Starting phenix.real_space_refine on Tue Oct 15 02:19:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ssb_40750/10_2024/8ssb_40750.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ssb_40750/10_2024/8ssb_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ssb_40750/10_2024/8ssb_40750.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ssb_40750/10_2024/8ssb_40750.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ssb_40750/10_2024/8ssb_40750.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ssb_40750/10_2024/8ssb_40750.cif" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 18 5.49 5 S 132 5.16 5 C 12575 2.51 5 N 2907 2.21 5 O 3416 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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: 11.00, per 1000 atoms: 0.58 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: 4.76 Conformation dependent library (CDL) restraints added in 2.4 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: 1.72 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: 5.35 Time building geometry restraints manager: 5.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2884 1.31 - 1.44: 5292 1.44 - 1.57: 11003 1.57 - 1.69: 36 1.69 - 1.82: 212 Bond restraints: 19427 Sorted by residual: bond pdb=" C ASP C 519 " pdb=" N PRO C 520 " ideal model delta sigma weight residual 1.336 1.386 -0.051 1.08e-02 8.57e+03 2.20e+01 bond pdb=" C ASP A 519 " pdb=" N PRO A 520 " ideal model delta sigma weight residual 1.336 1.386 -0.050 1.08e-02 8.57e+03 2.15e+01 bond pdb=" C31 PCW C1102 " pdb=" O2 PCW C1102 " ideal model delta sigma weight residual 1.333 1.424 -0.091 2.00e-02 2.50e+03 2.07e+01 bond pdb=" C VAL F 69 " pdb=" N PRO F 70 " ideal model delta sigma weight residual 1.335 1.394 -0.059 1.30e-02 5.92e+03 2.06e+01 bond pdb=" C VAL E 69 " pdb=" N PRO E 70 " ideal model delta sigma weight residual 1.335 1.394 -0.059 1.30e-02 5.92e+03 2.03e+01 ... (remaining 19422 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 24810 3.09 - 6.18: 933 6.18 - 9.27: 255 9.27 - 12.37: 48 12.37 - 15.46: 14 Bond angle restraints: 26060 Sorted by residual: angle pdb=" C ASN A 411 " pdb=" N HIS A 412 " pdb=" CA HIS A 412 " ideal model delta sigma weight residual 121.54 134.09 -12.55 1.91e+00 2.74e-01 4.32e+01 angle pdb=" C ASN C 411 " pdb=" N HIS C 412 " pdb=" CA HIS C 412 " ideal model delta sigma weight residual 121.54 134.05 -12.51 1.91e+00 2.74e-01 4.29e+01 angle pdb=" C ASP C 454 " pdb=" N ALA C 455 " pdb=" CA ALA C 455 " ideal model delta sigma weight residual 120.79 129.69 -8.90 1.39e+00 5.18e-01 4.10e+01 angle pdb=" C ASP A 454 " pdb=" N ALA A 455 " pdb=" CA ALA A 455 " ideal model delta sigma weight residual 120.79 129.69 -8.90 1.39e+00 5.18e-01 4.10e+01 angle pdb=" C ILE C 591 " pdb=" N SER C 592 " pdb=" CA SER C 592 " ideal model delta sigma weight residual 121.80 137.26 -15.46 2.44e+00 1.68e-01 4.01e+01 ... (remaining 26055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.54: 11207 35.54 - 71.09: 379 71.09 - 106.63: 37 106.63 - 142.17: 8 142.17 - 177.72: 2 Dihedral angle restraints: 11633 sinusoidal: 4991 harmonic: 6642 Sorted by residual: dihedral pdb=" CA SER A 403 " pdb=" C SER A 403 " pdb=" N PRO A 404 " pdb=" CA PRO A 404 " ideal model delta harmonic sigma weight residual 180.00 -119.87 -60.13 0 5.00e+00 4.00e-02 1.45e+02 dihedral pdb=" CA SER C 403 " pdb=" C SER C 403 " pdb=" N PRO C 404 " pdb=" CA PRO C 404 " ideal model delta harmonic sigma weight residual 180.00 -119.88 -60.12 0 5.00e+00 4.00e-02 1.45e+02 dihedral pdb=" CA LYS C 458 " pdb=" C LYS C 458 " pdb=" N ILE C 459 " pdb=" CA ILE C 459 " ideal model delta harmonic sigma weight residual -180.00 -125.97 -54.03 0 5.00e+00 4.00e-02 1.17e+02 ... (remaining 11630 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2198 0.064 - 0.128: 522 0.128 - 0.192: 88 0.192 - 0.256: 20 0.256 - 0.320: 8 Chirality restraints: 2836 Sorted by residual: chirality pdb=" C2 PCW B1101 " pdb=" C1 PCW B1101 " pdb=" C3 PCW B1101 " pdb=" O2 PCW B1101 " both_signs ideal model delta sigma weight residual False -2.32 -2.64 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CB ILE D 459 " pdb=" CA ILE D 459 " pdb=" CG1 ILE D 459 " pdb=" CG2 ILE D 459 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CB ILE B 459 " pdb=" CA ILE B 459 " pdb=" CG1 ILE B 459 " pdb=" CG2 ILE B 459 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.45e+00 ... (remaining 2833 not shown) Planarity restraints: 3142 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 716 " -0.067 5.00e-02 4.00e+02 1.01e-01 1.62e+01 pdb=" N PRO B 717 " 0.174 5.00e-02 4.00e+02 pdb=" CA PRO B 717 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 717 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 716 " 0.067 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO D 717 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO D 717 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO D 717 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 403 " 0.052 5.00e-02 4.00e+02 7.74e-02 9.57e+00 pdb=" N PRO A 404 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO A 404 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 404 " 0.042 5.00e-02 4.00e+02 ... (remaining 3139 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4708 2.79 - 3.31: 17672 3.31 - 3.84: 31682 3.84 - 4.37: 37273 4.37 - 4.90: 60640 Nonbonded interactions: 151975 Sorted by model distance: nonbonded pdb=" OG SER A 729 " pdb=" OG SER D 729 " model vdw 2.258 3.040 nonbonded pdb=" O ASP B 490 " pdb=" OG1 THR B 736 " model vdw 2.268 3.040 nonbonded pdb=" O ASP D 490 " pdb=" OG1 THR D 736 " model vdw 2.268 3.040 nonbonded pdb=" OE1 GLU C 705 " pdb=" OH TYR C 732 " model vdw 2.278 3.040 nonbonded pdb=" OE1 GLU A 705 " pdb=" OH TYR A 732 " model vdw 2.278 3.040 ... (remaining 151970 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 394 through 1035 or resid 1101 or (resid 1102 through 1103 \ and (name N or name C1 or name C11 or name C12 or name C13 or name C14 or name \ C15 or name C16 or name C17 or name C18 or name C19 or name C2 or name C20 or na \ me C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or \ name C37 or name C38 or name C39 or name C4 or name C40 or name C41 or name C42 \ or name C43 or name C44 or name C45 or name C5 or name C6 or name C7 or name C8 \ or name O11 or name O1P or name O2 or name O2P or name O3 or name O31 or name O \ 3P or name O4P or name P )) or (resid 1104 through 1106 and (name C13 or name C1 \ 4 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or nam \ e C21 or name C22 or name C23)) or resid 1108 through 1109)) selection = (chain 'C' and (resid 394 through 1035 or resid 1101 through 1102 or (resid 1103 \ and (name N or name C1 or name C11 or name C12 or name C13 or name C14 or name \ C15 or name C16 or name C17 or name C18 or name C19 or name C2 or name C20 or na \ me C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or \ name C37 or name C38 or name C39 or name C4 or name C40 or name C41 or name C42 \ or name C43 or name C44 or name C45 or name C5 or name C6 or name C7 or name C8 \ or name O11 or name O1P or name