: 0.810 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: 0.000 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.980 ------------------------------------------------------------------------------- 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 : 1.911 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: 0.3398 time to fit residues: 329.3483 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 : 1.905 ------------------------------------------------------------------------------- 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 = 65)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.113562 restraints weight = 33476.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.114589 restraints weight = 19327.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.114822 restraints weight = 15181.136| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 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 : 18.349 160.930 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 4.90782 ( 2436) SS BOND : bond 0.01422 ( 6) SS BOND : angle 2.21848 ( 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 : 1.922 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: 0.9200 (OUTLIER) cc_final: 0.8626 (tp) REVERT: A 585 MET cc_start: 0.8337 (mpt) cc_final: 0.8022 (mpt) REVERT: A 619 ASN cc_start: 0.8219 (m110) cc_final: 0.7421 (t0) REVERT: A 670 MET cc_start: 0.9117 (mtm) cc_final: 0.8898 (mtm) REVERT: A 879 LYS cc_start: 0.8402 (ttpt) cc_final: 0.7858 (mmtm) REVERT: A 1016 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8595 (mt) REVERT: B 400 ILE cc_start: 0.6922 (tt) cc_final: 0.6681 (mp) REVERT: B 419 GLU cc_start: 0.8289 (mm-30) cc_final: 0.8079 (tp30) REVERT: B 463 MET cc_start: 0.7247 (ptp) cc_final: 0.6863 (ptp) REVERT: B 493 LYS cc_start: 0.8959 (mttp) cc_final: 0.8493 (tttm) REVERT: B 669 LYS cc_start: 0.9160 (pttt) cc_final: 0.8949 (pttt) REVERT: B 713 GLU cc_start: 0.8990 (tm-30) cc_final: 0.8691 (tm-30) REVERT: B 714 GLN cc_start: 0.8024 (tp-100) cc_final: 0.7310 (tp40) REVERT: B 721 MET cc_start: 0.7901 (ppp) cc_final: 0.7657 (ppp) REVERT: B 748 LEU cc_start: 0.9533 (tp) cc_final: 0.9123 (pp) REVERT: B 760 ASP cc_start: 0.9294 (m-30) cc_final: 0.8767 (t70) REVERT: B 764 ASN cc_start: 0.8877 (m-40) cc_final: 0.8199 (m-40) REVERT: C 450 TYR cc_start: 0.7119 (m-80) cc_final: 0.6374 (m-80) REVERT: C 518 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8511 (pp) REVERT: C 581 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9052 (tp) REVERT: C 714 GLN cc_start: 0.8563 (mm-40) cc_final: 0.7974 (mm-40) REVERT: C 880 MET cc_start: 0.7871 (tmm) cc_final: 0.7605 (tmm) REVERT: C 891 PHE cc_start: 0.5732 (m-80) cc_final: 0.5397 (m-10) REVERT: C 926 ARG cc_start: 0.6381 (ttm-80) cc_final: 0.5744 (tmt170) REVERT: C 991 ARG cc_start: 0.6828 (mmt-90) cc_final: 0.6341 (mmt90) REVERT: C 1000 ASN cc_start: 0.7940 (m-40) cc_final: 0.7392 (m110) REVERT: D 421 TYR cc_start: 0.7963 (m-10) cc_final: 0.7702 (m-10) REVERT: D 493 LYS cc_start: 0.8720 (mttp) cc_final: 0.8154 (tttm) REVERT: D 533 TYR cc_start: 0.8718 (t80) cc_final: 0.8492 (t80) REVERT: D 702 TYR cc_start: 0.7623 (t80) cc_final: 0.7314 (t80) REVERT: D 714 GLN cc_start: 0.8431 (tp-100) cc_final: 0.7634 (tp40) REVERT: D 760 ASP cc_start: 0.9365 (m-30) cc_final: 0.8955 (t0) REVERT: D 762 LEU cc_start: 0.9317 (mm) cc_final: 0.9108 (mm) REVERT: E 75 HIS cc_start: 0.7526 (t70) cc_final: 0.6131 (t70) REVERT: E 78 PHE cc_start: 0.7845 (m-80) cc_final: 0.7420 (m-80) REVERT: E 87 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7547 (mm-30) REVERT: E 94 ASN cc_start: 0.7711 (p0) cc_final: 0.7358 (p0) REVERT: E 95 ILE cc_start: 0.8520 (tp) cc_final: 0.7783 (tt) REVERT: E 99 PHE cc_start: 0.7971 (m-10) cc_final: 0.7693 (m-80) REVERT: E 101 HIS cc_start: 0.7519 (m170) cc_final: 0.6463 (m170) REVERT: F 78 PHE cc_start: 0.7708 (m-80) cc_final: 0.7426 (m-80) REVERT: F 99 PHE cc_start: 0.7575 (m-10) cc_final: 0.7099 (t80) REVERT: F 104 ARG cc_start: 0.8808 (tpt90) cc_final: 0.8403 (tpt-90) outliers start: 77 outliers final: 28 residues processed: 514 average time/residue: 0.3453 time to fit residues: 268.4199 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 : 2.098 ------------------------------------------------------------------------------- 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: 6.9990 chunk 34 optimal weight: 3.9990 chunk 188 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 196 optimal weight: 0.3980 chunk 213 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 GLN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.161726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.107142 restraints weight = 33453.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.108170 restraints weight = 20267.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.108311 restraints weight = 15171.210| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.4615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 19433 Z= 0.233 Angle : 0.832 12.030 26072 Z= 0.425 Chirality : 0.047 0.213 2836 Planarity : 0.006 0.080 3142 Dihedral : 17.447 150.287 3213 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.57 % Allowed : 11.26 % Favored : 88.16 % Rotamer: Outliers : 5.11 % Allowed : 17.82 % Favored : 77.07 % 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: -2.89 (0.16), residues: 2264 helix: -0.82 (0.13), residues: 1340 sheet: -3.90 (0.38), residues: 120 loop : -3.45 (0.20), residues: 804 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 0.037 0.002 TYR D 450 ARG 0.011 0.001 ARG F 108 Details of bonding type rmsd hydrogen bonds : bond 0.04537 ( 834) hydrogen bonds : angle 4.53708 ( 2436) SS BOND : bond 0.01061 ( 6) SS BOND : angle 1.95709 ( 12) covalent geometry : bond 0.00546 (19427) covalent geometry : angle 0.83067 (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 508 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 408 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 TYR cc_start: 0.7476 (m-80) cc_final: 0.7027 (m-80) REVERT: A 581 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9015 (tp) REVERT: A 705 GLU cc_start: 0.7479 (mt-10) cc_final: 0.6234 (mt-10) REVERT: A 714 GLN cc_start: 0.9157 (OUTLIER) cc_final: 0.8880 (mm-40) REVERT: A 924 MET cc_start: 0.7150 (mmm) cc_final: 0.6476 (mmp) REVERT: A 926 ARG cc_start: 0.7348 (ptm160) cc_final: 0.6957 (ptm160) REVERT: B 419 GLU cc_start: 0.8240 (mm-30) cc_final: 0.8025 (tp30) REVERT: B 714 GLN cc_start: 0.8156 (tp-100) cc_final: 0.7443 (tp40) REVERT: B 721 MET cc_start: 0.8017 (ppp) cc_final: 0.7810 (ppp) REVERT: B 748 LEU cc_start: 0.9458 (tp) cc_final: 0.9010 (pp) REVERT: B 760 ASP cc_start: 0.9180 (m-30) cc_final: 0.8807 (t0) REVERT: B 762 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9027 (mm) REVERT: C 450 TYR cc_start: 0.7319 (m-80) cc_final: 0.6430 (m-80) REVERT: C 518 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8999 (pp) REVERT: C 581 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.8896 (tp) REVERT: C 865 GLU cc_start: 0.7625 (mm-30) cc_final: 0.6832 (mm-30) REVERT: C 890 CYS cc_start: 0.2331 (t) cc_final: 0.1964 (t) REVERT: C 926 ARG cc_start: 0.6557 (ttm-80) cc_final: 0.5834 (tmt170) REVERT: C 991 ARG cc_start: 0.6773 (mmt-90) cc_final: 0.6267 (mmt90) REVERT: C 999 PHE cc_start: 0.6998 (OUTLIER) cc_final: 0.6657 (m-10) REVERT: C 1000 ASN cc_start: 0.8301 (m-40) cc_final: 0.7633 (m-40) REVERT: D 419 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7790 (tp30) REVERT: D 431 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8121 (mp0) REVERT: D 460 TRP cc_start: 0.6482 (m-90) cc_final: 0.6111 (m-90) REVERT: D 493 LYS cc_start: 0.8733 (mttp) cc_final: 0.8234 (mtpp) REVERT: D 714 GLN cc_start: 0.8485 (tp-100) cc_final: 0.7776 (tm-30) REVERT: D 760 ASP cc_start: 0.9278 (m-30) cc_final: 0.8851 (t0) REVERT: D 761 LYS cc_start: 0.9430 (mmmt) cc_final: 0.9084 (mmtt) REVERT: E 75 HIS cc_start: 0.7632 (t70) cc_final: 0.6744 (t70) REVERT: E 78 PHE cc_start: 0.7907 (m-80) cc_final: 0.7659 (m-80) REVERT: E 87 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7711 (mm-30) REVERT: E 94 ASN cc_start: 0.7751 (p0) cc_final: 0.7450 (p0) REVERT: E 95 ILE cc_start: 0.8566 (tp) cc_final: 0.7850 (tt) REVERT: E 99 PHE cc_start: 0.7957 (m-10) cc_final: 0.7629 (m-80) REVERT: E 101 HIS cc_start: 0.7947 (m170) cc_final: 0.7429 (m-70) REVERT: E 134 GLU cc_start: 0.7437 (tm-30) cc_final: 0.7235 (tm-30) REVERT: F 99 PHE cc_start: 0.7634 (m-10) cc_final: 0.7162 (t80) REVERT: F 104 ARG cc_start: 0.8699 (tpt90) cc_final: 0.8275 (tpt-90) outliers start: 100 outliers final: 38 residues processed: 467 average time/residue: 0.3002 time to fit residues: 213.7008 Evaluate side-chains 398 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 353 time to evaluate : 1.936 ------------------------------------------------------------------------------- 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 502 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 638 ASP 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 445 VAL Chi-restraints excluded: chain C residue 469 TYR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 589 CYS 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 484 VAL 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 120 VAL Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 69 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 76 optimal weight: 0.9980 chunk 184 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 153 optimal weight: 0.7980 chunk 133 optimal weight: 0.9980 chunk 100 optimal weight: 9.9990 chunk 169 optimal weight: 20.0000 chunk 112 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN A 714 GLN ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 GLN ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 508 GLN D 575 ASN ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.164561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.111061 restraints weight = 33618.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.112236 restraints weight = 20056.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.112804 restraints weight = 14806.594| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.5112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19433 Z= 0.157 Angle : 0.787 12.410 26072 Z= 0.397 Chirality : 0.045 0.212 2836 Planarity : 0.005 0.075 3142 Dihedral : 16.528 143.869 3213 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.64 % Favored : 89.05 % Rotamer: Outliers : 4.19 % Allowed : 20.68 % Favored : 75.13 % 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: -2.25 (0.17), residues: 2264 helix: -0.19 (0.14), residues: 1346 sheet: -3.42 (0.37), residues: 148 loop : -3.44 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 460 HIS 0.016 0.002 HIS F 101 PHE 0.035 0.002 PHE A 943 TYR 0.037 0.002 TYR D 450 ARG 0.004 0.000 ARG F 108 Details of bonding type rmsd hydrogen bonds : bond 0.03853 ( 834) hydrogen bonds : angle 4.22840 ( 2436) SS BOND : bond 0.01150 ( 6) SS BOND : angle 3.00624 ( 12) covalent geometry : bond 0.00356 (19427) covalent geometry : angle 0.78476 (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 489 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 407 time to evaluate : 2.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 TYR cc_start: 0.7384 (m-80) cc_final: 0.6887 (m-80) REVERT: A 581 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.8988 (tp) REVERT: A 619 ASN cc_start: 0.9215 (OUTLIER) cc_final: 0.7145 (t0) REVERT: A 755 GLU cc_start: 0.8943 (mp0) cc_final: 0.8566 (mp0) REVERT: A 926 ARG cc_start: 0.7180 (ptm160) cc_final: 0.6753 (ptm160) REVERT: A 1000 ASN cc_start: 0.7915 (m-40) cc_final: 0.7075 (m-40) REVERT: A 1003 TYR cc_start: 0.7982 (m-80) cc_final: 0.7135 (m-80) REVERT: B 401 LEU cc_start: 0.9086 (pp) cc_final: 0.8788 (tt) REVERT: B 638 ASP cc_start: 0.8895 (p0) cc_final: 0.8595 (p0) REVERT: B 714 GLN cc_start: 0.8214 (tp-100) cc_final: 0.7420 (tp40) REVERT: B 748 LEU cc_start: 0.9461 (tp) cc_final: 0.9021 (pp) REVERT: B 760 ASP cc_start: 0.9114 (m-30) cc_final: 0.8607 (t70) REVERT: B 762 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8968 (mm) REVERT: B 764 ASN cc_start: 0.8837 (m-40) cc_final: 0.8374 (m110) REVERT: C 450 TYR cc_start: 0.7270 (m-80) cc_final: 0.6580 (m-80) REVERT: C 518 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8919 (pp) REVERT: C 524 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7656 (pt0) REVERT: C 581 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.8908 (tp) REVERT: C 619 ASN cc_start: 0.9063 (OUTLIER) cc_final: 0.6998 (t0) REVERT: C 713 GLU cc_start: 0.8580 (pp20) cc_final: 0.8040 (pp20) REVERT: C 714 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8107 (mm110) REVERT: C 864 LEU cc_start: 0.7384 (mt) cc_final: 0.7000 (mp) REVERT: C 926 ARG cc_start: 0.6778 (ttm-80) cc_final: 0.5917 (tmt170) REVERT: C 1000 ASN cc_start: 0.7994 (m-40) cc_final: 0.7315 (m-40) REVERT: D 401 LEU cc_start: 0.8789 (pp) cc_final: 0.8551 (tt) REVERT: D 419 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7627 (tp30) REVERT: D 431 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8139 (mp0) REVERT: D 493 LYS cc_start: 0.8650 (mttp) cc_final: 0.8071 (mtpp) REVERT: D 637 GLU cc_start: 0.8542 (pt0) cc_final: 0.8318 (pm20) REVERT: D 714 GLN cc_start: 0.8447 (tp-100) cc_final: 0.7658 (tp40) REVERT: D 760 ASP cc_start: 0.9205 (m-30) cc_final: 0.8644 (t0) REVERT: D 761 LYS cc_start: 0.9384 (mmmt) cc_final: 0.9084 (mmtm) REVERT: D 764 ASN cc_start: 0.9006 (m-40) cc_final: 0.8568 (m-40) REVERT: D 781 LYS cc_start: 0.5228 (tptt) cc_final: 0.4337 (mtpt) REVERT: E 75 HIS cc_start: 0.7587 (t70) cc_final: 0.6742 (t70) REVERT: E 87 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7609 (tp30) REVERT: E 94 ASN cc_start: 0.7710 (p0) cc_final: 0.7422 (p0) REVERT: E 95 ILE cc_start: 0.8501 (tp) cc_final: 0.7778 (tt) REVERT: E 99 PHE cc_start: 0.7939 (m-10) cc_final: 0.7609 (m-80) REVERT: E 101 HIS cc_start: 0.7888 (m170) cc_final: 0.7438 (m-70) REVERT: E 134 GLU cc_start: 0.7373 (tm-30) cc_final: 0.6870 (tm-30) REVERT: F 87 GLU cc_start: 0.7483 (mm-30) cc_final: 0.7263 (tp30) REVERT: F 99 PHE cc_start: 0.7639 (m-10) cc_final: 0.7131 (t80) REVERT: F 104 ARG cc_start: 0.8691 (tpt90) cc_final: 0.8322 (tpt-90) REVERT: F 123 MET cc_start: 0.5918 (mmm) cc_final: 0.5695 (mmm) outliers start: 82 outliers final: 42 residues processed: 459 average time/residue: 0.2921 time to fit residues: 206.7838 Evaluate side-chains 410 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 360 time to evaluate : 2.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 469 TYR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1005 TRP Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 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 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 619 ASN Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain C residue 900 CYS Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain 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 573 ILE 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 24 VAL Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 124 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 118 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 154 optimal weight: 2.9990 chunk 196 optimal weight: 8.9990 chunk 148 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 642 GLN A 874 GLN ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 HIS 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 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 = 0.4175 r_free = 0.4175 target = 0.162652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.105196 restraints weight = 33779.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.108558 restraints weight = 19406.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.110725 restraints weight = 14606.234| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.5441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 19433 Z= 0.196 Angle : 0.787 12.871 26072 Z= 0.398 Chirality : 0.046 0.181 2836 Planarity : 0.005 0.071 3142 Dihedral : 16.230 140.023 3213 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.95 % Favored : 88.74 % Rotamer: Outliers : 5.06 % Allowed : 21.96 % Favored : 72.98 % 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: -1.98 (0.18), residues: 2264 helix: 0.07 (0.14), residues: 1344 sheet: -3.46 (0.39), residues: 124 loop : -3.43 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 460 HIS 0.020 0.002 HIS F 101 PHE 0.030 0.002 PHE A 943 TYR 0.033 0.002 TYR D 450 ARG 0.008 0.001 ARG E 108 Details of bonding type rmsd hydrogen bonds : bond 0.03934 ( 834) hydrogen bonds : angle 4.21669 ( 2436) SS BOND : bond 0.00568 ( 6) SS BOND : angle 1.46839 ( 12) covalent geometry : bond 0.00460 (19427) covalent geometry : angle 0.78666 (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 472 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 373 time to evaluate : 2.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 TYR cc_start: 0.7634 (m-80) cc_final: 0.7140 (m-80) REVERT: A 581 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.8951 (tp) REVERT: A 619 ASN cc_start: 0.9197 (OUTLIER) cc_final: 0.7127 (t0) REVERT: A 755 GLU cc_start: 0.8933 (mp0) cc_final: 0.8518 (mp0) REVERT: A 926 ARG cc_start: 0.7147 (ptm160) cc_final: 0.6903 (ptm160) REVERT: A 1000 ASN cc_start: 0.7868 (m-40) cc_final: 0.7180 (m-40) REVERT: A 1029 MET cc_start: 0.8042 (mmm) cc_final: 0.7812 (mtt) REVERT: B 401 LEU cc_start: 0.9139 (pp) cc_final: 0.8798 (tp) REVERT: B 419 GLU cc_start: 0.6989 (tp30) cc_final: 0.6548 (tp30) REVERT: B 714 GLN cc_start: 0.8315 (tp-100) cc_final: 0.7555 (tp40) REVERT: B 760 ASP cc_start: 0.9038 (m-30) cc_final: 0.8753 (t70) REVERT: B 762 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8868 (mm) REVERT: C 450 TYR cc_start: 0.7456 (m-80) cc_final: 0.6672 (m-80) REVERT: C 518 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.9029 (pp) REVERT: C 581 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.8819 (tp) REVERT: C 585 MET cc_start: 0.8226 (mpt) cc_final: 0.7722 (mpt) REVERT: C 619 ASN cc_start: 0.9115 (OUTLIER) cc_final: 0.7089 (t0) REVERT: C 713 GLU cc_start: 0.8642 (pp20) cc_final: 0.8393 (pp20) REVERT: C 926 ARG cc_start: 0.6731 (ttm-80) cc_final: 0.5933 (tmt170) REVERT: C 999 PHE cc_start: 0.6800 (OUTLIER) cc_final: 0.6382 (m-80) REVERT: C 1000 ASN cc_start: 0.8006 (m-40) cc_final: 0.7620 (m-40) REVERT: D 401 LEU cc_start: 0.8796 (pp) cc_final: 0.8486 (tt) REVERT: D 419 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7517 (tp30) REVERT: D 431 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8132 (mp0) REVERT: D 493 LYS cc_start: 0.8610 (mttp) cc_final: 0.8132 (mtpp) REVERT: D 637 GLU cc_start: 0.8572 (pt0) cc_final: 0.8320 (pm20) REVERT: D 714 GLN cc_start: 0.8454 (tp-100) cc_final: 0.7700 (tp40) REVERT: D 748 LEU cc_start: 0.9423 (tp) cc_final: 0.9022 (pp) REVERT: D 760 ASP cc_start: 0.9121 (m-30) cc_final: 0.8568 (t0) REVERT: D 764 ASN cc_start: 0.9028 (m-40) cc_final: 0.8410 (m-40) REVERT: E 75 HIS cc_start: 0.7566 (t70) cc_final: 0.7169 (t70) REVERT: E 95 ILE cc_start: 0.8499 (tp) cc_final: 0.7587 (tt) REVERT: E 99 PHE cc_start: 0.7935 (m-10) cc_final: 0.7610 (m-80) REVERT: E 101 HIS cc_start: 0.7954 (m170) cc_final: 0.7447 (m-70) REVERT: E 134 GLU cc_start: 0.7350 (tm-30) cc_final: 0.7045 (tm-30) REVERT: F 99 PHE cc_start: 0.7642 (m-10) cc_final: 0.7178 (t80) REVERT: F 104 ARG cc_start: 0.8702 (tpt90) cc_final: 0.8419 (tpt-90) REVERT: F 123 MET cc_start: 0.5896 (mmm) cc_final: 0.5684 (mmm) outliers start: 99 outliers final: 61 residues processed: 432 average time/residue: 0.3024 time to fit residues: 200.4675 Evaluate side-chains 417 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 348 time to evaluate : 2.