Starting phenix.real_space_refine on Wed Jan 22 11:33:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b61_44234/01_2025/9b61_44234.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b61_44234/01_2025/9b61_44234.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b61_44234/01_2025/9b61_44234.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b61_44234/01_2025/9b61_44234.map" model { file = "/net/cci-nas-00/data/ceres_data/9b61_44234/01_2025/9b61_44234.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b61_44234/01_2025/9b61_44234.cif" } resolution = 2.81 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= 0.000 sd= 0.001 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: 4 Type Number sf(0) Gaussians S 128 5.16 5 C 12003 2.51 5 N 2954 2.21 5 O 3362 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 18447 Number of models: 1 Model: "" Number of chains: 8 Chain: "H" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1456 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1456 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3131 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 404, 3116 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 12} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 391} Chain breaks: 3 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Conformer: "B" Number of residues, atoms: 404, 3116 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 12} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 391} Chain breaks: 3 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 bond proxies already assigned to first conformer: 3166 Chain: "B" Number of atoms: 3178 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 411, 3167 Classifications: {'peptide': 411} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 11} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 397} Chain breaks: 2 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 39 Conformer: "B" Number of residues, atoms: 411, 3167 Classifications: {'peptide': 411} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 11} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 397} Chain breaks: 2 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 39 bond proxies already assigned to first conformer: 3223 Chain: "A" Number of atoms: 3109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3109 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 12} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 391} Chain breaks: 3 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "D" Number of atoms: 3181 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 411, 3165 Classifications: {'peptide': 411} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 12} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 397} Chain breaks: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Conformer: "B" Number of residues, atoms: 411, 3165 Classifications: {'peptide': 411} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 12} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 397} Chain breaks: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 bond proxies already assigned to first conformer: 3216 Chain: "E" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1468 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 186} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1468 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 186} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AHIS C 435 " occ=0.58 ... (18 atoms not shown) pdb=" NE2BHIS C 435 " occ=0.42 residue: pdb=" N APHE B 623 " occ=0.34 ... (20 atoms not shown) pdb=" CZ BPHE B 623 " occ=0.66 residue: pdb=" N APHE D 623 " occ=0.51 ... (20 atoms not shown) pdb=" CZ BPHE D 623 " occ=0.49 Time building chain proxies: 15.44, per 1000 atoms: 0.84 Number of scatterers: 18447 At special positions: 0 Unit cell: (113.16, 111.52, 146.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 128 16.00 O 3362 8.00 N 2954 7.00 C 12003 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.03 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.04 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.03 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.02 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.03 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " 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: 4.99 Conformation dependent library (CDL) restraints added in 4.0 seconds 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4378 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 22 sheets defined 60.8% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'H' and resid 5 through 30 Processing helix chain 'H' and resid 92 through 105 removed outlier: 3.535A pdb=" N TYR H 96 " --> pdb=" O ASP H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 128 removed outlier: 4.080A pdb=" N GLU H 126 " --> pdb=" O ILE H 122 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 162 removed outlier: 4.045A pdb=" N LEU H 136 " --> pdb=" O HIS H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 214 Processing helix chain 'F' and resid 6 through 30 Processing helix chain 'F' and resid 92 through 105 removed outlier: 3.562A pdb=" N TYR F 96 " --> pdb=" O ASP F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 125 Processing helix chain 'F' and resid 132 through 162 removed outlier: 4.091A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 214 Processing helix chain 'C' and resid 416 through 419 removed outlier: 4.034A pdb=" N GLU C 419 " --> pdb=" O GLU C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 416 through 419' Processing helix chain 'C' and resid 423 through 437 removed outlier: 3.959A pdb=" N ASP C 427 " --> pdb=" O GLY C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 469 removed outlier: 3.524A pdb=" N GLY C 465 " --> pdb=" O ASN C 461 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU C 467 " --> pdb=" O MET C 463 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL C 468 " --> pdb=" O VAL C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 515 through 519 removed outlier: 3.751A pdb=" N LEU C 518 " --> pdb=" O PHE C 515 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP C 519 " --> pdb=" O SER C 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 515 through 519' Processing helix chain 'C' and resid 522 through 546 Processing helix chain 'C' and resid 547 through 551 Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 595 through 630 Processing helix chain 'C' and resid 635 through 642 removed outlier: 3.540A pdb=" N LEU C 639 " --> pdb=" O SER C 635 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN C 642 " --> pdb=" O ASP C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 662 removed outlier: 3.895A pdb=" N GLU C 657 " --> pdb=" O GLY C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 676 removed outlier: 3.756A pdb=" N LYS C 669 " --> pdb=" O ALA C 665 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR C 672 " --> pdb=" O ASP C 668 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR C 673 " --> pdb=" O LYS C 669 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N MET C 674 " --> pdb=" O MET C 670 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER C 676 " --> pdb=" O THR C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 696 removed outlier: 3.614A pdb=" N LYS C 695 " --> pdb=" O ALA C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 705 through 715 removed outlier: 3.507A pdb=" N GLU C 710 " --> pdb=" O