O2 or name O2P or name O3 or name O31 or name O \ 3P or name O4P or name P )) or resid 1104 through 1108)) } ncs_group { reference = (chain 'B' and (resid 394 through 821 or resid 1101 through 1102 or (resid 1103 \ and (name N or name C1 or name C11 or name C12 or name C13 or name C14 or name C \ 15 or name C16 or name C17 or name C18 or name C19 or name C2 or name C3 or name \ C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or \ name C38 or name C39 or name C4 or name C40 or name C41 or name C5 or name C6 or \ name C7 or name C8 or name O11 or name O1P or name O2 or name O2P or name O3 or \ name O31 or name O3P or name O4P or name P )) or (resid 1105 and (name N or nam \ e C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or \ name C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name C22 \ or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name C \ 36 or name C37 or name C38 or name C39 or name C4 or name C40 or name C41 or nam \ e C5 or name C6 or name C7 or name C8 or name O11 or name O1P or name O2 or name \ O2P or name O3 or name O31 or name O3P or name O4P or name P )))) selection = (chain 'D' and (resid 394 through 821 or resid 1101 through 1102 or (resid 1103 \ and (name N or name C1 or name C11 or name C12 or name C13 or name C14 or name C \ 15 or name C16 or name C17 or name C18 or name C19 or name C2 or name C3 or name \ C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or \ name C38 or name C39 or name C4 or name C40 or name C41 or name C5 or name C6 or \ name C7 or name C8 or name O11 or name O1P or name O2 or name O2P or name O3 or \ name O31 or name O3P or name O4P or name P )) or resid 1104)) } ncs_group { reference = (chain 'E' and (resid 2 through 159 or (resid 202 and (name C13 or name C14 or n \ ame C15 or name C16 or name C17 or name C18 or name C19 or name C20)))) selection = (chain 'F' and (resid 2 through 159 or (resid 202 and (name C13 or name C14 or n \ ame C15 or name C16 or name C17 or name C18 or name C19 or name C20)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.160 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: 0.030 Extract box with map and model: 0.700 Check model and map are aligned: 0.150 Set scattering table: 0.170 Process input model: 41.030 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.040 ------------------------------------------------------------------------------- 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 19427 Z= 0.581 Angle : 1.545 15.457 26060 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 *********************** 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 fitting. rotamer outliers: 14 poor density : 650 time to evaluate : 2.056 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: 0.3442 time to fit residues: 332.7745 Evaluate side-chains 387 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 384 time to evaluate : 1.938 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 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 19427 Z= 0.238 Angle : 0.829 11.605 26060 Z= 0.428 Chirality : 0.046 0.198 2836 Planarity : 0.006 0.079 3142 Dihedral : 18.349 160.931 3219 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.62 % Allowed : 10.16 % Favored : 89.22 % Rotamer: Outliers : 3.93 % Allowed : 16.45 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.95 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.99 (0.15), residues: 2264 helix: -1.86 (0.12), residues: 1356 sheet: -4.26 (0.35), residues: 120 loop : -3.63 (0.19), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 671 HIS 0.013 0.002 HIS E 107 PHE 0.030 0.002 PHE A 901 TYR 0.035 0.002 TYR D 450 ARG 0.007 0.001 ARG C 684 *********************** 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 fitting. rotamer outliers: 77 poor density : 463 time to evaluate : 2.173 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 407 MET cc_start: 0.7965 (mmm) cc_final: 0.7752 (mmm) REVERT: A 581 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8567 (tp) REVERT: A 585 MET cc_start: 0.8441 (mpt) cc_final: 0.8107 (mpt) REVERT: A 619 ASN cc_start: 0.8077 (m110) cc_final: 0.7333 (t0) REVERT: A 670 MET cc_start: 0.9301 (mtm) cc_final: 0.8988 (mtm) REVERT: A 879 LYS cc_start: 0.8410 (ttpt) cc_final: 0.7830 (mmtm) REVERT: A 1016 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8489 (mt) REVERT: A 1019 SER cc_start: 0.8856 (t) cc_final: 0.8610 (p) REVERT: A 1029 MET cc_start: 0.7745 (mmm) cc_final: 0.7524 (mtp) REVERT: B 400 ILE cc_start: 0.7002 (tt) cc_final: 0.6787 (mp) REVERT: B 463 MET cc_start: 0.7111 (ptp) cc_final: 0.6755 (ptp) REVERT: B 493 LYS cc_start: 0.8951 (mttp) cc_final: 0.8454 (tttm) REVERT: B 626 VAL cc_start: 0.9302 (t) cc_final: 0.9058 (m) REVERT: B 669 LYS cc_start: 0.9168 (pttt) cc_final: 0.8964 (pttt) REVERT: B 713 GLU cc_start: 0.9059 (tm-30) cc_final: 0.8752 (tm-30) REVERT: B 714 GLN cc_start: 0.8045 (tp-100) cc_final: 0.7334 (tp40) REVERT: B 721 MET cc_start: 0.7892 (ppp) cc_final: 0.7588 (ppp) REVERT: B 748 LEU cc_start: 0.9511 (tp) cc_final: 0.9103 (pp) REVERT: B 760 ASP cc_start: 0.9305 (m-30) cc_final: 0.8774 (t70) REVERT: B 764 ASN cc_start: 0.8866 (m-40) cc_final: 0.8184 (m-40) REVERT: C 450 TYR cc_start: 0.7353 (m-80) cc_final: 0.6399 (m-80) REVERT: C 489 ILE cc_start: 0.9225 (OUTLIER) cc_final: 0.9005 (pp) REVERT: C 518 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8596 (pp) REVERT: C 581 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.9027 (tp) REVERT: C 714 GLN cc_start: 0.8630 (mm-40) cc_final: 0.8055 (mm-40) REVERT: C 880 MET cc_start: 0.7535 (tmm) cc_final: 0.7196 (tmm) REVERT: C 891 PHE cc_start: 0.5842 (m-80) cc_final: 0.5442 (m-10) REVERT: C 926 ARG cc_start: 0.6592 (ttm-80) cc_final: 0.5830 (tmt170) REVERT: C 991 ARG cc_start: 0.6721 (mmt-90) cc_final: 0.6224 (mmt90) REVERT: C 1000 ASN cc_start: 0.7713 (m-40) cc_final: 0.7143 (m110) REVERT: C 1029 MET cc_start: 0.7993 (mmm) cc_final: 0.7785 (mtp) REVERT: D 421 TYR cc_start: 0.7975 (m-10) cc_final: 0.7718 (m-10) REVERT: D 493 LYS cc_start: 0.8622 (mttp) cc_final: 0.7880 (tttm) REVERT: D 533 TYR cc_start: 0.8797 (t80) cc_final: 0.8543 (t80) REVERT: D 702 TYR cc_start: 0.7726 (t80) cc_final: 0.7199 (t80) REVERT: D 714 GLN cc_start: 0.8463 (tp-100) cc_final: 0.7644 (tp40) REVERT: D 760 ASP cc_start: 0.9528 (m-30) cc_final: 0.9049 (t0) REVERT: D 762 LEU cc_start: 0.9399 (mm) cc_final: 0.9192 (mm) REVERT: E 75 HIS cc_start: 0.7353 (t70) cc_final: 0.6444 (t70) REVERT: E 78 PHE cc_start: 0.7456 (m-80) cc_final: 0.7173 (m-80) REVERT: E 87 GLU cc_start: 0.7429 (mm-30) cc_final: 0.7195 (mm-30) REVERT: E 94 ASN cc_start: 0.7588 (p0) cc_final: 0.7377 (p0) REVERT: E 95 ILE cc_start: 0.8330 (tp) cc_final: 0.7408 (tt) REVERT: E 101 HIS cc_start: 0.7268 (m170) cc_final: 0.6376 (m170) outliers start: 77 outliers final: 28 residues processed: 514 average time/residue: 0.3396 time to fit residues: 262.6844 Evaluate side-chains 406 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 373 time to evaluate : 2.044 ------------------------------------------------------------------------------- 