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 469 TYR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 638 ASP 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 1005 TRP Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 495 PHE 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 524 GLU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 619 ASN Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain C residue 900 CYS Chi-restraints excluded: chain C residue 986 ASP Chi-restraints excluded: chain C residue 999 PHE Chi-restraints excluded: chain C residue 1005 TRP Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain C residue 1019 SER 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 573 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 120 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: 2.9990 chunk 79 optimal weight: 0.3980 chunk 171 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 86 optimal weight: 7.9990 chunk 75 optimal weight: 0.3980 chunk 13 optimal weight: 0.9990 chunk 162 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS A 642 GLN ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 874 GLN D 575 ASN ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.165896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.111139 restraints weight = 33813.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.114120 restraints weight = 20059.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.114491 restraints weight = 13989.155| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.5752 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= 0.147 Angle : 0.784 13.338 26072 Z= 0.395 Chirality : 0.045 0.257 2836 Planarity : 0.005 0.067 3142 Dihedral : 15.562 134.277 3213 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.22 % Allowed : 10.73 % Favored : 89.05 % Rotamer: Outliers : 4.39 % Allowed : 23.03 % Favored : 72.57 % 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: -1.62 (0.18), residues: 2264 helix: 0.34 (0.15), residues: 1344 sheet: -2.69 (0.40), residues: 138 loop : -3.36 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 460 HIS 0.016 0.002 HIS F 101 PHE 0.031 0.002 PHE A 943 TYR 0.030 0.002 TYR D 450 ARG 0.008 0.000 ARG E 108 Details of bonding type rmsd hydrogen bonds : bond 0.03597 ( 834) hydrogen bonds : angle 3.99540 ( 2436) SS BOND : bond 0.01228 ( 6) SS BOND : angle 3.79119 ( 12) covalent geometry : bond 0.00330 (19427) covalent geometry : angle 0.77986 (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 474 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 388 time to evaluate : 1.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 TYR cc_start: 0.7572 (m-80) cc_final: 0.7040 (m-80) REVERT: A 524 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7301 (pt0) REVERT: A 581 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.8850 (tp) REVERT: A 619 ASN cc_start: 0.9172 (OUTLIER) cc_final: 0.7113 (t0) REVERT: A 926 ARG cc_start: 0.7025 (ptm160) cc_final: 0.6787 (ptm160) REVERT: A 988 MET cc_start: 0.8731 (mmp) cc_final: 0.8409 (mmm) REVERT: A 1000 ASN cc_start: 0.7766 (m-40) cc_final: 0.7123 (m-40) REVERT: A 1029 MET cc_start: 0.8012 (mmm) cc_final: 0.7723 (mtt) REVERT: B 419 GLU cc_start: 0.6787 (tp30) cc_final: 0.6582 (tp30) REVERT: B 491 PHE cc_start: 0.6163 (OUTLIER) cc_final: 0.5848 (t80) REVERT: B 633 ILE cc_start: 0.8466 (OUTLIER) cc_final: 0.8264 (mp) REVERT: B 692 ARG cc_start: 0.8383 (tpt-90) cc_final: 0.7702 (mtp85) REVERT: B 714 GLN cc_start: 0.8298 (tp-100) cc_final: 0.7506 (tp40) REVERT: B 748 LEU cc_start: 0.9382 (tp) cc_final: 0.9139 (pp) REVERT: B 760 ASP cc_start: 0.9122 (m-30) cc_final: 0.8547 (t70) REVERT: B 764 ASN cc_start: 0.8869 (m-40) cc_final: 0.8381 (m110) REVERT: C 450 TYR cc_start: 0.7318 (m-80) cc_final: 0.6506 (m-80) REVERT: C 518 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8885 (pp) REVERT: C 581 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8860 (tp) REVERT: C 619 ASN cc_start: 0.9032 (OUTLIER) cc_final: 0.7094 (t0) REVERT: C 688 GLU cc_start: 0.7734 (pt0) cc_final: 0.7202 (tp30) REVERT: C 713 GLU cc_start: 0.8637 (pp20) cc_final: 0.8216 (pp20) REVERT: C 714 GLN cc_start: 0.8775 (mm-40) cc_final: 0.8274 (mm110) REVERT: C 926 ARG cc_start: 0.6751 (ttm-80) cc_final: 0.5965 (tmt170) REVERT: C 988 MET cc_start: 0.8554 (mmm) cc_final: 0.8293 (mmm) REVERT: C 1000 ASN cc_start: 0.7806 (m-40) cc_final: 0.7579 (m-40) REVERT: D 401 LEU cc_start: 0.8877 (pp) cc_final: 0.8632 (tt) REVERT: D 419 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7562 (tp30) REVERT: D 431 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8122 (mp0) REVERT: D 450 TYR cc_start: 0.5404 (OUTLIER) cc_final: 0.4120 (m-80) REVERT: D 493 LYS cc_start: 0.8599 (mttp) cc_final: 0.8170 (mtpp) REVERT: D 519 ASP cc_start: 0.7879 (OUTLIER) cc_final: 0.7639 (m-30) REVERT: D 637 GLU cc_start: 0.8593 (pt0) cc_final: 0.8322 (pm20) REVERT: D 673 TYR cc_start: 0.7955 (m-80) cc_final: 0.7584 (m-80) REVERT: D 714 GLN cc_start: 0.8413 (tp-100) cc_final: 0.7854 (tm-30) REVERT: D 748 LEU cc_start: 0.9437 (tp) cc_final: 0.9075 (pp) REVERT: D 760 ASP cc_start: 0.9184 (m-30) cc_final: 0.8592 (t0) REVERT: D 764 ASN cc_start: 0.9007 (m-40) cc_final: 0.8434 (m-40) REVERT: D 781 LYS cc_start: 0.5474 (tptt) cc_final: 0.5072 (mtpp) REVERT: D 783 LYS cc_start: 0.6824 (pmtt) cc_final: 0.6487 (ptpp) REVERT: E 75 HIS cc_start: 0.7581 (t70) cc_final: 0.7186 (t70) REVERT: E 87 GLU cc_start: 0.7525 (tp30) cc_final: 0.7211 (tp30) REVERT: E 99 PHE cc_start: 0.7916 (m-10) cc_final: 0.7705 (t80) REVERT: E 101 HIS cc_start: 0.7903 (m170) cc_final: 0.7394 (m-70) REVERT: E 108 ARG cc_start: 0.6410 (mmm160) cc_final: 0.5788 (mmm160) REVERT: F 64 LEU cc_start: 0.7557 (mt) cc_final: 0.7168 (pp) REVERT: F 87 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7271 (tt0) REVERT: F 99 PHE cc_start: 0.7586 (m-10) cc_final: 0.7074 (t80) REVERT: F 114 GLU cc_start: 0.6760 (tm-30) cc_final: 0.6408 (tm-30) outliers start: 86 outliers final: 52 residues processed: 440 average time/residue: 0.2909 time to fit residues: 197.7555 Evaluate side-chains 416 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 354 time to evaluate : 1.946 ------------------------------------------------------------------------------- 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 812 ILE Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1005 TRP Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 