SER C 706 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TYR C 711 " --> pdb=" O THR C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 757 removed outlier: 3.602A pdb=" N VAL C 746 " --> pdb=" O LEU C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 769 removed outlier: 3.587A pdb=" N TRP C 767 " --> pdb=" O LYS C 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 791 Processing helix chain 'C' and resid 792 through 825 removed outlier: 3.562A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 461 through 469 removed outlier: 4.078A pdb=" N GLU B 466 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU B 467 " --> pdb=" O MET B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 489 removed outlier: 3.743A pdb=" N VAL B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 removed outlier: 4.016A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 546 Processing helix chain 'B' and resid 547 through 551 removed outlier: 4.024A pdb=" N TRP B 551 " --> pdb=" O PRO B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 626 Processing helix chain 'B' and resid 635 through 642 Processing helix chain 'B' and resid 653 through 660 removed outlier: 3.672A pdb=" N PHE B 659 " --> pdb=" O THR B 655 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ARG B 660 " --> pdb=" O LYS B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 670 removed outlier: 3.687A pdb=" N MET B 670 " --> pdb=" O VAL B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 677 Processing helix chain 'B' and resid 685 through 695 removed outlier: 3.659A pdb=" N VAL B 690 " --> pdb=" O THR B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 715 removed outlier: 3.710A pdb=" N GLN B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'B' and resid 788 through 791 Processing helix chain 'B' and resid 792 through 825 Processing helix chain 'A' and resid 416 through 419 removed outlier: 3.507A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 419' Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 461 through 469 removed outlier: 3.738A pdb=" N GLU A 466 " --> pdb=" O GLY A 462 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A 467 " --> pdb=" O MET A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 488 removed outlier: 3.952A pdb=" N VAL A 488 " --> pdb=" O VAL A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.802A pdb=" N LEU A 518 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 546 Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 595 through 630 Processing helix chain 'A' and resid 635 through 642 Processing helix chain 'A' and resid 653 through 661 Processing helix chain 'A' and resid 664 through 675 removed outlier: 4.314A pdb=" N MET A 670 " --> pdb=" O VAL A 666 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP A 671 " --> pdb=" O PHE A 667 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR A 673 " --> pdb=" O LYS A 669 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N MET A 674 " --> pdb=" O MET A 670 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG A 675 " --> pdb=" O TRP A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 696 Processing helix chain 'A' and resid 706 through 714 removed outlier: 3.507A pdb=" N ILE A 712 " --> pdb=" O MET A 708 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN A 714 " --> pdb=" O GLU A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 757 Processing helix chain 'A' and resid 757 through 769 Processing helix chain 'A' and resid 788 through 791 Processing helix chain 'A' and resid 792 through 825 Processing helix chain 'D' and resid 416 through 419 removed outlier: 3.722A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 461 through 469 removed outlier: 3.721A pdb=" N GLU D 466 " --> pdb=" O GLY D 462 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU D 467 " --> pdb=" O MET D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 489 removed outlier: 3.797A pdb=" N VAL D 488 " --> pdb=" O VAL D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 519 removed outlier: 4.022A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 546 Processing helix chain 'D' and resid 547 through 551 removed outlier: 3.543A pdb=" N TRP D 551 " --> pdb=" O PRO D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 626 Processing helix chain 'D' and resid 635 through 642 Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 664 through 675 removed outlier: 3.581A pdb=" N TYR D 673 " --> pdb=" O LYS D 669 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N MET D 674 " --> pdb=" O MET D 670 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ARG D 675 " --> pdb=" O TRP D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 697 removed outlier: 3.667A pdb=" N LYS D 697 " --> pdb=" O VAL D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 714 removed outlier: 3.556A pdb=" N ILE D 712 " --> pdb=" O MET D 708 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 753 removed outlier: 3.623A pdb=" N VAL D 746 " --> pdb=" O LEU D 742 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU D 753 " --> pdb=" O ALA D 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 769 Processing helix chain 'D' and resid 788 through 825 removed outlier: 3.838A pdb=" N VAL D 792 " --> pdb=" O SER D 788 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N GLY D 794 " --> pdb=" O SER D 790 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL D 795 " --> pdb=" O ASN D 791 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 30 Processing helix chain 'E' and resid 92 through 105 Processing helix chain 'E' and resid 105 through 125 Processing helix chain 'E' and resid 133 through 161 Processing helix chain 'E' and resid 177 through 214 removed outlier: 3.539A pdb=" N PHE E 187 " --> pdb=" O GLY E 183 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE E 188 " --> pdb=" O ALA E 184 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU E 208 " --> pdb=" O ARG E 204 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG E 209 " --> pdb=" O HIS E 205 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA E 214 " --> pdb=" O ALA E 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 30 removed outlier: 3.723A pdb=" N GLN G 9 " --> pdb=" O ASP G 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 105 Processing helix chain 'G' and resid 105 through 125 Processing helix chain 'G' and resid 132 through 161 removed outlier: 3.922A pdb=" N LEU G 136 " --> pdb=" O HIS G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 214 removed outlier: 3.532A pdb=" N LEU G 185 " --> pdb=" O TYR G 181 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE G 187 " --> pdb=" O GLY G 183 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU G 208 " --> pdb=" O ARG G 204 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA G 214 " --> pdb=" O ALA G 210 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 66 through 68 removed outlier: 3.533A pdb=" N VAL H 57 " --> pdb=" O GLY H 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 77 through 79 removed outlier: 3.724A pdb=" N VAL F 57 " --> pdb=" O GLY F 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 440 through 444 removed outlier: 3.713A pdb=" N ILE C 474 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N THR C 398 " --> pdb=" O ILE C 474 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 407 through 408 removed outlier: 4.104A pdb=" N GLU C 422 " --> pdb=" O MET C 407 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 489 through 491 