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 489 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 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 115 optimal weight: 0.0470 chunk 64 optimal weight: 10.0000 chunk 172 optimal weight: 1.9990 chunk 140 optimal weight: 0.3980 chunk 57 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 224 optimal weight: 2.9990 chunk 184 optimal weight: 0.7980 chunk 205 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 166 optimal weight: 10.0000 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 714 GLN B 435 HIS C 950 HIS ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 ASN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19427 Z= 0.198 Angle : 0.774 12.244 26060 Z= 0.392 Chirality : 0.045 0.230 2836 Planarity : 0.006 0.074 3142 Dihedral : 16.871 149.738 3213 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.82 % Favored : 88.87 % Rotamer: Outliers : 4.34 % Allowed : 17.62 % Favored : 78.04 % 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: -2.74 (0.17), residues: 2264 helix: -0.72 (0.13), residues: 1334 sheet: -3.53 (0.36), residues: 146 loop : -3.35 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 460 HIS 0.016 0.002 HIS F 101 PHE 0.024 0.002 PHE A 546 TYR 0.032 0.002 TYR D 450 ARG 0.010 0.001 ARG F 108 *********************** 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 525 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 440 time to evaluate : 2.607 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: 0.7388 (m-80) cc_final: 0.6568 (m-80) REVERT: A 581 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8672 (tp) REVERT: A 585 MET cc_start: 0.8408 (mpt) cc_final: 0.8041 (mpt) REVERT: A 705 GLU cc_start: 0.7213 (mt-10) cc_final: 0.6583 (mt-10) REVERT: A 714 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.8681 (mm-40) REVERT: A 924 MET cc_start: 0.7065 (mmm) cc_final: 0.6367 (mmp) REVERT: A 926 ARG cc_start: 0.7141 (ptm160) cc_final: 0.6741 (ptm160) REVERT: A 1000 ASN cc_start: 0.7875 (m-40) cc_final: 0.7216 (m-40) REVERT: A 1019 SER cc_start: 0.8966 (t) cc_final: 0.8701 (p) REVERT: A 1029 MET cc_start: 0.7733 (mmm) cc_final: 0.7490 (mtp) REVERT: B 400 ILE cc_start: 0.7065 (tt) cc_final: 0.6380 (tt) REVERT: B 419 GLU cc_start: 0.6833 (tp30) cc_final: 0.6513 (tp30) REVERT: B 626 VAL cc_start: 0.9285 (t) cc_final: 0.9071 (m) REVERT: B 714 GLN cc_start: 0.8061 (tp-100) cc_final: 0.7402 (tp40) REVERT: B 748 LEU cc_start: 0.9443 (tp) cc_final: 0.8988 (pp) REVERT: B 760 ASP cc_start: 0.9195 (m-30) cc_final: 0.8650 (t70) REVERT: B 762 LEU cc_start: 0.9308 (mm) cc_final: 0.8973 (mm) REVERT: B 764 ASN cc_start: 0.8821 (m-40) cc_final: 0.8066 (m110) REVERT: C 450 TYR cc_start: 0.7294 (m-80) cc_final: 0.6189 (m-80) REVERT: C 518 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8747 (pp) REVERT: C 524 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7626 (pt0) REVERT: C 581 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8870 (tp) REVERT: C 713 GLU cc_start: 0.8605 (pp20) cc_final: 0.7820 (pp20) REVERT: C 714 GLN cc_start: 0.8650 (mm-40) cc_final: 0.7822 (mm110) REVERT: C 865 GLU cc_start: 0.7538 (mm-30) cc_final: 0.6716 (mm-30) REVERT: C 926 ARG cc_start: 0.6624 (ttm-80) cc_final: 0.5748 (tmt170) REVERT: C 936 LEU cc_start: 0.8759 (tp) cc_final: 0.8444 (mt) REVERT: C 988 MET cc_start: 0.8519 (mmm) cc_final: 0.8270 (mmm) REVERT: C 991 ARG cc_start: 0.6588 (mmt-90) cc_final: 0.6220 (mmt90) REVERT: C 1000 ASN cc_start: 0.7856 (m-40) cc_final: 0.6999 (m-40) REVERT: D 419 GLU cc_start: 0.8363 (mm-30) cc_final: 0.7841 (tp30) REVERT: D 431 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8185 (mp0) REVERT: D 493 LYS cc_start: 0.8572 (mttp) cc_final: 0.7817 (mtpp) REVERT: D 650 LEU cc_start: 0.8257 (tp) cc_final: 0.8042 (tp) REVERT: D 702 TYR cc_start: 0.7671 (t80) cc_final: 0.7423 (t80) REVERT: D 714 GLN cc_start: 0.8475 (tp-100) cc_final: 0.7665 (tp40) REVERT: D 760 ASP cc_start: 0.9463 (m-30) cc_final: 0.8948 (t0) REVERT: E 75 HIS cc_start: 0.7408 (t70) cc_final: 0.6472 (t70) REVERT: E 101 HIS cc_start: 0.7374 (m170) cc_final: 0.6685 (m170) REVERT: F 123 MET cc_start: 0.6007 (mmm) cc_final: 0.5779 (mmm) outliers start: 85 outliers final: 31 residues processed: 490 average time/residue: 0.2930 time to fit residues: 219.9145 Evaluate side-chains 415 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 378 time to evaluate : 1.531 ------------------------------------------------------------------------------- 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 483 LEU Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 714 GLN Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 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 638 ASP Chi-restraints excluded: chain C residue 900 CYS Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 524 GLU 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 32 ASP Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 124 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 9.9990 chunk 155 optimal weight: 6.9990 chunk 107 optimal weight: 0.1980 chunk 22 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 139 optimal weight: 0.6980 chunk 208 optimal weight: 1.9990 chunk 220 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 chunk 197 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 HIS A 619 ASN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 714 GLN B 435 HIS ** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 508 GLN D 575 ASN ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 HIS F 94 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19427 Z= 0.237 Angle : 0.778 12.411 26060 Z= 0.393 Chirality : 0.045 0.206 2836 Planarity : 0.005 0.071 3142 Dihedral : 16.304 145.021 3213 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.69 % Favored : 89.00 % Rotamer: Outliers : 4.19 % Allowed : 20.33 % Favored : 75.49 % 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: -2.29 (0.17), residues: 2264 helix: -0.22 (0.14), residues: 1342 sheet: -3.35 (0.36), residues: 148 loop : -3.49 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 460 HIS 0.013 0.002 HIS F 101 PHE 0.038 0.002 PHE A 943 TYR 0.028 0.002 TYR D 450 ARG 0.006 0.001 ARG B 420 *********************** 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 475 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 393 time to evaluate : 2.133 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: 0.7410 (m-80) cc_final: 0.6476 (m-80) REVERT: A 581 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8859 (tp) REVERT: A 755 GLU cc_start: 0.9005 (mp0) cc_final: 0.8513 (mp0) REVERT: A 1000 ASN cc_start: 0.7976 (m-40) cc_final: 0.7152 (m-40) REVERT: A 1001 TYR cc_start: 0.8339 (p90) cc_final: 0.8004 (p90) REVERT: A 1019 SER cc_start: 0.9003 (t) cc_final: 0.8710 (p) REVERT: B 637 GLU cc_start: 0.8551 (pt0) cc_final: 0.8302 (pp20) REVERT: B 638 ASP cc_start: 0.8983 (p0) cc_final: 0.8650 (p0) REVERT: B 714 GLN cc_start: 0.8221 (tp-100) cc_final: 0.7344 (tp40) REVERT: B 748 LEU cc_start: 0.9451 (tp) cc_final: 0.9000 (pp) REVERT: B 760 ASP