403 SER 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 619 ASN Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain C residue 900 CYS Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 450 TYR Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 495 PHE Chi-restraints excluded: chain D residue 519 ASP Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 151 TYR Chi-restraints excluded: chain F residue 24 VAL 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: 0.9980 chunk 27 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 215 optimal weight: 0.9990 chunk 181 optimal weight: 0.3980 chunk 208 optimal weight: 9.9990 chunk 219 optimal weight: 0.2980 chunk 134 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 187 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 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** 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** 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 = 0.4218 r_free = 0.4218 target = 0.166315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.109947 restraints weight = 33411.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.113573 restraints weight = 19144.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.114036 restraints weight = 13530.825| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.6020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 19433 Z= 0.151 Angle : 0.786 13.345 26072 Z= 0.391 Chirality : 0.045 0.232 2836 Planarity : 0.005 0.070 3142 Dihedral : 15.110 128.365 3213 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.69 % Favored : 89.22 % Rotamer: Outliers : 4.09 % Allowed : 24.87 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 4.69 % Twisted General : 0.68 % 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: -1.46 (0.18), residues: 2264 helix: 0.55 (0.15), residues: 1332 sheet: -3.12 (0.36), residues: 158 loop : -3.27 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.001 TRP B 460 HIS 0.014 0.002 HIS F 101 PHE 0.033 0.002 PHE A 943 TYR 0.031 0.002 TYR B 450 ARG 0.007 0.000 ARG A 453 Details of bonding type rmsd hydrogen bonds : bond 0.03645 ( 834) hydrogen bonds : angle 3.92627 ( 2436) SS BOND : bond 0.00939 ( 6) SS BOND : angle 2.48874 ( 12) covalent geometry : bond 0.00345 (19427) covalent geometry : angle 0.78449 (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 453 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 373 time to evaluate : 1.939 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: A 450 TYR cc_start: 0.7497 (m-80) cc_final: 0.7018 (m-10) REVERT: A 524 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7332 (pt0) REVERT: A 581 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.8840 (tp) REVERT: A 619 ASN cc_start: 0.9181 (OUTLIER) cc_final: 0.7244 (t0) REVERT: A 926 ARG cc_start: 0.6916 (ptm160) cc_final: 0.6675 (ptm160) REVERT: A 988 MET cc_start: 0.8718 (mmp) cc_final: 0.8388 (mmm) REVERT: A 1000 ASN cc_start: 0.7617 (m-40) cc_final: 0.7084 (m110) REVERT: A 1029 MET cc_start: 0.7911 (mmm) cc_final: 0.7689 (mtt) REVERT: B 491 PHE cc_start: 0.6034 (OUTLIER) cc_final: 0.5798 (t80) REVERT: B 714 GLN cc_start: 0.8318 (tp-100) cc_final: 0.7559 (tm-30) REVERT: B 760 ASP cc_start: 0.9142 (m-30) cc_final: 0.8716 (t70) REVERT: C 408 MET cc_start: 0.7550 (tpp) cc_final: 0.6918 (tpp) REVERT: C 450 TYR cc_start: 0.7218 (m-80) cc_final: 0.6287 (m-80) REVERT: C 518 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8929 (pp) REVERT: C 581 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.8808 (tp) REVERT: C 591 ILE cc_start: 0.7270 (OUTLIER) cc_final: 0.7005 (tp) REVERT: C 619 ASN cc_start: 0.9047 (OUTLIER) cc_final: 0.7168 (t0) REVERT: C 688 GLU cc_start: 0.7763 (pt0) cc_final: 0.7243 (tp30) REVERT: C 713 GLU cc_start: 0.8699 (pp20) cc_final: 0.8259 (pp20) REVERT: C 714 GLN cc_start: 0.8770 (mm-40) cc_final: 0.8268 (mm110) REVERT: C 926 ARG cc_start: 0.6686 (ttm-80) cc_final: 0.5944 (tmt170) REVERT: C 1000 ASN cc_start: 0.7709 (m-40) cc_final: 0.7476 (m-40) REVERT: D 407 MET cc_start: 0.7747 (mpp) cc_final: 0.7183 (mpp) REVERT: D 419 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7467 (tp30) REVERT: D 431 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8088 (mp0) REVERT: D 450 TYR cc_start: 0.5239 (OUTLIER) cc_final: 0.4123 (m-80) REVERT: D 493 LYS cc_start: 0.8646 (mttp) cc_final: 0.8211 (mtpp) REVERT: D 519 ASP cc_start: 0.7852 (OUTLIER) cc_final: 0.7613 (m-30) REVERT: D 637 GLU cc_start: 0.8567 (pt0) cc_final: 0.8301 (pm20) REVERT: D 682 PHE cc_start: 0.7511 (OUTLIER) cc_final: 0.7256 (m-80) REVERT: D 714 GLN cc_start: 0.8389 (tp-100) cc_final: 0.7825 (tm-30) REVERT: D 760 ASP cc_start: 0.9137 (m-30) cc_final: 0.8684 (t0) REVERT: E 75 HIS cc_start: 0.7639 (t70) cc_final: 0.7242 (t70) REVERT: E 87 GLU cc_start: 0.7557 (tp30) cc_final: 0.7199 (tp30) REVERT: E 99 PHE cc_start: 0.7905 (m-10) cc_final: 0.7546 (t80) REVERT: E 101 HIS cc_start: 0.7993 (m170) cc_final: 0.7477 (m-70) REVERT: E 106 PHE cc_start: 0.7623 (p90) cc_final: 0.7292 (t80) REVERT: E 108 ARG cc_start: 0.6390 (mmm160) cc_final: 0.5906 (mmm160) REVERT: E 123 MET cc_start: 0.5865 (mmm) cc_final: 0.5626 (mmm) REVERT: F 64 LEU cc_start: 0.7415 (mt) cc_final: 0.7076 (pp) REVERT: F 65 ARG cc_start: 0.7865 (ptt90) cc_final: 0.7599 (ptt90) REVERT: F 99 PHE cc_start: 0.7581 (m-10) cc_final: 0.7188 (t80) outliers start: 80 outliers final: 56 residues processed: 421 average time/residue: 0.3003 time to fit residues: 196.7719 Evaluate side-chains 403 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 336 time to evaluate : 1.932 ------------------------------------------------------------------------------- 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 812 ILE Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1005 TRP Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 469 TYR Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 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 619 ASN Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 900 CYS Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 450 TYR Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 519 ASP Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 682 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 69 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 151 TYR Chi-restraints excluded: chain F residue 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 150 optimal weight: 0.7980 chunk 223 optimal weight: 10.0000 chunk 78 optimal weight: 0.3980 chunk 28 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 chunk 187 optimal weight: 10.0000 chunk 69 optimal weight: 30.0000 chunk 146 optimal weight: 2.9990 chunk 193 optimal weight: 4.