Processing sheet with id=AA6, first strand: chain 'C' and resid 496 through 498 removed outlier: 3.612A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 502 through 505 removed outlier: 4.422A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL C 723 " --> pdb=" O ILE C 502 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE C 504 " --> pdb=" O MET C 721 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.698A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 440 through 444 removed outlier: 5.834A pdb=" N VAL B 396 " --> pdb=" O ILE B 474 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE B 476 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N THR B 398 " --> pdb=" O ILE B 476 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ALA B 477 " --> pdb=" O ASP B 733 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ASP B 733 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU B 479 " --> pdb=" O GLY B 731 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N GLY B 731 " --> pdb=" O LEU B 479 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 440 through 444 removed outlier: 5.834A pdb=" N VAL B 396 " --> pdb=" O ILE B 474 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE B 476 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N THR B 398 " --> pdb=" O ILE B 476 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ALA B 477 " --> pdb=" O ASP B 733 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ASP B 733 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU B 479 " --> pdb=" O GLY B 731 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N GLY B 731 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AB3, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.507A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.143A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 440 through 444 removed outlier: 6.121A pdb=" N VAL A 396 " --> pdb=" O ILE A 474 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 407 through 408 removed outlier: 3.862A pdb=" N GLU A 422 " --> pdb=" O MET A 407 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 489 through 498 removed outlier: 4.642A pdb=" N ILE A 734 " --> pdb=" O SER A 492 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N TYR A 732 " --> pdb=" O PRO A 494 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N MET A 496 " --> pdb=" O LYS A 730 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LYS A 730 " --> pdb=" O MET A 496 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 646 through 648 removed outlier: 8.684A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYR A 702 " --> pdb=" O MET A 503 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET A 503 " --> pdb=" O TYR A 702 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 504 " --> pdb=" O MET A 721 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 440 through 444 removed outlier: 6.931A pdb=" N ILE D 474 " --> pdb=" O THR D 398 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ALA D 477 " --> pdb=" O ASP D 733 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ASP D 733 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU D 479 " --> pdb=" O GLY D 731 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLY D 731 " --> pdb=" O LEU D 479 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 440 through 444 removed outlier: 6.931A pdb=" N ILE D 474 " --> pdb=" O THR D 398 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ALA D 477 " --> pdb=" O ASP D 733 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ASP D 733 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU D 479 " --> pdb=" O GLY D 731 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLY D 731 " --> pdb=" O LEU D 479 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU D 498 " --> pdb=" O LYS D 730 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AC2, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.636A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.278A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 9.032A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU D 704 " --> pdb=" O SER D 501 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL D 723 " --> pdb=" O ILE D 502 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 78 through 79 removed outlier: 3.636A pdb=" N LYS E 78 " --> pdb=" O THR E 66 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR E 66 " --> pdb=" O LYS E 78 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 77 through 79 1144 hydrogen bonds defined for protein. 3349 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: 6.64 Time building geometry restraints manager: 5.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.05 - 1.21: 2 1.21 - 1.36: 5719 1.36 - 1.51: 6074 1.51 - 1.67: 6860 1.67 - 1.82: 208 Bond restraints: 18863 Sorted by residual: bond pdb=" CG PRO A 745 " pdb=" CD PRO A 745 " ideal model delta sigma weight residual 1.503 1.173 0.330 3.40e-02 8.65e+02 9.41e+01 bond pdb=" CB PRO A 745 " pdb=" CG PRO A 745 " ideal model delta sigma weight residual 1.492 1.052 0.440 5.00e-02 4.00e+02 7.74e+01 bond pdb=" CG PRO B 478 " pdb=" CD PRO B 478 " ideal model delta sigma weight residual 1.503 1.413 0.090 3.40e-02 8.65e+02 7.06e+00 bond pdb=" N PRO A 745 " pdb=" CD PRO A 745 " ideal model delta sigma weight residual 1.473 1.510 -0.037 1.40e-02 5.10e+03 7.04e+00 bond pdb=" CA PRO A 745 " pdb=" CB PRO A 745 " ideal model delta sigma weight residual 1.534 1.557 -0.024 1.49e-02 4.50e+03 2.49e+00 ... (remaining 18858 not shown) Histogram of bond angle deviations from ideal: 0.00 - 12.05: 25518 12.05 - 24.10: 2 24.10 - 36.15: 2 36.15 - 48.20: 0 48.20 - 60.25: 1 Bond angle restraints: 25523 Sorted by residual: angle pdb=" CB PRO A 745 " pdb=" CG PRO A 745 " pdb=" CD PRO A 745 " ideal model delta sigma weight residual 106.10 166.35 -60.25 3.20e+00 9.77e-02 3.55e+02 angle pdb=" N PRO A 745 " pdb=" CD PRO A 745 " pdb=" CG PRO A 745 " ideal model delta sigma weight residual 103.20 76.27 26.93 1.50e+00 4.44e-01 3.22e+02 angle pdb=" CA PRO A 745 " pdb=" CB PRO A 745 " pdb=" CG PRO A 745 " ideal model delta sigma weight residual 104.50 76.91 27.59 1.90e+00 2.77e-01 2.11e+02 angle pdb=" CA PRO A 745 " pdb=" N PRO A 745 " pdb=" CD PRO A 745 " ideal model delta sigma weight residual 112.00 102.04 9.96 1.40e+00 5.10e-01 5.06e+01 angle pdb=" N PRO B 478 " pdb=" CD PRO B 478 " pdb=" CG PRO B 478 " ideal model delta sigma weight residual 103.20 93.71 9.49 1.50e+00 4.44e-01 4.01e+01 ... (remaining 25518 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 9362 17.57 - 35.15: 1213 35.15 - 52.72: 359 52.72 - 70.29: 58 70.29 - 87.86: 25 Dihedral angle restraints: 11017 sinusoidal: 4159 harmonic: 6858 Sorted by residual: dihedral pdb=" CB CYS H 40 " pdb=" SG CYS H 40 " pdb=" SG CYS H 68 " pdb=" CB CYS H 68 " ideal model delta sinusoidal sigma weight residual 93.00 168.87 -75.87 1 1.00e+01 1.00e-02 7.26e+01 dihedral pdb=" CB CYS G 40 " pdb=" SG CYS G 40 " pdb=" SG CYS G 68 " pdb=" CB CYS G 68 " ideal model delta sinusoidal sigma weight residual 93.00 137.68 -44.68 1 1.00e+01 1.00e-02 2.77e+01 dihedral pdb=" CB CYS G 67 " pdb=" SG CYS G 67 " pdb=" SG CYS G 77 " pdb=" CB CYS G 77 " ideal model delta sinusoidal sigma weight residual -86.00 -129.24 43.24 1 1.00e+01 1.00e-02 2.61e+01 ... (remaining 11014 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1923 0.033 - 0.066: 696 0.066 - 0.099: 190 0.099 - 0.132: 67 0.132 - 0.165: 7 Chirality restraints: 2883 Sorted by residual: chirality