cc_start: 0.9173 (m-30) cc_final: 0.8588 (t70) REVERT: B 764 ASN cc_start: 0.8824 (m-40) cc_final: 0.8346 (m110) REVERT: C 450 TYR cc_start: 0.7305 (m-80) cc_final: 0.6302 (m-80) REVERT: C 518 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8895 (pp) REVERT: C 581 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.8937 (tp) REVERT: C 713 GLU cc_start: 0.8617 (pp20) cc_final: 0.7928 (pp20) REVERT: C 714 GLN cc_start: 0.8716 (mm-40) cc_final: 0.7942 (mm110) REVERT: C 748 LEU cc_start: 0.9045 (pp) cc_final: 0.8775 (mt) REVERT: C 864 LEU cc_start: 0.6332 (mt) cc_final: 0.5889 (mp) REVERT: C 865 GLU cc_start: 0.7069 (mm-30) cc_final: 0.6774 (mm-30) REVERT: C 882 LEU cc_start: 0.7731 (pp) cc_final: 0.7526 (pp) REVERT: C 926 ARG cc_start: 0.6848 (ttm-80) cc_final: 0.5844 (tmt170) REVERT: C 969 SER cc_start: 0.8965 (p) cc_final: 0.8652 (t) REVERT: C 999 PHE cc_start: 0.6869 (OUTLIER) cc_final: 0.6352 (m-80) REVERT: C 1000 ASN cc_start: 0.7901 (m-40) cc_final: 0.7073 (m-40) REVERT: D 419 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7662 (tp30) REVERT: D 431 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8180 (mp0) REVERT: D 460 TRP cc_start: 0.6428 (m-10) cc_final: 0.6010 (m-90) REVERT: D 493 LYS cc_start: 0.8558 (mttp) cc_final: 0.7948 (mtpp) REVERT: D 714 GLN cc_start: 0.8488 (tp-100) cc_final: 0.7685 (tp40) REVERT: D 748 LEU cc_start: 0.9532 (tp) cc_final: 0.9040 (pp) REVERT: D 760 ASP cc_start: 0.9447 (m-30) cc_final: 0.8865 (t70) REVERT: D 781 LYS cc_start: 0.5426 (tptt) cc_final: 0.4978 (mtpp) REVERT: D 783 LYS cc_start: 0.6870 (pmtt) cc_final: 0.6420 (ptpp) REVERT: E 14 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8484 (mp) REVERT: E 75 HIS cc_start: 0.7277 (t-90) cc_final: 0.6630 (t70) REVERT: E 101 HIS cc_start: 0.7371 (m170) cc_final: 0.6578 (m170) REVERT: E 134 GLU cc_start: 0.7411 (tm-30) cc_final: 0.6857 (tm-30) REVERT: F 104 ARG cc_start: 0.8212 (tpt-90) cc_final: 0.7943 (tpt-90) REVERT: C 1107 GLU cc_start: 0.5285 (tp30) cc_final: 0.4589 (mm-30) outliers start: 82 outliers final: 47 residues processed: 447 average time/residue: 0.3024 time to fit residues: 207.9619 Evaluate side-chains 410 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 357 time to evaluate : 1.527 ------------------------------------------------------------------------------- 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 674 MET 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 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 481 ILE Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 469 TYR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain C residue 900 CYS Chi-restraints excluded: chain C residue 999 PHE Chi-restraints excluded: chain C residue 1016 LEU Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 637 GLU Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 124 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 6.9990 chunk 125 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 164 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 188 optimal weight: 1.9990 chunk 152 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 112 optimal weight: 0.9990 chunk 197 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 HIS A 642 GLN A 874 GLN ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 GLN ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 874 GLN ** C 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 ASN ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN F 107 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.5473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19427 Z= 0.246 Angle : 0.761 12.446 26060 Z= 0.386 Chirality : 0.045 0.211 2836 Planarity : 0.005 0.068 3142 Dihedral : 15.847 140.404 3213 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.34 % Favored : 89.40 % Rotamer: Outliers : 5.46 % Allowed : 20.89 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.86 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.18), residues: 2264 helix: 0.17 (0.14), residues: 1336 sheet: -3.48 (0.34), residues: 156 loop : -3.43 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP B 460 HIS 0.018 0.002 HIS F 101 PHE 0.032 0.002 PHE A 943 TYR 0.034 0.002 TYR D 450 ARG 0.007 0.001 ARG E 108 *********************** 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 492 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 385 time to evaluate : 2.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 TYR cc_start: 0.7667 (m-80) cc_final: 0.6680 (m-80) REVERT: A 524 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7134 (pt0) REVERT: A 581 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8949 (tp) REVERT: A 619 ASN cc_start: 0.8801 (OUTLIER) cc_final: 0.7045 (t0) REVERT: A 755 GLU cc_start: 0.9009 (mp0) cc_final: 0.8543 (mp0) REVERT: A 998 TYR cc_start: 0.7832 (p90) cc_final: 0.7405 (p90) REVERT: A 1000 ASN cc_start: 0.7919 (m-40) cc_final: 0.7324 (m-40) REVERT: A 1003 TYR cc_start: 0.7707 (m-80) cc_final: 0.6931 (m-80) REVERT: A 1019 SER cc_start: 0.9051 (t) cc_final: 0.8762 (p) REVERT: A 1029 MET cc_start: 0.7426 (mmp) cc_final: 0.6912 (mtp) REVERT: B 401 LEU cc_start: 0.8940 (tp) cc_final: 0.8696 (pt) REVERT: B 629 MET cc_start: 0.8655 (tpp) cc_final: 0.8078 (mtt) REVERT: B 713 GLU cc_start: 0.9059 (tm-30) cc_final: 0.8835 (tm-30) REVERT: B 714 GLN cc_start: 0.8270 (tp-100) cc_final: 0.7521 (tp40) REVERT: B 760 ASP cc_start: 0.9141 (m-30) cc_final: 0.8778 (t70) REVERT: B 762 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8921 (mm) REVERT: C 450 TYR cc_start: 0.7484 (m-80) cc_final: 0.6311 (m-80) REVERT: C 518 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8974 (pp) REVERT: C 581 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8905 (tp) REVERT: C 688 GLU cc_start: 0.8294 (pt0) cc_final: 0.7445 (tp30) REVERT: C 713 GLU cc_start: 0.8629 (pp20) cc_final: 0.8081 (pp20) REVERT: C 714 GLN cc_start: 0.8800 (mm-40) cc_final: 0.8196 (mm110) REVERT: C 748 LEU cc_start: 0.9038 (pp) cc_final: 0.8768 (mt) REVERT: C 926 ARG cc_start: 0.7045 (ttm-80) cc_final: 0.5995 (tmt170) REVERT: C 969 SER cc_start: 0.8891 (p) cc_final: 0.8663 (t) REVERT: C 999 PHE cc_start: 0.6846 (OUTLIER) cc_final: 0.6303 (m-80) REVERT: C 1000 ASN cc_start: 0.7901 (m-40) cc_final: 0.7426 (m-40) REVERT: C 1005 TRP cc_start: 0.6592 (m-90) cc_final: 0.6289 (m-10) REVERT: D 419 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7698 (tp30) REVERT: D 431 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8180 (mp0) REVERT: D 493 LYS cc_start: 0.8552 (mttp) cc_final: 0.7976 (mtpp) REVERT: D 519 ASP cc_start: 0.8218 (OUTLIER) cc_final: 0.7919 (m-30) REVERT: D 637 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8090 (pm20) REVERT: D 714 GLN cc_start: 0.8484 (tp-100) cc_final: 0.7870 (tm-30) REVERT: D 748 LEU cc_start: 0.9502 (tp) cc_final: 0.9029 (pp) REVERT: D 760 ASP cc_start: 0.9428 (m-30) cc_final: 0.8715 (t0) REVERT: D 764 ASN cc_start: 0.9139 (m-40) cc_final: 0.8565 (m-40) REVERT: E 75 HIS cc_start: 0.7297 (t-90) cc_final: 0.6609 (t70) REVERT: E 101 HIS cc_start: 0.7545 (m170) cc_final: 0.6592 (m170) REVERT: E 123 MET cc_start: 0.5911 (mmm) cc_final: 0.4921 (mmm) REVERT: E 134 GLU cc_start: 0.7295 (tm-30) cc_final: 0.6868 (tm-30) REVERT: C 1107 GLU cc_start: 0.5274 (tp30) cc_final: 0.4949 (mm-30) outliers start: 107 outliers final: 57 residues processed: 453 average time/residue: 0.2973 time to fit residues: 209.2405 Evaluate side-chains 413 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 347 time to evaluate : 2.