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN ** 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 756 GLN 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 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 = 0.4178 r_free = 0.4178 target = 0.163242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.105718 restraints weight = 33504.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.110016 restraints weight = 20612.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.110692 restraints weight = 13208.784| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.6154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 19433 Z= 0.211 Angle : 0.823 14.716 26072 Z= 0.413 Chirality : 0.047 0.221 2836 Planarity : 0.005 0.074 3142 Dihedral : 15.294 129.641 3213 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.26 % Favored : 88.65 % Rotamer: Outliers : 4.65 % Allowed : 25.23 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 6.25 % 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: -1.41 (0.18), residues: 2264 helix: 0.56 (0.15), residues: 1322 sheet: -2.19 (0.42), residues: 134 loop : -3.34 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP B 460 HIS 0.010 0.001 HIS F 101 PHE 0.043 0.002 PHE A 943 TYR 0.035 0.002 TYR B 450 ARG 0.006 0.001 ARG A 453 Details of bonding type rmsd hydrogen bonds : bond 0.03843 ( 834) hydrogen bonds : angle 4.08729 ( 2436) SS BOND : bond 0.00770 ( 6) SS BOND : angle 1.94598 ( 12) covalent geometry : bond 0.00495 (19427) covalent geometry : angle 0.82263 (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 448 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 357 time to evaluate : 2.110 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: A 524 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7263 (pt0) REVERT: A 581 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.8776 (tp) REVERT: A 585 MET cc_start: 0.8247 (mpt) cc_final: 0.7616 (mpt) REVERT: A 619 ASN cc_start: 0.9236 (OUTLIER) cc_final: 0.7305 (t0) REVERT: A 865 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7299 (mm-30) REVERT: A 985 ASN cc_start: 0.8304 (m-40) cc_final: 0.7987 (m110) REVERT: A 988 MET cc_start: 0.8762 (mmp) cc_final: 0.8450 (mmm) REVERT: A 1000 ASN cc_start: 0.7638 (m-40) cc_final: 0.7098 (m110) REVERT: B 407 MET cc_start: 0.7297 (mpp) cc_final: 0.6880 (mpp) REVERT: B 714 GLN cc_start: 0.8229 (tp-100) cc_final: 0.7554 (tp40) REVERT: B 760 ASP cc_start: 0.9092 (m-30) cc_final: 0.8669 (t70) REVERT: B 772 GLU cc_start: 0.5524 (mm-30) cc_final: 0.4626 (mt-10) REVERT: C 518 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.9002 (pp) REVERT: C 581 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.8782 (tp) REVERT: C 585 MET cc_start: 0.8248 (mpt) cc_final: 0.7644 (mpt) REVERT: C 591 ILE cc_start: 0.7321 (OUTLIER) cc_final: 0.6942 (tp) REVERT: C 619 ASN cc_start: 0.9174 (OUTLIER) cc_final: 0.7201 (t0) REVERT: C 688 GLU cc_start: 0.7822 (pt0) cc_final: 0.7365 (tp30) REVERT: C 713 GLU cc_start: 0.8712 (pp20) cc_final: 0.8432 (pp20) REVERT: C 781 LYS cc_start: 0.7976 (mppt) cc_final: 0.7357 (pttp) REVERT: C 926 ARG cc_start: 0.6665 (ttm-80) cc_final: 0.5928 (tmt170) REVERT: C 1000 ASN cc_start: 0.7887 (m-40) cc_final: 0.7274 (m-40) REVERT: D 401 LEU cc_start: 0.9029 (pp) cc_final: 0.8734 (tt) REVERT: D 407 MET cc_start: 0.7531 (mpp) cc_final: 0.7175 (mpp) REVERT: D 419 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7502 (tp30) REVERT: D 431 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8056 (mp0) REVERT: D 450 TYR cc_start: 0.5202 (OUTLIER) cc_final: 0.4338 (m-80) REVERT: D 493 LYS cc_start: 0.8691 (mttp) cc_final: 0.8252 (mtpp) REVERT: D 519 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7636 (m-30) REVERT: D 637 GLU cc_start: 0.8540 (pt0) cc_final: 0.8275 (pm20) REVERT: D 714 GLN cc_start: 0.8441 (tp-100) cc_final: 0.7826 (tm-30) REVERT: D 748 LEU cc_start: 0.9289 (mm) cc_final: 0.9034 (pp) REVERT: E 75 HIS cc_start: 0.7717 (t70) cc_final: 0.7380 (t70) REVERT: E 87 GLU cc_start: 0.7667 (tp30) cc_final: 0.7337 (tp30) REVERT: E 99 PHE cc_start: 0.7918 (m-10) cc_final: 0.7562 (t80) REVERT: E 101 HIS cc_start: 0.8148 (m170) cc_final: 0.7536 (m-70) REVERT: E 106 PHE cc_start: 0.7571 (p90) cc_final: 0.7350 (t80) REVERT: E 123 MET cc_start: 0.5983 (mmm) cc_final: 0.5762 (mmm) REVERT: F 64 LEU cc_start: 0.7603 (mt) cc_final: 0.7215 (pp) REVERT: F 65 ARG cc_start: 0.7891 (ptt90) cc_final: 0.7639 (ptt90) REVERT: F 99 PHE cc_start: 0.7445 (m-10) cc_final: 0.7008 (t80) REVERT: F 151 TYR cc_start: 0.6890 (OUTLIER) cc_final: 0.6412 (t80) outliers start: 91 outliers final: 59 residues processed: 408 average time/residue: 0.2900 time to fit residues: 185.6379 Evaluate side-chains 408 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 338 time to evaluate : 2.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 469 TYR Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 524 GLU 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 812 ILE Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1005 TRP Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 469 TYR Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 619 ASN Chi-restraints excluded: chain C residue 626 VAL 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 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 450 TYR Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 495 PHE Chi-restraints excluded: chain D residue 519 ASP Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 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 118 ASP Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 151 TYR Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 118 ASP Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 124 ASN Chi-restraints excluded: chain F residue 151 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 194 optimal weight: 0.8980 chunk 195 optimal weight: 5.9990 chunk 113 optimal weight: 0.5980 chunk 111 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 119 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 79 optimal weight: 0.4980 chunk 48 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN ** 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 883 HIS C 950 HIS D 575 ASN ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.166641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.110441 restraints weight = 33598.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.113243 restraints weight = 19834.