pdb=" CA ASP E 86 " pdb=" N ASP E 86 " pdb=" C ASP E 86 " pdb=" CB ASP E 86 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.81e-01 chirality pdb=" CG LEU H 115 " pdb=" CB LEU H 115 " pdb=" CD1 LEU H 115 " pdb=" CD2 LEU H 115 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.66e-01 chirality pdb=" CA THR C 744 " pdb=" N THR C 744 " pdb=" C THR C 744 " pdb=" CB THR C 744 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.62e-01 ... (remaining 2880 not shown) Planarity restraints: 3153 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 477 " 0.054 5.00e-02 4.00e+02 7.78e-02 9.69e+00 pdb=" N PRO B 478 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO B 478 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 478 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 671 " 0.012 2.00e-02 2.50e+03 1.60e-02 6.42e+00 pdb=" CG TRP A 671 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP A 671 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP A 671 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 671 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 671 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 671 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 671 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 671 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 671 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 819 " -0.189 9.50e-02 1.11e+02 8.56e-02 5.93e+00 pdb=" NE ARG C 819 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG C 819 " -0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG C 819 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG C 819 " 0.000 2.00e-02 2.50e+03 ... (remaining 3150 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 489 2.70 - 3.25: 18839 3.25 - 3.80: 31542 3.80 - 4.35: 38218 4.35 - 4.90: 63587 Nonbonded interactions: 152675 Sorted by model distance: nonbonded pdb=" OE1 GLU C 524 " pdb=" OH TYR G 176 " model vdw 2.154 3.040 nonbonded pdb=" N GLU C 637 " pdb=" OE1 GLU C 637 " model vdw 2.190 3.120 nonbonded pdb=" N GLN B 508 " pdb=" OE1 GLN B 508 " model vdw 2.211 3.120 nonbonded pdb=" N GLU A 705 " pdb=" OE1 GLU A 705 " model vdw 2.213 3.120 nonbonded pdb=" OE1 GLU A 524 " pdb=" OH TYR E 176 " model vdw 2.232 3.040 ... (remaining 152670 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 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 434 or resid 436 through 438 o \ r (resid 439 and (name N or name CA or name C or name O or name CB or name CG )) \ or resid 440 through 575 or (resid 576 and (name N or name CA or name C or name \ O or name CB )) or resid 577 through 622 or resid 624 through 626 or (resid 627 \ and (name N or name CA or name C or name O or name CB )) or resid 628 through 6 \ 83 or (resid 684 and (name N or name CA or name C or name O or name CB )) or res \ id 685 through 763 or resid 765 through 812 or (resid 813 and (name N or name CA \ or name C or name O or name CB )) or resid 814 through 818 or (resid 819 throug \ h 820 and (name N or name CA or name C or name O or name CB )) or resid 821 thro \ ugh 825)) selection = (chain 'B' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 434 or resid 436 through 438 o \ r (resid 439 and (name N or name CA or name C or name O or name CB or name CG )) \ or resid 440 through 506 or (resid 511 and (name N or name CA or name C or name \ O or name CB )) or resid 512 through 575 or (resid 576 and (name N or name CA o \ r name C or name O or name CB )) or resid 577 through 593 or (resid 594 and (nam \ e N or name CA or name C or name O or name CB )) or resid 595 through 622 or res \ id 624 through 626 or (resid 627 and (name N or name CA or name C or name O or n \ ame CB )) or resid 628 through 760 or (resid 761 and (name N or name CA or name \ C or name O or name CB )) or resid 762 through 763 or (resid 765 and (name N or \ name CA or name C or name O or name CB )) or resid 766 through 773 or (resid 784 \ and (name N or name CA or name C or name O or name CB )) or resid 785 through 8 \ 25)) selection = (chain 'C' and (resid 393 through 434 or resid 436 through 593 or (resid 594 and \ (name N or name CA or name C or name O or name CB )) or resid 595 through 622 o \ r resid 624 through 626 or (resid 627 and (name N or name CA or name C or name O \ or name CB )) or resid 628 through 666 or (resid 667 and (name N or name CA or \ name C or name O or name CB )) or resid 668 through 683 or (resid 684 and (name \ N or name CA or name C or name O or name CB )) or resid 685 through 763 or resid \ 765 through 812 or (resid 813 and (name N or name CA or name C or name O or nam \ e CB )) or resid 814 through 818 or (resid 819 through 820 and (name N or name C \ A or name C or name O or name CB )) or resid 821 through 825)) selection = (chain 'D' and (resid 393 through 434 or resid 436 through 506 or (resid 511 and \ (name N or name CA or name C or name O or name CB )) or resid 512 through 575 o \ r (resid 576 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 77 through 593 or (resid 594 and (name N or name CA or name C or name O or name \ CB )) or resid 595 through 622 or resid 624 through 666 or (resid 667 and (name \ N or name CA or name C or name O or name CB )) or resid 668 through 760 or (resi \ d 761 and (name N or name CA or name C or name O or name CB )) or resid 762 thro \ ugh 763 or (resid 765 and (name N or name CA or name C or name O or name CB )) o \ r resid 766 through 773 or (resid 784 and (name N or name CA or name C or name O \ or name CB )) or resid 785 through 825)) } ncs_group { reference = (chain 'E' and resid 5 through 214) selection = (chain 'F' and (resid 5 through 41 or resid 55 through 214)) selection = (chain 'G' and resid 5 through 214) selection = (chain 'H' and (resid 5 through 41 or resid 55 through 214)) } 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=0.34 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.780 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 49.640 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 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 : 0.005 0.440 18863 Z= 0.370 Angle : 0.801 60.254 25523 Z= 0.373 Chirality : 0.039 0.165 2883 Planarity : 0.004 0.086 3153 Dihedral : 17.298 87.863 6603 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.10 % Allowed : 33.97 % Favored : 62.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.40 (0.18), residues: 2343 helix: 2.24 (0.14), residues: 1313 sheet: -1.27 (0.40), residues: 162 loop : -0.68 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 671 HIS 0.008 0.001 HIS F 132 PHE 0.022 0.001 PHE E 73 TYR 0.022 0.001 TYR B 673 ARG 0.021 0.001 ARG C 819 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 308 time to evaluate : 1.989 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: F 31 ASP cc_start: 0.7765 (m-30) cc_final: 0.7432 (m-30) REVERT: F 200 MET cc_start: 0.7788 (mtt) cc_final: 0.7213 (mtt) REVERT: C 819 ARG cc_start: 0.7187 (ttp80) cc_final: 0.6760 (ttm-80) REVERT: B 782 GLU cc_start: 0.5819 (pp20) cc_final: 0.5388 (pm20) REVERT: E 129 LYS cc_start: 0.8369 (mmmm) cc_final: 0.8070 (mppt) outliers start: 57 outliers final: 54 residues processed: 360 average time/residue: 1.3467 time to fit residues: 546.6655 Evaluate side-chains 354 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 300 time to evaluate : 2.