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 469 TYR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 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 1015 LEU Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 469 TYR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain C residue 900 CYS Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 999 PHE Chi-restraints excluded: chain C residue 1016 LEU Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 495 PHE Chi-restraints excluded: chain D residue 504 ILE Chi-restraints excluded: chain D residue 519 ASP Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 637 GLU Chi-restraints excluded: chain D residue 747 ASN Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 151 TYR Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 124 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 0.8980 chunk 198 optimal weight: 0.5980 chunk 43 optimal weight: 8.9990 chunk 129 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 220 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 115 optimal weight: 0.0770 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN A 874 GLN ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 GLN ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 94 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.5820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19427 Z= 0.202 Angle : 0.772 14.678 26060 Z= 0.387 Chirality : 0.045 0.247 2836 Planarity : 0.005 0.066 3142 Dihedral : 15.322 134.370 3213 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.22 % Allowed : 10.91 % Favored : 88.87 % Rotamer: Outliers : 4.14 % Allowed : 23.24 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.81 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.18), residues: 2264 helix: 0.41 (0.15), residues: 1332 sheet: -2.66 (0.40), residues: 140 loop : -3.33 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP B 460 HIS 0.018 0.002 HIS F 101 PHE 0.032 0.002 PHE A 943 TYR 0.047 0.002 TYR B 673 ARG 0.009 0.001 ARG E 108 *********************** 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 483 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 402 time to evaluate : 2.246 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: 0.7627 (m-80) cc_final: 0.6669 (m-80) REVERT: A 524 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7466 (pt0) REVERT: A 581 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8813 (tp) REVERT: A 619 ASN cc_start: 0.8694 (OUTLIER) cc_final: 0.6909 (t0) REVERT: A 755 GLU cc_start: 0.9026 (mp0) cc_final: 0.8628 (mp0) REVERT: A 891 PHE cc_start: 0.6120 (m-10) cc_final: 0.5332 (m-10) REVERT: A 988 MET cc_start: 0.8651 (mmp) cc_final: 0.8245 (mmm) REVERT: A 998 TYR cc_start: 0.7942 (p90) cc_final: 0.7482 (p90) REVERT: A 1000 ASN cc_start: 0.7833 (m-40) cc_final: 0.7299 (m110) REVERT: A 1003 TYR cc_start: 0.7776 (m-80) cc_final: 0.7436 (m-80) REVERT: A 1019 SER cc_start: 0.9113 (t) cc_final: 0.8779 (p) REVERT: A 1029 MET cc_start: 0.7263 (mmp) cc_final: 0.6990 (mtp) REVERT: B 401 LEU cc_start: 0.8842 (tp) cc_final: 0.8633 (pt) REVERT: B 407 MET cc_start: 0.7628 (mpp) cc_final: 0.7366 (mpp) REVERT: B 573 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8254 (tp) REVERT: B 629 MET cc_start: 0.8642 (tpp) cc_final: 0.8100 (mtt) REVERT: B 638 ASP cc_start: 0.9012 (p0) cc_final: 0.8680 (p0) REVERT: B 682 PHE cc_start: 0.7635 (OUTLIER) cc_final: 0.7344 (m-80) REVERT: B 714 GLN cc_start: 0.8277 (tp-100) cc_final: 0.7513 (tp40) REVERT: B 760 ASP cc_start: 0.9119 (m-30) cc_final: 0.8558 (t70) REVERT: B 764 ASN cc_start: 0.8841 (m-40) cc_final: 0.8310 (m110) REVERT: C 408 MET cc_start: 0.7186 (tpp) cc_final: 0.6667 (tpp) REVERT: C 450 TYR cc_start: 0.7365 (m-80) cc_final: 0.6409 (m-80) REVERT: C 518 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8951 (pp) REVERT: C 581 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8865 (tp) REVERT: C 688 GLU cc_start: 0.8210 (pt0) cc_final: 0.7330 (tp30) REVERT: C 713 GLU cc_start: 0.8677 (pp20) cc_final: 0.8141 (pp20) REVERT: C 714 GLN cc_start: 0.8814 (mm-40) cc_final: 0.8213 (mm110) REVERT: C 748 LEU cc_start: 0.8957 (pp) cc_final: 0.8710 (mt) REVERT: C 926 ARG cc_start: 0.6900 (ttm-80) cc_final: 0.5789 (tmt170) REVERT: C 969 SER cc_start: 0.8862 (p) cc_final: 0.8607 (t) REVERT: C 988 MET cc_start: 0.8540 (mmm) cc_final: 0.8323 (mmm) REVERT: C 1000 ASN cc_start: 0.7821 (m-40) cc_final: 0.7351 (m-40) REVERT: C 1005 TRP cc_start: 0.6535 (m-90) cc_final: 0.6239 (m-10) REVERT: D 407 MET cc_start: 0.7630 (mpp) cc_final: 0.7420 (mpp) REVERT: D 419 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7769 (tp30) REVERT: D 431 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8102 (mp0) REVERT: D 460 TRP cc_start: 0.6180 (m-10) cc_final: 0.4764 (m-10) REVERT: D 493 LYS cc_start: 0.8550 (mttp) cc_final: 0.7877 (mtpp) REVERT: D 519 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7890 (m-30) REVERT: D 714 GLN cc_start: 0.8453 (tp-100) cc_final: 0.7627 (tp40) REVERT: D 748 LEU cc_start: 0.9495 (tp) cc_final: 0.9058 (pp) REVERT: D 760 ASP cc_start: 0.9394 (m-30) cc_final: 0.8696 (t0) REVERT: D 764 ASN cc_start: 0.9084 (m-40) cc_final: 0.8538 (m-40) REVERT: D 781 LYS cc_start: 0.5685 (tptt) cc_final: 0.5059 (mtpp) REVERT: D 783 LYS cc_start: 0.6894 (pmtt) cc_final: 0.6356 (ptpp) REVERT: E 108 ARG cc_start: 0.6357 (mmm160) cc_final: 0.5791 (mmm160) REVERT: E 123 MET cc_start: 0.6152 (mmm) cc_final: 0.5945 (mmm) REVERT: E 134 GLU cc_start: 0.7301 (tm-30) cc_final: 0.6825 (tm-30) REVERT: F 64 LEU cc_start: 0.7476 (mt) cc_final: 0.7210 (pp) REVERT: F 147 PHE cc_start: 0.8541 (m-80) cc_final: 0.8213 (m-80) REVERT: C 1107 GLU cc_start: 0.5134 (tp30) cc_final: 0.4917 (mm-30) outliers start: 81 outliers final: 56 residues processed: 450 average time/residue: 0.3065 time to fit residues: 211.4039 Evaluate side-chains 423 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 359 time to evaluate : 2.