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.114736 restraints weight = 14075.411| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.6403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19433 Z= 0.150 Angle : 0.806 14.849 26072 Z= 0.401 Chirality : 0.046 0.225 2836 Planarity : 0.005 0.071 3142 Dihedral : 14.741 125.657 3213 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.04 % Favored : 88.91 % Rotamer: Outliers : 4.03 % Allowed : 26.05 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.63 % 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: -1.25 (0.18), residues: 2264 helix: 0.70 (0.15), residues: 1324 sheet: -2.01 (0.40), residues: 144 loop : -3.34 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.002 TRP B 460 HIS 0.010 0.001 HIS F 101 PHE 0.034 0.002 PHE A 943 TYR 0.043 0.002 TYR B 673 ARG 0.009 0.000 ARG E 108 Details of bonding type rmsd hydrogen bonds : bond 0.03581 ( 834) hydrogen bonds : angle 3.95683 ( 2436) SS BOND : bond 0.00640 ( 6) SS BOND : angle 3.27309 ( 12) covalent geometry : bond 0.00341 (19427) covalent geometry : angle 0.80288 (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 434 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 355 time to evaluate : 2.106 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 524 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7385 (pt0) REVERT: A 581 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.8777 (tp) REVERT: A 619 ASN cc_start: 0.9124 (OUTLIER) cc_final: 0.7137 (t0) REVERT: A 985 ASN cc_start: 0.8313 (m-40) cc_final: 0.7893 (m110) REVERT: A 988 MET cc_start: 0.8757 (mmp) cc_final: 0.8430 (mmm) REVERT: A 1000 ASN cc_start: 0.7566 (m-40) cc_final: 0.7017 (m110) REVERT: A 1029 MET cc_start: 0.7626 (mtp) cc_final: 0.7381 (mtt) REVERT: B 407 MET cc_start: 0.7383 (mpp) cc_final: 0.7025 (mpp) REVERT: B 714 GLN cc_start: 0.8232 (tp-100) cc_final: 0.7629 (tm-30) REVERT: B 760 ASP cc_start: 0.9118 (m-30) cc_final: 0.8680 (t70) REVERT: B 772 GLU cc_start: 0.5313 (mm-30) cc_final: 0.4599 (mt-10) REVERT: C 518 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8857 (pp) REVERT: C 581 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8774 (tp) REVERT: C 591 ILE cc_start: 0.7072 (OUTLIER) cc_final: 0.6801 (tp) REVERT: C 619 ASN cc_start: 0.9127 (OUTLIER) cc_final: 0.7205 (t0) REVERT: C 688 GLU cc_start: 0.7741 (pt0) cc_final: 0.7266 (tp30) REVERT: C 713 GLU cc_start: 0.8705 (pp20) cc_final: 0.8359 (pp20) REVERT: C 714 GLN cc_start: 0.8792 (mm-40) cc_final: 0.8383 (mm110) REVERT: C 926 ARG cc_start: 0.6639 (ttm-80) cc_final: 0.6009 (tmt170) REVERT: C 1000 ASN cc_start: 0.7766 (m-40) cc_final: 0.7183 (m-40) REVERT: D 407 MET cc_start: 0.7389 (mpp) cc_final: 0.6989 (mpp) REVERT: D 419 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7409 (tp30) REVERT: D 431 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8104 (mp0) REVERT: D 450 TYR cc_start: 0.5217 (OUTLIER) cc_final: 0.4614 (m-80) REVERT: D 493 LYS cc_start: 0.8627 (mttp) cc_final: 0.8226 (mtpp) REVERT: D 637 GLU cc_start: 0.8514 (pt0) cc_final: 0.8257 (pm20) REVERT: D 714 GLN cc_start: 0.8410 (tp-100) cc_final: 0.7657 (tm-30) REVERT: D 748 LEU cc_start: 0.9306 (mm) cc_final: 0.9051 (pp) REVERT: E 75 HIS cc_start: 0.7732 (t70) cc_final: 0.7291 (t70) REVERT: E 87 GLU cc_start: 0.7646 (tp30) cc_final: 0.7245 (tp30) REVERT: E 99 PHE cc_start: 0.7967 (m-10) cc_final: 0.7598 (t80) REVERT: E 101 HIS cc_start: 0.8018 (m170) cc_final: 0.7383 (m-70) REVERT: E 106 PHE cc_start: 0.7516 (p90) cc_final: 0.7289 (t80) REVERT: E 108 ARG cc_start: 0.6408 (mmm160) cc_final: 0.5792 (mmm160) REVERT: E 123 MET cc_start: 0.6135 (mmm) cc_final: 0.5621 (mmm) REVERT: F 64 LEU cc_start: 0.7474 (mt) cc_final: 0.7154 (pp) REVERT: F 87 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7551 (tp30) REVERT: F 99 PHE cc_start: 0.7327 (m-10) cc_final: 0.6842 (t80) outliers start: 79 outliers final: 56 residues processed: 403 average time/residue: 0.2917 time to fit residues: 183.9994 Evaluate side-chains 401 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 336 time to evaluate : 2.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 469 TYR Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 524 GLU 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 759 LEU Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1005 TRP Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 467 LEU 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 573 ILE 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 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 591 ILE Chi-restraints excluded: chain C residue 619 ASN Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 768 TYR 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 395 VAL Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 450 TYR Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 151 TYR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 118 ASP 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 160 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 178 optimal weight: 1.9990 chunk 165 optimal weight: 0.3980 chunk 175 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 104 optimal weight: 7.9990 chunk 81 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 194 optimal weight: 0.8980 chunk 141 optimal weight: 8.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 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 950 HIS ** 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** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.170401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.115728 restraints weight = 33305.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.120340 restraints weight = 18039.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.120693 restraints weight = 11835.860| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.6562 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= 0.156 Angle : 0.815 14.767 26072 Z= 0.403 Chirality : 0.047 0.305 2836 Planarity : 0.005 0.071 3142 Dihedral : 14.410 123.917 3213 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.64 % Favored : 89.31 % Rotamer: Outliers : 3.63 % Allowed : 27.02 % Favored : 69.