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain C residue 473 ASP Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 694 ARG Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 726 ASN Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 790 SER Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 699 LYS Chi-restraints excluded: chain D residue 818 SER Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 205 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 0.9980 chunk 177 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 chunk 111 optimal weight: 7.9990 chunk 136 optimal weight: 0.5980 chunk 212 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 726 ASN A 709 ASN A 714 GLN ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.222919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.165264 restraints weight = 60209.001| |-----------------------------------------------------------------------------| r_work (start): 0.4116 rms_B_bonded: 7.13 r_work: 0.3414 rms_B_bonded: 5.43 restraints_weight: 2.0000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3362 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3361 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 18863 Z= 0.217 Angle : 0.604 10.579 25523 Z= 0.304 Chirality : 0.040 0.158 2883 Planarity : 0.004 0.052 3153 Dihedral : 5.903 59.750 2641 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.29 % Allowed : 30.25 % Favored : 65.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.56 (0.18), residues: 2343 helix: 2.32 (0.14), residues: 1366 sheet: -1.51 (0.40), residues: 146 loop : -0.70 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 766 HIS 0.003 0.001 HIS E 199 PHE 0.015 0.001 PHE E 73 TYR 0.020 0.001 TYR C 424 ARG 0.012 0.001 ARG C 819 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 327 time to evaluate : 1.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 99 ARG cc_start: 0.7832 (mtp180) cc_final: 0.7590 (mtp180) REVERT: H 160 ASN cc_start: 0.7559 (m-40) cc_final: 0.7354 (m-40) REVERT: H 192 MET cc_start: 0.7606 (OUTLIER) cc_final: 0.7374 (mtt) REVERT: H 200 MET cc_start: 0.8394 (tpp) cc_final: 0.7801 (mtp) REVERT: H 204 ARG cc_start: 0.7410 (mmp-170) cc_final: 0.7195 (mmp-170) REVERT: F 31 ASP cc_start: 0.8107 (m-30) cc_final: 0.7714 (m-30) REVERT: F 134 ILE cc_start: 0.7463 (pp) cc_final: 0.7250 (pt) REVERT: F 196 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8336 (tt) REVERT: F 204 ARG cc_start: 0.7501 (mmp-170) cc_final: 0.6974 (tpm170) REVERT: C 627 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7948 (mp0) REVERT: C 694 ARG cc_start: 0.8622 (mtp85) cc_final: 0.8257 (mmt-90) REVERT: B 694 ARG cc_start: 0.7862 (mpp80) cc_final: 0.7555 (ptt-90) REVERT: A 671 TRP cc_start: 0.7694 (t60) cc_final: 0.7463 (t60) REVERT: D 496 MET cc_start: 0.8072 (ptp) cc_final: 0.7007 (mtm) REVERT: D 678 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7341 (mp0) REVERT: E 6 ARG cc_start: 0.8350 (mmm-85) cc_final: 0.7813 (mmm160) REVERT: E 129 LYS cc_start: 0.8347 (mmmm) cc_final: 0.8047 (mppt) outliers start: 80 outliers final: 29 residues processed: 378 average time/residue: 1.3903 time to fit residues: 590.1701 Evaluate side-chains 333 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 301 time to evaluate : 2.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain A residue 435 HIS Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 740 SER Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 179 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 87 optimal weight: 8.9990 chunk 81 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 202 optimal weight: 0.8980 chunk 177 optimal weight: 1.9990 chunk 218 optimal weight: 5.9990 chunk 208 optimal weight: 0.3980 chunk 217 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 193 optimal weight: 9.9990 chunk 111 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 726 ASN A 709 ASN A 714 GLN ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4771 r_free = 0.4771 target = 0.222099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.166054 restraints weight = 66069.500| |-----------------------------------------------------------------------------| r_work (start): 0.4112 rms_B_bonded: 8.15 r_work: 0.3372 rms_B_bonded: 5.76 restraints_weight: 2.0000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3333 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3333 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18863 Z= 0.222 Angle : 0.587 10.531 25523 Z= 0.293 Chirality : 0.040 0.158 2883 Planarity : 0.004 0.050 3153 Dihedral : 4.684 58.249 2578 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.88 % Allowed : 30.66 % Favored : 65.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 2343 helix: 2.35 (0.14), residues: 1375 sheet: -1.42 (0.41), residues: 139 loop : -0.79 (0.21), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 671 HIS 0.008 0.001 HIS G 82 PHE 0.015 0.001 PHE G 97 TYR 0.018 0.001 TYR C 424 ARG 0.011 0.001 ARG C 819 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 318 time to evaluate : 2.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 192 MET cc_start: 0.7572 (OUTLIER) cc_final: 0.7334 (mtt) REVERT: H 204 ARG cc_start: 0.7355 (mmp-170) cc_final: 0.7148 (mmp-170) REVERT: F 31 ASP cc_start: 0.8151 (m-30) cc_final: 0.7701 (m-30) REVERT: F 196 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8324 (tt) REVERT: F 204 ARG cc_start: 0.7509 (mmp-170) cc_final: 0.6989 (tpm170) REVERT: C 408 MET cc_start: 0.6390 (tpt) cc_final: 0.5852 (tpp) REVERT: C 627 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8116 (mp0) REVERT: B 670 MET cc_start: 0.8385 (ppp) cc_final: 0.7750 (ppp) REVERT: B 694 ARG cc_start: 0.7909 (mpp80) cc_final: 0.7560 (ptt-90) REVERT: B 708 MET cc_start: 0.8448 (tpp) cc_final: 0.8081 (tpp) REVERT: A 713 GLU cc_start: 0.8715 (pp20) cc_final: 0.8491 (pp20) REVERT: A 767 TRP cc_start: 0.7150 (m-90) cc_final: 0.6852 (m-90) REVERT: D 545 ARG cc_start: 0.8764 (mtt180) cc_final: 0.8429 (mmt90) REVERT: D 660 ARG cc_start: 0.7917 (ttm110) cc_final: 0.7604 (mtm-85) REVERT: D 782 GLU cc_start: 0.7224 (mp0) cc_final: 0.6943 (mp0) REVERT: E 6 ARG cc_start: 0.8335 (mmm-85) cc_final: 0.7832 (mmm160) REVERT: E 129 LYS cc_start: 0.8272 (mmmm) cc_final: 0.7988 (mppt) REVERT: G 11 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7942 (tm) REVERT: G 78 LYS cc_start: 0.7454 (ttpt) cc_final: 0.7197 (ptpt) REVERT: G 206 LYS cc_start: 0.7811 (OUTLIER) cc_final: 0.7594 (ttpp) outliers start: 72 outliers final: 39 residues processed: 362 average time/residue: 1.3801 time to fit residues: 561.4336 Evaluate side-chains 347 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 303 time to evaluate : 1.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain A residue 435 HIS Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain G residue 206 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 132 optimal weight: 3.9990 chunk 174 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 133 optimal weight: 0.8980 chunk 107 optimal weight: 30.0000 chunk 52 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 chunk 187 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 149 ASN B 726 ASN A 709 ASN A 714 GLN D 764 ASN A ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4767 r_free = 0.4767 target = 0.221631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.164245 restraints weight = 62598.390| |-----------------------------------------------------------------------------| r_work (start): 0.4111 rms_B_bonded: 7.39 r_work: 0.3385 rms_B_bonded: 5.46 restraints_weight: 2.0000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3332 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3332 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18863 Z= 0.223 Angle : 0.588 10.600 25523 Z= 0.293 Chirality : 0.040 0.154 2883 Planarity : 0.004 0.048 3153 Dihedral : 4.430 57.172 2573 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.81 % Allowed : 29.73 % Favored : 65.