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 469 TYR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 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 1015 LEU Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 682 PHE Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 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 576 SER Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 900 CYS Chi-restraints excluded: chain C residue 1016 LEU 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 519 ASP Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain F residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 125 optimal weight: 0.9990 chunk 161 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 185 optimal weight: 7.9990 chunk 123 optimal weight: 3.9990 chunk 219 optimal weight: 0.6980 chunk 137 optimal weight: 0.5980 chunk 133 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.6080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 19427 Z= 0.213 Angle : 0.779 19.170 26060 Z= 0.387 Chirality : 0.045 0.208 2836 Planarity : 0.005 0.064 3142 Dihedral : 15.000 128.654 3213 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.82 % Favored : 89.00 % Rotamer: Outliers : 4.65 % Allowed : 24.11 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 6.25 % 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: -1.42 (0.18), residues: 2264 helix: 0.61 (0.15), residues: 1316 sheet: -3.38 (0.40), residues: 116 loop : -3.23 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.002 TRP B 460 HIS 0.015 0.002 HIS F 101 PHE 0.032 0.002 PHE A 943 TYR 0.025 0.001 TYR D 450 ARG 0.006 0.000 ARG E 108 *********************** 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 484 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 393 time to evaluate : 2.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 TYR cc_start: 0.7740 (m-80) cc_final: 0.6912 (m-80) REVERT: A 581 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8861 (tp) REVERT: A 619 ASN cc_start: 0.8737 (OUTLIER) cc_final: 0.8061 (t0) REVERT: A 688 GLU cc_start: 0.8010 (pt0) cc_final: 0.7270 (tp30) REVERT: A 755 GLU cc_start: 0.8954 (mp0) cc_final: 0.8727 (mp0) REVERT: A 926 ARG cc_start: 0.6728 (ptm160) cc_final: 0.6344 (ptm160) REVERT: A 988 MET cc_start: 0.8673 (mmp) cc_final: 0.8372 (mmm) REVERT: A 998 TYR cc_start: 0.7934 (p90) cc_final: 0.7412 (p90) REVERT: A 1000 ASN cc_start: 0.7769 (m-40) cc_final: 0.7231 (m110) REVERT: A 1019 SER cc_start: 0.9148 (t) cc_final: 0.8823 (p) REVERT: B 401 LEU cc_start: 0.8878 (tp) cc_final: 0.8648 (pt) REVERT: B 407 MET cc_start: 0.7744 (mpp) cc_final: 0.7522 (mpp) REVERT: B 714 GLN cc_start: 0.8315 (tp-100) cc_final: 0.7587 (tm-30) REVERT: B 760 ASP cc_start: 0.9152 (m-30) cc_final: 0.8506 (t70) REVERT: B 764 ASN cc_start: 0.8847 (m-40) cc_final: 0.8302 (m110) REVERT: C 408 MET cc_start: 0.7154 (tpp) cc_final: 0.6629 (tpp) REVERT: C 450 TYR cc_start: 0.7294 (m-80) cc_final: 0.6384 (m-80) REVERT: C 518 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8962 (pp) REVERT: C 581 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8819 (tp) REVERT: C 688 GLU cc_start: 0.8221 (pt0) cc_final: 0.7380 (tp30) REVERT: C 713 GLU cc_start: 0.8710 (pp20) cc_final: 0.8234 (pp20) REVERT: C 714 GLN cc_start: 0.8822 (mm-40) cc_final: 0.8290 (mm110) REVERT: C 748 LEU cc_start: 0.8990 (pp) cc_final: 0.8761 (mt) REVERT: C 926 ARG cc_start: 0.6825 (ttm-80) cc_final: 0.5758 (tmt170) REVERT: C 969 SER cc_start: 0.8835 (p) cc_final: 0.8516 (t) REVERT: C 1000 ASN cc_start: 0.7860 (m-40) cc_final: 0.7008 (m-40) REVERT: C 1005 TRP cc_start: 0.6557 (m-90) cc_final: 0.6237 (m-10) REVERT: D 407 MET cc_start: 0.7856 (mpp) cc_final: 0.7406 (mpp) REVERT: D 419 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7552 (tp30) REVERT: D 431 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8083 (mp0) REVERT: D 493 LYS cc_start: 0.8579 (mttp) cc_final: 0.7936 (mtpp) REVERT: D 519 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7883 (m-30) REVERT: D 673 TYR cc_start: 0.8304 (m-80) cc_final: 0.7845 (m-80) REVERT: D 682 PHE cc_start: 0.7414 (OUTLIER) cc_final: 0.7168 (m-80) REVERT: D 714 GLN cc_start: 0.8452 (tp-100) cc_final: 0.7663 (tp40) REVERT: D 760 ASP cc_start: 0.9364 (m-30) cc_final: 0.8688 (t0) REVERT: D 764 ASN cc_start: 0.9162 (m-40) cc_final: 0.8569 (m-40) REVERT: E 106 PHE cc_start: 0.7074 (p90) cc_final: 0.6554 (t80) REVERT: E 108 ARG cc_start: 0.6396 (mmm160) cc_final: 0.6031 (mmm160) REVERT: E 123 MET cc_start: 0.6154 (mmm) cc_final: 0.5590 (mmm) REVERT: F 65 ARG cc_start: 0.7833 (ptt90) cc_final: 0.7609 (ptt90) REVERT: F 147 PHE cc_start: 0.8493 (m-80) cc_final: 0.8202 (m-80) REVERT: C 1107 GLU cc_start: 0.5323 (tp30) cc_final: 0.4820 (mm-30) outliers start: 91 outliers final: 57 residues processed: 452 average time/residue: 0.2979 time to fit residues: 207.8454 Evaluate side-chains 413 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 349 time to evaluate : 2.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 469 TYR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 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 1015 LEU Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 469 TYR Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain C residue 900 CYS Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 984 ILE Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain C residue 1016 LEU 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 519 ASP Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 682 PHE Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 747 ASN Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 151 TYR Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 124 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 66 optimal weight: 0.4980 chunk 43 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 172 optimal weight: 0.7980 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 756 GLN ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.6276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 19427 Z= 0.267 Angle : 0.807 15.388 26060 Z= 0.402 Chirality : 0.046 0.207 2836 Planarity : 0.005 0.067 3142 Dihedral : 14.935 127.672 3213 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.87 % Favored : 89.05 % Rotamer: Outliers : 4.34 % Allowed : 25.23 % Favored : 70.43 % 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: -1.37 (0.18), residues: 2264 helix: 0.61 (0.15), residues: 1330 sheet: -2.75 (0.38), residues: 152 loop : -3.28 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 887 HIS 0.013 0.002 HIS F 101 PHE 0.032 0.002 PHE A 943 TYR 0.030 0.002 TYR D 450 ARG 0.005 0.001 ARG E 108 *********************** 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 425 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 340 time to evaluate : 2.234 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: A 450 TYR cc_start: 0.7784 (m-80) cc_final: 0.7152 (m-80) REVERT: A 581 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.8886 (tp) REVERT: A 619 ASN cc_start: 0.8880 (OUTLIER) cc_final: 0.7808 (t0) REVERT: A 688 GLU cc_start: 0.8067 (pt0) cc_final: 0.7216 (tp30) REVERT: A 755 GLU cc_start: 0.8945 (mp0) cc_final: 0.8723 (mp0) REVERT: A 926 ARG cc_start: 0.6708 (ptm160) cc_final: 0.6333 (ptm160) REVERT: A 988 MET cc_start: 0.8679 (mmp) cc_final: 0.8354 (mmm) REVERT: A 998 TYR cc_start: 0.7988 (p90) cc_final: 0.7513 (p90) REVERT: A 1000 ASN cc_start: 0.7759 (m-40) cc_final: 0.7257 (m110) REVERT: A 1019 SER cc_start: 0.9188 (t) cc_final: 0.8850 (p) REVERT: B 401 LEU cc_start: 0.8845 (tp) cc_final: 0.8640 (pt) REVERT: B 407 MET cc_start: 0.7791 (mpp) cc_final: 0.7326 (mpp) REVERT: B 629 MET cc_start: 0.8523 (tpp) cc_final: 0.7940 (mtt) REVERT: B 714 GLN cc_start: 0.8332 (tp-100) cc_final: 0.7626 (tm-30) REVERT: B 721 MET cc_start: 0.8445 (ppp) cc_final: 0.8216 (ppp) REVERT: B 748 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.8987 (pp) REVERT: B 760 ASP cc_start: 0.9126 (m-30) cc_final: 0.8688 (t70) REVERT: C 408 MET cc_start: 0.7519 (tpp) cc_final: 0.7219 (tpp) REVERT: C 450 TYR cc_start: 0.7591 (m-80) cc_final: 0.6818 (m-80) REVERT: C 581 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8748 (tp) REVERT: C 585 MET cc_start: 0.8291 (mpt) cc_final: 0.7719 (mpt) REVERT: C 688 GLU cc_start: 0.8247 (pt0) cc_final: 0.7453 (tp30) REVERT: C 713 GLU cc_start: 0.8712 (pp20) cc_final: 0.8421 (pp20) REVERT: C 748 LEU cc_start: 0.8988 (pp) cc_final: 0.8768 (mt) REVERT: C 865 GLU cc_start: 0.6911 (mm-30) cc_final: 0.6666 (mm-30) REVERT: C 926 ARG cc_start: 0.6781 (ttm-80) cc_final: 0.5860 (tmt170) REVERT: C 1000 ASN cc_start: 0.7924 (m-40) cc_final: 0.7089 (m-40) REVERT: D 407 MET cc_start: 0.7704 (mpp) cc_final: 0.7459 (mpp) REVERT: D 419 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7671 (tp30) REVERT: D 431 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8075 (mp0) REVERT: D 493 LYS cc_start: 0.8592 (mttp) cc_final: 0.8038 (mtpp) REVERT: D 519 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.7909 (m-30) REVERT: D 682 PHE cc_start: 0.7543 (m-80) cc_final: 0.7244 (m-80) REVERT: D 714 GLN cc_start: 0.8492 (tp-100) cc_final: 0.7765 (tp40) REVERT: D 721 MET cc_start: 0.8292 (ppp) cc_final: 0.7951 (ppp) REVERT: D 748 LEU cc_start: 0.9335 (tp) cc_final: 0.8982 (pp) REVERT: D 760 ASP cc_start: 0.9326 (m-30) cc_final: 0.8755 (t0) REVERT: E 106 PHE cc_start: 0.7102 (p90) cc_final: 0.6649 (t80) REVERT: E 108 ARG cc_start: 0.6384 (mmm160) cc_final: 0.6129 (mmm160) REVERT: F 65 ARG cc_start: 0.7836 (ptt90) cc_final: 0.7589 (ptt90) REVERT: F 123 MET cc_start: 0.5377 (mmm) cc_final: 0.5009 (mmm) REVERT: F 147 PHE cc_start: 0.8622 (m-80) cc_final: 0.8308 (m-80) outliers start: 85 outliers final: 62 residues processed: 394 average time/residue: 0.2968 time to fit residues: 181.3089 Evaluate side-chains 391 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 323 time to evaluate : 2.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 469 TYR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 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 1015 LEU Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 469 TYR Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 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 882 LEU Chi-restraints excluded: chain C residue 900 CYS Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain C residue 1016 LEU Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 495 PHE Chi-restraints excluded: chain D residue 519 ASP Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 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 80 LEU Chi-restraints excluded: chain F residue 118 ASP Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 124 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 0.6980 chunk 210 optimal weight: 10.0000 chunk 192 optimal weight: 2.9990 chunk 204 optimal weight: 7.9990 chunk 123 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 160 optimal weight: 10.0000 chunk 62 optimal weight: 0.1980 chunk 185 optimal weight: 0.9990 chunk 193 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 587 GLN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.6410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 19427 Z= 0.259 Angle : 0.813 15.199 26060 Z= 0.404 Chirality : 0.047 0.225 2836 Planarity : 0.005 0.069 3142 Dihedral : 14.740 127.254 3213 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.95 % Favored : 89.00 % Rotamer: Outliers : 3.68 % Allowed : 26.15 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 7.81 % Twisted General : 0.54 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.18), residues: 2264 helix: 0.67 (0.15), residues: 1330 sheet: -2.42 (0.41), residues: 136 loop : -3.33 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 887 HIS 0.011 0.002 HIS F 101 PHE 0.033 0.002 PHE A1028 TYR 0.027 0.002 TYR D 450 ARG 0.004 0.000 ARG E 104 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 348 time to evaluate : 2.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 TYR cc_start: 0.7707 (m-80) cc_final: 0.7296 (m-10) REVERT: A 581 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8751 (tp) REVERT: A 585 MET cc_start: 0.8298 (mpt) cc_final: 0.7724 (mpt) REVERT: A 619 ASN cc_start: 0.8847 (OUTLIER) cc_final: 0.8268 (t0) REVERT: A 721 MET cc_start: 0.8864 (pmm) cc_final: 0.8462 (pmm) REVERT: A 755 GLU cc_start: 0.8969 (mp0) cc_final: 0.8741 (mp0) REVERT: A 926 ARG cc_start: 0.6656 (ptm160) cc_final: 0.6282 (ptm160) REVERT: A 988 MET cc_start: 0.8692 (mmp) cc_final: 0.8393 (mmm) REVERT: A 998 TYR cc_start: 0.7947 (p90) cc_final: 0.7456 (p90) REVERT: A 1000 ASN cc_start: 0.7738 (m-40) cc_final: 0.7221 (m110) REVERT: A 1019 SER cc_start: 0.9216 (t) cc_final: 0.8870 (p) REVERT: B 407 MET cc_start: 0.7840 (mpp) cc_final: 0.7351 (mpp) REVERT: B 714 GLN cc_start: 0.8291 (tp-100) cc_final: 0.7637 (tm-30) REVERT: B 748 LEU cc_start: 0.9436 (tp) cc_final: 0.8986 (pp) REVERT: B 760 ASP cc_start: 0.9120 (m-30) cc_final: 0.8679 (t70) REVERT: C 408 MET cc_start: 0.7592 (tpp) cc_final: 0.7345 (tpp) REVERT: C 450 TYR cc_start: 0.7584 (m-80) cc_final: 0.6916 (m-80) REVERT: C 581 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8765 (tp) REVERT: C 688 GLU cc_start: 0.8240 (pt0) cc_final: 0.7460 (tp30) REVERT: C 713 GLU cc_start: 0.8714 (pp20) cc_final: 0.8422 (pp20) REVERT: C 748 LEU cc_start: 0.8974 (pp) cc_final: 0.8761 (mt) REVERT: C 926 ARG cc_start: 0.6703 (ttm-80) cc_final: 0.5757 (tmt170) REVERT: C 1000 ASN cc_start: 0.7899 (m-40) cc_final: 0.7136 (m-40) REVERT: D 407 MET cc_start: 0.7762 (mpp) cc_final: 0.7525 (mpp) REVERT: D 408 MET cc_start: 0.6162 (tpp) cc_final: 0.5917 (tpp) REVERT: D 419 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7606 (tp30) REVERT: D 431 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8033 (mp0) REVERT: D 460 TRP cc_start: 0.6191 (m-10) cc_final: 0.5398 (m-90) REVERT: D 493 LYS cc_start: 0.8639 (mttp) cc_final: 0.8102 (mtpp) REVERT: D 519 ASP cc_start: 0.8214 (OUTLIER) cc_final: 0.7910 (m-30) REVERT: D 714 GLN cc_start: 0.8524 (tp-100) cc_final: 0.7753 (tm-30) REVERT: D 748 LEU cc_start: 0.9425 (tp) cc_final: 0.9040 (pp) REVERT: D 760 ASP cc_start: 0.9302 (m-30) cc_final: 0.8730 (t70) REVERT: D 761 LYS cc_start: 0.9391 (mmmt) cc_final: 0.9040 (mmtm) REVERT: E 106 PHE cc_start: 0.7148 (p90) cc_final: 0.6768 (t80) REVERT: E 123 MET cc_start: 0.5445 (mmm) cc_final: 0.5063 (mmm) REVERT: F 65 ARG cc_start: 0.7876 (ptt90) cc_final: 0.7651 (ptt90) REVERT: F 123 MET cc_start: 0.5571 (mmm) cc_final: 0.5223 (mmm) outliers start: 72 outliers final: 58 residues processed: 397 average time/residue: 0.2962 time to fit residues: 182.3719 Evaluate side-chains 390 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 327 time to evaluate : 2.