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 4.69 % Twisted General : 0.50 % 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: -1.25 (0.18), residues: 2264 helix: 0.79 (0.15), residues: 1296 sheet: -2.83 (0.41), residues: 124 loop : -3.21 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 887 HIS 0.012 0.001 HIS F 101 PHE 0.031 0.002 PHE A1028 TYR 0.038 0.002 TYR F 100 ARG 0.010 0.000 ARG E 108 Details of bonding type rmsd hydrogen bonds : bond 0.03576 ( 834) hydrogen bonds : angle 3.97007 ( 2436) SS BOND : bond 0.00713 ( 6) SS BOND : angle 3.22981 ( 12) covalent geometry : bond 0.00359 (19427) covalent geometry : angle 0.81250 (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 433 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 362 time to evaluate : 1.940 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: A 524 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7191 (pt0) REVERT: A 581 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8692 (tp) REVERT: A 585 MET cc_start: 0.8134 (mpt) cc_final: 0.7571 (mpt) REVERT: A 619 ASN cc_start: 0.9094 (OUTLIER) cc_final: 0.7155 (t0) REVERT: A 854 ILE cc_start: 0.9322 (mm) cc_final: 0.8917 (tt) REVERT: A 865 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7268 (mm-30) REVERT: A 926 ARG cc_start: 0.6674 (ptm160) cc_final: 0.6261 (ptm160) REVERT: A 985 ASN cc_start: 0.8356 (m-40) cc_final: 0.7849 (m110) REVERT: A 988 MET cc_start: 0.8754 (mmp) cc_final: 0.8446 (mmm) REVERT: A 1000 ASN cc_start: 0.7563 (m-40) cc_final: 0.7024 (m110) REVERT: A 1029 MET cc_start: 0.7654 (mtp) cc_final: 0.7453 (mtt) REVERT: B 407 MET cc_start: 0.7377 (mpp) cc_final: 0.7004 (mpp) REVERT: B 449 LYS cc_start: 0.7896 (tppt) cc_final: 0.7613 (mmmm) REVERT: B 714 GLN cc_start: 0.8256 (tp-100) cc_final: 0.7603 (tm-30) REVERT: B 760 ASP cc_start: 0.9088 (m-30) cc_final: 0.8613 (t70) REVERT: C 449 LYS cc_start: 0.8809 (mptp) cc_final: 0.8561 (mppt) REVERT: C 450 TYR cc_start: 0.7580 (m-80) cc_final: 0.7274 (m-80) REVERT: C 518 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8894 (pp) REVERT: C 581 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.8725 (tp) REVERT: C 591 ILE cc_start: 0.6860 (OUTLIER) cc_final: 0.6603 (tp) REVERT: C 619 ASN cc_start: 0.9098 (OUTLIER) cc_final: 0.7075 (t0) REVERT: C 688 GLU cc_start: 0.7716 (pt0) cc_final: 0.7277 (tp30) REVERT: C 781 LYS cc_start: 0.7974 (mppt) cc_final: 0.7409 (pttp) REVERT: C 874 GLN cc_start: 0.6388 (mm-40) cc_final: 0.6100 (tp-100) REVERT: C 926 ARG cc_start: 0.6554 (ttm-80) cc_final: 0.5868 (tmt170) REVERT: C 988 MET cc_start: 0.8586 (mmm) cc_final: 0.8368 (mmm) REVERT: C 1000 ASN cc_start: 0.7689 (m-40) cc_final: 0.7178 (m-40) REVERT: D 407 MET cc_start: 0.7439 (mpp) cc_final: 0.7060 (mpp) REVERT: D 431 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8107 (mp0) REVERT: D 460 TRP cc_start: 0.6180 (m-90) cc_final: 0.5862 (m-90) REVERT: D 493 LYS cc_start: 0.8609 (mttp) cc_final: 0.8237 (mtpp) REVERT: D 637 GLU cc_start: 0.8527 (pt0) cc_final: 0.8253 (pm20) REVERT: D 714 GLN cc_start: 0.8397 (tp-100) cc_final: 0.7641 (tm-30) REVERT: D 748 LEU cc_start: 0.9298 (mm) cc_final: 0.9041 (pp) REVERT: E 75 HIS cc_start: 0.7735 (t70) cc_final: 0.7287 (t70) REVERT: E 87 GLU cc_start: 0.7656 (tp30) cc_final: 0.7283 (tp30) REVERT: E 99 PHE cc_start: 0.7998 (m-10) cc_final: 0.7615 (t80) REVERT: E 101 HIS cc_start: 0.8077 (m170) cc_final: 0.7320 (m-70) REVERT: E 108 ARG cc_start: 0.6474 (mmm160) cc_final: 0.5828 (mmm160) REVERT: E 123 MET cc_start: 0.6174 (mmm) cc_final: 0.5699 (mmm) REVERT: F 64 LEU cc_start: 0.7455 (mt) cc_final: 0.7161 (pp) REVERT: F 99 PHE cc_start: 0.7063 (m-10) cc_final: 0.6557 (t80) REVERT: F 151 TYR cc_start: 0.6777 (OUTLIER) cc_final: 0.6495 (t80) outliers start: 71 outliers final: 52 residues processed: 402 average time/residue: 0.2916 time to fit residues: 181.9368 Evaluate side-chains 407 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 346 time to evaluate : 2.126 ------------------------------------------------------------------------------- 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 524 GLU 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 759 LEU 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 1005 TRP Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 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 576 SER Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 619 ASN Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 768 TYR Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain C residue 882 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 395 VAL Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 546 PHE 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 118 ASP Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 151 TYR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 118 ASP Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 151 TYR Chi-restraints excluded: chain F residue 153 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 181 optimal weight: 0.9980 chunk 191 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 156 optimal weight: 0.0770 chunk 27 optimal weight: 0.4980 chunk 16 optimal weight: 0.5980 chunk 198 optimal weight: 0.8980 chunk 177 optimal weight: 1.9990 chunk 126 optimal weight: 0.0770 chunk 139 optimal weight: 0.6980 chunk 166 optimal weight: 8.9990 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 950 HIS C 985 ASN ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.175611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.124323 restraints weight = 32921.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.129332 restraints weight = 17613.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.129307 restraints weight = 11382.345| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.6846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 19433 Z= 0.144 Angle : 0.807 14.817 26072 Z= 0.399 Chirality : 0.046 0.341 2836 Planarity : 0.005 0.068 3142 Dihedral : 13.759 119.943 3213 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.25 % Favored : 89.75 % Rotamer: Outliers : 2.96 % Allowed : 27.78 % Favored : 69.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.36 % 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: -1.03 (0.18), residues: 2264 helix: 1.00 (0.15), residues: 1274 sheet: -3.22 (0.38), residues: 134 loop : -2.97 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 887 HIS 0.010 0.001 HIS F 101 PHE 0.031 0.002 PHE A1028 TYR 0.033 0.002 TYR F 100 ARG 0.009 0.000 ARG E 108 Details of bonding type rmsd hydrogen bonds : bond 0.03413 ( 834) hydrogen bonds : angle 3.89952 ( 2436) SS BOND : bond 0.00607 ( 6) SS BOND : angle 3.00741 ( 12) covalent geometry : bond 0.00319 (19427) covalent geometry : angle 0.80459 (26060) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7533.19 seconds wall clock time: 131 minutes 12.15 seconds (7872.15 seconds total)