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.58 (0.18), residues: 2343 helix: 2.37 (0.14), residues: 1368 sheet: -1.42 (0.40), residues: 139 loop : -0.78 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 671 HIS 0.007 0.001 HIS F 205 PHE 0.016 0.001 PHE E 73 TYR 0.015 0.001 TYR C 424 ARG 0.006 0.000 ARG C 819 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 324 time to evaluate : 1.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 ASP cc_start: 0.1702 (OUTLIER) cc_final: 0.1294 (p0) REVERT: H 192 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.7384 (mtt) REVERT: H 204 ARG cc_start: 0.7350 (mmp-170) cc_final: 0.7119 (mmp-170) REVERT: F 31 ASP cc_start: 0.8086 (m-30) cc_final: 0.7771 (m-30) REVERT: F 78 LYS cc_start: 0.8550 (ptmt) cc_final: 0.7945 (pttm) REVERT: F 196 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8281 (tt) REVERT: F 204 ARG cc_start: 0.7511 (mmp-170) cc_final: 0.6906 (tpm170) REVERT: C 408 MET cc_start: 0.6415 (tpt) cc_final: 0.5755 (tpp) REVERT: B 694 ARG cc_start: 0.7934 (mpp80) cc_final: 0.7709 (tpp80) REVERT: B 708 MET cc_start: 0.8519 (tpp) cc_final: 0.8047 (tpp) REVERT: B 783 LYS cc_start: 0.7522 (OUTLIER) cc_final: 0.7269 (tptm) REVERT: A 420 ARG cc_start: 0.8065 (mtm110) cc_final: 0.7812 (mtm110) REVERT: A 713 GLU cc_start: 0.8763 (pp20) cc_final: 0.8475 (pp20) REVERT: A 764 ASN cc_start: 0.8523 (p0) cc_final: 0.8299 (p0) REVERT: A 767 TRP cc_start: 0.7166 (m-90) cc_final: 0.6804 (m-90) REVERT: D 496 MET cc_start: 0.7969 (ptp) cc_final: 0.7026 (mtm) REVERT: D 678 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7536 (mp0) REVERT: D 782 GLU cc_start: 0.7210 (mp0) cc_final: 0.6955 (mp0) REVERT: E 6 ARG cc_start: 0.8252 (mmm-85) cc_final: 0.7809 (mmm160) REVERT: E 129 LYS cc_start: 0.8304 (mmmm) cc_final: 0.8035 (mppt) REVERT: G 5 ASP cc_start: 0.7406 (t70) cc_final: 0.7205 (t70) REVERT: G 11 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7951 (tm) REVERT: G 59 THR cc_start: 0.6787 (OUTLIER) cc_final: 0.6433 (t) REVERT: G 78 LYS cc_start: 0.7457 (ttpt) cc_final: 0.7249 (ptpt) REVERT: G 156 TYR cc_start: 0.8822 (t80) cc_final: 0.8424 (t80) REVERT: G 206 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.7623 (ttpp) outliers start: 90 outliers final: 45 residues processed: 378 average time/residue: 1.3344 time to fit residues: 567.1850 Evaluate side-chains 353 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 301 time to evaluate : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 200 MET Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 783 LYS Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain A residue 435 HIS Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 740 SER Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 200 MET Chi-restraints excluded: chain G residue 206 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 208 optimal weight: 4.9990 chunk 228 optimal weight: 4.9990 chunk 204 optimal weight: 4.9990 chunk 173 optimal weight: 3.9990 chunk 148 optimal weight: 20.0000 chunk 105 optimal weight: 7.9990 chunk 195 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 191 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 149 ASN C 461 ASN B 726 ASN A 714 GLN ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.218063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.138566 restraints weight = 59799.726| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 5.91 r_work: 0.3339 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3333 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3333 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 18863 Z= 0.434 Angle : 0.669 11.391 25523 Z= 0.338 Chirality : 0.044 0.203 2883 Planarity : 0.004 0.052 3153 Dihedral : 4.376 54.750 2568 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 5.43 % Allowed : 29.42 % Favored : 65.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.11 (0.17), residues: 2343 helix: 1.96 (0.14), residues: 1351 sheet: -1.34 (0.36), residues: 184 loop : -0.85 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 671 HIS 0.008 0.001 HIS F 205 PHE 0.021 0.002 PHE C 584 TYR 0.017 0.002 TYR B 549 ARG 0.009 0.001 ARG A 660 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 305 time to evaluate : 2.168 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: H 86 ASP cc_start: 0.2069 (OUTLIER) cc_final: 0.1624 (p0) REVERT: H 204 ARG cc_start: 0.7376 (mmp-170) cc_final: 0.7170 (mmp-170) REVERT: F 31 ASP cc_start: 0.8149 (m-30) cc_final: 0.7862 (m-30) REVERT: F 191 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.7054 (mp0) REVERT: F 196 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8177 (tt) REVERT: F 204 ARG cc_start: 0.7483 (OUTLIER) cc_final: 0.6970 (tpm170) REVERT: F 206 LYS cc_start: 0.6600 (tmmt) cc_final: 0.6021 (mtpp) REVERT: C 408 MET cc_start: 0.6769 (tpt) cc_final: 0.6045 (tpp) REVERT: C 673 TYR cc_start: 0.8133 (t80) cc_final: 0.7810 (t80) REVERT: B 497 SER cc_start: 0.8738 (m) cc_final: 0.8532 (t) REVERT: B 670 MET cc_start: 0.8359 (ppp) cc_final: 0.7960 (pmm) REVERT: B 674 MET cc_start: 0.7853 (pmm) cc_final: 0.7093 (pmm) REVERT: B 675 ARG cc_start: 0.7899 (mmt180) cc_final: 0.7148 (mmt180) REVERT: B 708 MET cc_start: 0.8608 (tpp) cc_final: 0.8326 (tpp) REVERT: B 782 GLU cc_start: 0.6264 (pp20) cc_final: 0.6031 (pm20) REVERT: D 594 ARG cc_start: 0.9126 (OUTLIER) cc_final: 0.8821 (mtp85) REVERT: D 629 MET cc_start: 0.6954 (tpt) cc_final: 0.6672 (tpt) REVERT: D 660 ARG cc_start: 0.7842 (ttm110) cc_final: 0.7397 (mtm-85) REVERT: D 678 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7613 (mp0) REVERT: D 782 GLU cc_start: 0.7219 (mp0) cc_final: 0.6982 (mp0) REVERT: E 6 ARG cc_start: 0.8368 (mmm-85) cc_final: 0.7846 (mmm160) REVERT: E 99 ARG cc_start: 0.7090 (mpp80) cc_final: 0.6651 (mpp80) REVERT: E 129 LYS cc_start: 0.8267 (mmmm) cc_final: 0.8015 (mppt) REVERT: G 5 ASP cc_start: 0.7462 (t70) cc_final: 0.7258 (t70) REVERT: G 37 ARG cc_start: 0.7889 (mtt-85) cc_final: 0.7682 (mtp-110) REVERT: G 67 CYS cc_start: 0.6565 (OUTLIER) cc_final: 0.6298 (m) REVERT: G 69 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.7092 (mt) REVERT: G 206 LYS cc_start: 0.7812 (OUTLIER) cc_final: 0.7609 (ttpp) outliers start: 102 outliers final: 55 residues processed: 368 average time/residue: 1.3018 time to fit residues: 539.1839 Evaluate side-chains 355 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 292 time to evaluate : 1.