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 469 TYR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 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 1007 PHE Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 467 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 502 ILE Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 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 882 LEU Chi-restraints excluded: chain C residue 900 CYS Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain C residue 1016 LEU Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 519 ASP Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 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 80 LEU 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 124 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 150 optimal weight: 0.7980 chunk 227 optimal weight: 4.9990 chunk 209 optimal weight: 3.9990 chunk 180 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 143 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.6535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 19427 Z= 0.252 Angle : 0.812 15.445 26060 Z= 0.403 Chirality : 0.047 0.247 2836 Planarity : 0.005 0.068 3142 Dihedral : 14.498 126.276 3213 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.78 % Favored : 89.18 % Rotamer: Outliers : 3.32 % Allowed : 27.22 % Favored : 69.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 7.81 % Twisted General : 0.54 % 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: -1.28 (0.18), residues: 2264 helix: 0.70 (0.15), residues: 1334 sheet: -2.61 (0.49), residues: 96 loop : -3.35 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 887 HIS 0.009 0.002 HIS F 101 PHE 0.034 0.002 PHE A1028 TYR 0.030 0.002 TYR D 450 ARG 0.016 0.001 ARG E 108 ********************** 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 402 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 337 time to evaluate : 1.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 TYR cc_start: 0.7717 (m-80) cc_final: 0.7311 (m-10) REVERT: A 581 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8754 (tp) REVERT: A 619 ASN cc_start: 0.8830 (OUTLIER) cc_final: 0.8035 (t0) REVERT: A 721 MET cc_start: 0.8917 (pmm) cc_final: 0.8461 (pmm) REVERT: A 926 ARG cc_start: 0.6653 (ptm160) cc_final: 0.6282 (ptm160) REVERT: A 943 PHE cc_start: 0.8566 (t80) cc_final: 0.8316 (t80) REVERT: A 988 MET cc_start: 0.8687 (mmp) cc_final: 0.8434 (mmm) REVERT: A 998 TYR cc_start: 0.7928 (p90) cc_final: 0.7396 (p90) REVERT: A 1000 ASN cc_start: 0.7749 (m-40) cc_final: 0.7223 (m110) REVERT: A 1019 SER cc_start: 0.9253 (t) cc_final: 0.8898 (p) REVERT: B 407 MET cc_start: 0.7809 (mpp) cc_final: 0.7435 (mpp) REVERT: B 491 PHE cc_start: 0.6260 (t80) cc_final: 0.5978 (t80) REVERT: B 629 MET cc_start: 0.8363 (tpp) cc_final: 0.7951 (mtt) REVERT: B 714 GLN cc_start: 0.8341 (tp-100) cc_final: 0.7691 (tm-30) REVERT: B 748 LEU cc_start: 0.9443 (tp) cc_final: 0.9009 (pp) REVERT: B 760 ASP cc_start: 0.9101 (m-30) cc_final: 0.8677 (t70) REVERT: C 450 TYR cc_start: 0.7583 (m-80) cc_final: 0.7058 (m-80) REVERT: C 581 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8603 (tp) REVERT: C 585 MET cc_start: 0.8328 (mpt) cc_final: 0.7683 (mpt) REVERT: C 688 GLU cc_start: 0.8259 (pt0) cc_final: 0.7486 (tp30) REVERT: C 713 GLU cc_start: 0.8713 (pp20) cc_final: 0.8428 (pp20) REVERT: C 721 MET cc_start: 0.8381 (ptm) cc_final: 0.8117 (ptp) REVERT: C 748 LEU cc_start: 0.8969 (pp) cc_final: 0.8739 (mt) REVERT: C 926 ARG cc_start: 0.6669 (ttm-80) cc_final: 0.5713 (tmt170) REVERT: C 1000 ASN cc_start: 0.7921 (m-40) cc_final: 0.7182 (m-40) REVERT: D 407 MET cc_start: 0.7812 (mpp) cc_final: 0.7573 (mpp) REVERT: D 408 MET cc_start: 0.6117 (tpp) cc_final: 0.5615 (tpt) REVERT: D 419 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7566 (tp30) REVERT: D 431 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8101 (mp0) REVERT: D 493 LYS cc_start: 0.8613 (mttp) cc_final: 0.8064 (mtpp) REVERT: D 519 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7906 (m-30) REVERT: D 714 GLN cc_start: 0.8522 (tp-100) cc_final: 0.7749 (tm-30) REVERT: D 721 MET cc_start: 0.8335 (ppp) cc_final: 0.7989 (ppp) REVERT: D 748 LEU cc_start: 0.9475 (tp) cc_final: 0.9076 (pp) REVERT: D 760 ASP cc_start: 0.9319 (m-30) cc_final: 0.8767 (t0) REVERT: D 761 LYS cc_start: 0.9394 (mmmt) cc_final: 0.9087 (mmtt) REVERT: E 106 PHE cc_start: 0.7135 (p90) cc_final: 0.6734 (t80) REVERT: E 123 MET cc_start: 0.5601 (mmm) cc_final: 0.5252 (mmm) REVERT: F 123 MET cc_start: 0.5699 (mmm) cc_final: 0.5369 (mmm) outliers start: 65 outliers final: 55 residues processed: 383 average time/residue: 0.2918 time to fit residues: 174.5524 Evaluate side-chains 389 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 329 time to evaluate : 2.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 469 TYR Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 619 ASN Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 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 1007 PHE Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 469 TYR 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 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 882 LEU Chi-restraints excluded: chain C residue 900 CYS Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain C residue 1016 LEU Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 519 ASP Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 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 80 LEU Chi-restraints excluded: chain F residue 118 ASP Chi-restraints excluded: chain F residue 120 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 7.9990 chunk 55 optimal weight: 0.8980 chunk 166 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 181 optimal weight: 0.0040 chunk 75 optimal weight: 0.3980 chunk 186 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 159 optimal weight: 1.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 950 HIS C 985 ASN ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.171793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.116096 restraints weight = 33357.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.120340 restraints weight = 17020.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.123110 restraints weight = 12085.578| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.6752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 19427 Z= 0.208 Angle : 0.801 15.653 26060 Z= 0.395 Chirality : 0.046 0.250 2836 Planarity : 0.005 0.065 3142 Dihedral : 13.870 122.295 3213 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.25 % Favored : 89.71 % Rotamer: Outliers : 3.12 % Allowed : 27.37 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 6.25 % 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: -1.13 (0.18), residues: 2264 helix: 0.87 (0.15), residues: 1306 sheet: -3.45 (0.38), residues: 144 loop : -3.01 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 887 HIS 0.011 0.002 HIS F 101 PHE 0.032 0.002 PHE A1028 TYR 0.022 0.001 TYR D 450 ARG 0.013 0.000 ARG E 108 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4502.96 seconds wall clock time: 164 minutes 39.08 seconds (9879.08 seconds total)