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 121 CYS Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 200 MET Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain F residue 191 GLU Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 204 ARG Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain A residue 435 HIS Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 594 ARG Chi-restraints excluded: chain D residue 643 THR Chi-restraints excluded: chain D residue 740 SER Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 128 TYR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 200 MET Chi-restraints excluded: chain G residue 206 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 165 optimal weight: 1.9990 chunk 207 optimal weight: 0.9980 chunk 211 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 197 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 229 optimal weight: 1.9990 chunk 203 optimal weight: 8.9990 chunk 185 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 726 ASN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 714 GLN ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.221095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.145019 restraints weight = 63446.585| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 5.13 r_work: 0.3420 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3403 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3403 r_free = 0.3403 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3403 r_free = 0.3403 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3403 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18863 Z= 0.221 Angle : 0.612 10.713 25523 Z= 0.301 Chirality : 0.040 0.149 2883 Planarity : 0.004 0.052 3153 Dihedral : 4.086 52.621 2567 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.83 % Allowed : 30.82 % Favored : 65.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.39 (0.18), residues: 2343 helix: 2.25 (0.14), residues: 1353 sheet: -1.37 (0.39), residues: 160 loop : -0.88 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 671 HIS 0.007 0.001 HIS F 205 PHE 0.014 0.001 PHE C 584 TYR 0.015 0.001 TYR B 549 ARG 0.008 0.001 ARG G 204 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 318 time to evaluate : 2.215 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: H 86 ASP cc_start: 0.2119 (OUTLIER) cc_final: 0.1660 (p0) REVERT: H 192 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.7296 (mtt) REVERT: H 204 ARG cc_start: 0.7405 (mmp-170) cc_final: 0.7166 (mmp-170) REVERT: F 31 ASP cc_start: 0.8042 (m-30) cc_final: 0.7784 (m-30) REVERT: F 196 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8178 (tt) REVERT: F 204 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.6988 (tpm170) REVERT: F 206 LYS cc_start: 0.6613 (tmmt) cc_final: 0.6034 (mtpp) REVERT: C 408 MET cc_start: 0.6506 (tpt) cc_final: 0.5828 (tpp) REVERT: C 673 TYR cc_start: 0.7967 (t80) cc_final: 0.7552 (t80) REVERT: B 670 MET cc_start: 0.8409 (ppp) cc_final: 0.7992 (pmm) REVERT: B 674 MET cc_start: 0.7833 (pmm) cc_final: 0.7525 (pmm) REVERT: B 694 ARG cc_start: 0.7726 (mpp80) cc_final: 0.7180 (tpp-160) REVERT: B 708 MET cc_start: 0.8684 (tpp) cc_final: 0.8452 (tpp) REVERT: B 782 GLU cc_start: 0.6233 (pp20) cc_final: 0.6008 (pm20) REVERT: A 767 TRP cc_start: 0.7129 (m-90) cc_final: 0.6759 (m-90) REVERT: D 496 MET cc_start: 0.7949 (ptp) cc_final: 0.6918 (mtm) REVERT: D 594 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.8774 (mtp85) REVERT: D 660 ARG cc_start: 0.7960 (ttm110) cc_final: 0.7503 (mtm-85) REVERT: D 782 GLU cc_start: 0.7211 (mp0) cc_final: 0.6877 (mp0) REVERT: E 6 ARG cc_start: 0.8345 (mmm-85) cc_final: 0.7839 (mmm160) REVERT: E 99 ARG cc_start: 0.7087 (mpp80) cc_final: 0.6645 (mpp80) REVERT: E 129 LYS cc_start: 0.8264 (mmmm) cc_final: 0.8048 (mppt) REVERT: E 196 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8322 (tt) REVERT: G 78 LYS cc_start: 0.7578 (ttpt) cc_final: 0.7362 (ptpt) REVERT: G 117 MET cc_start: 0.7634 (mmp) cc_final: 0.7421 (mtm) REVERT: G 156 TYR cc_start: 0.8642 (t80) cc_final: 0.8410 (t80) REVERT: G 206 LYS cc_start: 0.7759 (OUTLIER) cc_final: 0.7517 (ttpp) outliers start: 71 outliers final: 46 residues processed: 356 average time/residue: 1.2898 time to fit residues: 516.3181 Evaluate side-chains 351 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 298 time to evaluate : 2.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 200 MET Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 204 ARG Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 594 ARG Chi-restraints excluded: chain D residue 740 SER Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 128 TYR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 206 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 188 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 103 optimal weight: 0.7980 chunk 174 optimal weight: 0.4980 chunk 221 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 169 optimal weight: 0.0980 chunk 90 optimal weight: 0.6980 chunk 180 optimal weight: 30.0000 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 149 ASN B 726 ASN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 714 GLN ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4776 r_free = 0.4776 target = 0.222879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.164635 restraints weight = 60962.281| |-----------------------------------------------------------------------------| r_work (start): 0.4111 rms_B_bonded: 7.23 r_work: 0.3413 rms_B_bonded: 5.47 restraints_weight: 2.0000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3364 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3364 r_free = 0.3364 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3364 r_free = 0.3364 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3364 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18863 Z= 0.178 Angle : 0.615 12.687 25523 Z= 0.298 Chirality : 0.039 0.155 2883 Planarity : 0.004 0.060 3153 Dihedral : 3.942 51.009 2567 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.90 % Allowed : 32.68 % Favored : 64.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.65 (0.18), residues: 2343 helix: 2.51 (0.14), residues: 1351 sheet: -1.31 (0.38), residues: 166 loop : -0.82 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 671 HIS 0.006 0.001 HIS F 205 PHE 0.011 0.001 PHE D 584 TYR 0.018 0.001 TYR B 549 ARG 0.014 0.001 ARG A 660 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 315 time to evaluate : 2.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 ASP cc_start: 0.2255 (OUTLIER) cc_final: 0.1804 (p0) REVERT: H 99 ARG cc_start: 0.7676 (mtp180) cc_final: 0.7405 (mtp180) REVERT: H 192 MET cc_start: 0.7450 (OUTLIER) cc_final: 0.7225 (mtt) REVERT: H 204 ARG cc_start: 0.7357 (mmp-170) cc_final: 0.7044 (mmp-170) REVERT: F 31 ASP cc_start: 0.8079 (m-30) cc_final: 0.7821 (m-30) REVERT: F 78 LYS cc_start: 0.8524 (ptmt) cc_final: 0.7795 (pttm) REVERT: F 204 ARG cc_start: 0.7459 (OUTLIER) cc_final: 0.6913 (tpm170) REVERT: C 408 MET cc_start: 0.6387 (tpt) cc_final: 0.5702 (tpp) REVERT: C 463 MET cc_start: 0.8592 (tpt) cc_final: 0.8326 (mmm) REVERT: C 627 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7970 (mp0) REVERT: C 673 TYR cc_start: 0.8061 (t80) cc_final: 0.7660 (t80) REVERT: C 819 ARG cc_start: 0.7020 (ttp80) cc_final: 0.6478 (tpp80) REVERT: B 670 MET cc_start: 0.8461 (ppp) cc_final: 0.7857 (pmt) REVERT: B 674 MET cc_start: 0.7888 (pmm) cc_final: 0.7602 (pmm) REVERT: B 694 ARG cc_start: 0.7847 (mpp80) cc_final: 0.7561 (tpp-160) REVERT: B 708 MET cc_start: 0.8726 (tpp) cc_final: 0.8394 (tpp) REVERT: B 782 GLU cc_start: 0.6306 (pp20) cc_final: 0.6030 (pm20) REVERT: A 674 MET cc_start: 0.7369 (pmm) cc_final: 0.6642 (pmm) REVERT: A 767 TRP cc_start: 0.7096 (m-90) cc_final: 0.6676 (m-90) REVERT: D 467 LEU cc_start: 0.8559 (tm) cc_final: 0.8348 (pp) REVERT: D 496 MET cc_start: 0.8019 (ptp) cc_final: 0.7040 (mtm) REVERT: D 660 ARG cc_start: 0.8044 (ttm110) cc_final: 0.7594 (mtm-85) REVERT: E 6 ARG cc_start: 0.8348 (mmm-85) cc_final: 0.7841 (mmm160) REVERT: E 99 ARG cc_start: 0.7089 (mpp80) cc_final: 0.6656 (mpp80) REVERT: E 129 LYS cc_start: 0.8200 (mmmm) cc_final: 0.7981 (mppt) REVERT: E 196 LEU cc_start: 0.8571 (tp) cc_final: 0.8363 (tt) REVERT: G 37 ARG cc_start: 0.7678 (mtt-85) cc_final: 0.7473 (mtt-85) REVERT: G 59 THR cc_start: 0.6584 (p) cc_final: 0.6132 (t) REVERT: G 156 TYR cc_start: 0.8607 (t80) cc_final: 0.8366 (t80) REVERT: G 185 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7178 (mm) REVERT: G 206 LYS cc_start: 0.7751 (OUTLIER) cc_final: 0.7513 (ttpp) outliers start: 53 outliers final: 31 residues processed: 348 average time/residue: 1.3159 time to fit residues: 515.7614 Evaluate side-chains 341 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 304 time to evaluate : 1.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 200 MET Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain F residue 204 ARG Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 740 SER Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 206 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 182 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 131 optimal weight: 0.6980 chunk 113 optimal weight: 0.7980 chunk 136 optimal weight: 0.9990 chunk 185 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 163 optimal weight: 5.9990 chunk 152 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 149 ASN B 726 ASN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 714 GLN ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.222186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.162698 restraints weight = 55712.709| |-----------------------------------------------------------------------------| r_work (start): 0.4087 rms_B_bonded: 6.34 r_work: 0.3411 rms_B_bonded: 5.20 restraints_weight: 2.0000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3362 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3362 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18863 Z= 0.194 Angle : 0.618 11.367 25523 Z= 0.302 Chirality : 0.040 0.176 2883 Planarity : 0.004 0.056 3153 Dihedral : 3.667 32.047 2562 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.21 % Allowed : 32.47 % Favored : 64.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.65 (0.18), residues: 2343 helix: 2.50 (0.14), residues: 1351 sheet: -1.19 (0.37), residues: 174 loop : -0.83 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 671 HIS 0.007 0.001 HIS F 205 PHE 0.012 0.001 PHE C 584 TYR 0.020 0.001 TYR B 549 ARG 0.009 0.001 ARG C 819 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 311 time to evaluate : 2.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 ASP cc_start: 0.2327 (OUTLIER) cc_final: 0.1874 (p0) REVERT: H 192 MET cc_start: 0.7509 (OUTLIER) cc_final: 0.7278 (mtt) REVERT: H 204 ARG cc_start: 0.7350 (mmp-170) cc_final: 0.7034 (mmp-170) REVERT: F 31 ASP cc_start: 0.8071 (m-30) cc_final: 0.7786 (m-30) REVERT: F 65 ARG cc_start: 0.7680 (pmt170) cc_final: 0.7326 (ptt-90) REVERT: F 78 LYS cc_start: 0.8502 (ptmt) cc_final: 0.7776 (pttm) REVERT: F 204 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.7059 (tpm170) REVERT: F 206 LYS cc_start: 0.6696 (tmmt) cc_final: 0.6088 (mtpp) REVERT: C 463 MET cc_start: 0.8612 (tpt) cc_final: 0.8383 (mmm) REVERT: C 673 TYR cc_start: 0.8074 (t80) cc_final: 0.7682 (t80) REVERT: C 819 ARG cc_start: 0.7008 (ttp80) cc_final: 0.6492 (tpp80) REVERT: B 407 MET cc_start: 0.7194 (pmm) cc_final: 0.6844 (pmm) REVERT: B 439 LYS cc_start: 0.7896 (pmtt) cc_final: 0.7658 (pmmt) REVERT: B 670 MET cc_start: 0.8412 (ppp) cc_final: 0.7839 (pmt) REVERT: B 674 MET cc_start: 0.7900 (pmm) cc_final: 0.7633 (pmm) REVERT: B 694 ARG cc_start: 0.7897 (mpp80) cc_final: 0.7602 (tpp-160) REVERT: B 708 MET cc_start: 0.8745 (tpp) cc_final: 0.8303 (tpp) REVERT: A 671 TRP cc_start: 0.8265 (t-100) cc_final: 0.7699 (t-100) REVERT: A 674 MET cc_start: 0.7464 (pmm) cc_final: 0.6617 (pmm) REVERT: A 767 TRP cc_start: 0.7152 (m-90) cc_final: 0.6698 (m-90) REVERT: D 467 LEU cc_start: 0.8587 (tm) cc_final: 0.8383 (pp) REVERT: D 496 MET cc_start: 0.8014 (ptp) cc_final: 0.7019 (mtm) REVERT: D 503 MET cc_start: 0.8704 (mmm) cc_final: 0.8170 (mmt) REVERT: E 6 ARG cc_start: 0.8343 (mmm-85) cc_final: 0.7847 (mmm160) REVERT: E 206 LYS cc_start: 0.8088 (ptmt) cc_final: 0.7868 (ttpt) REVERT: G 5 ASP cc_start: 0.7457 (t70) cc_final: 0.7244 (t70) REVERT: G 59 THR cc_start: 0.6555 (p) cc_final: 0.5903 (t) REVERT: G 78 LYS cc_start: 0.7361 (OUTLIER) cc_final: 0.7142 (ptpt) REVERT: G 185 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.7188 (mm) outliers start: 59 outliers final: 32 residues processed: 344 average time/residue: 1.3131 time to fit residues: 509.4275 Evaluate side-chains 334 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 297 time to evaluate : 2.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 200 MET Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 204 ARG Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 663 LYS Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain D residue 740 SER Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain G residue 78 LYS Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain G residue 195 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 5 optimal weight: 3.9990 chunk 172 optimal weight: 0.6980 chunk 192 optimal weight: 7.9990 chunk 111 optimal weight: 5.9990 chunk 220 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 128 optimal weight: 0.5980 chunk 124 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 232 optimal weight: 0.9990 chunk 135 optimal weight: 0.0000 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 726 ASN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 714 GLN ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.223133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.166390 restraints weight = 60723.389| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 7.28 r_work: 0.3391 rms_B_bonded: 5.55 restraints_weight: 2.0000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3361 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3361 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18863 Z= 0.183 Angle : 0.634 11.929 25523 Z= 0.308 Chirality : 0.040 0.171 2883 Planarity : 0.004 0.057 3153 Dihedral : 3.687 32.210 2562 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.64 % Allowed : 32.99 % Favored : 64.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.69 (0.18), residues: 2343 helix: 2.54 (0.14), residues: 1351 sheet: -1.13 (0.38), residues: 174 loop : -0.83 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 671 HIS 0.007 0.001 HIS F 205 PHE 0.011 0.001 PHE H 107 TYR 0.021 0.001 TYR B 549 ARG 0.009 0.001 ARG A 660 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 301 time to evaluate : 2.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 ASP cc_start: 0.2439 (OUTLIER) cc_final: 0.1982 (p0) REVERT: H 192 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.7274 (mtt) REVERT: H 204 ARG cc_start: 0.7338 (mmp-170) cc_final: 0.7022 (mmp-170) REVERT: F 31 ASP cc_start: 0.8100 (m-30) cc_final: 0.7853 (m-30) REVERT: F 78 LYS cc_start: 0.8595 (ptmt) cc_final: 0.7873 (pttm) REVERT: F 204 ARG cc_start: 0.7510 (OUTLIER) cc_final: 0.6992 (tpm170) REVERT: F 206 LYS cc_start: 0.6667 (tmmt) cc_final: 0.6099 (mtpp) REVERT: C 463 MET cc_start: 0.8627 (tpt) cc_final: 0.8397 (mmm) REVERT: C 673 TYR cc_start: 0.8022 (t80) cc_final: 0.7660 (t80) REVERT: C 819 ARG cc_start: 0.7036 (ttp80) cc_final: 0.6564 (tpp80) REVERT: B 407 MET cc_start: 0.7187 (pmm) cc_final: 0.6138 (pmm) REVERT: B 500 ILE cc_start: 0.7739 (OUTLIER) cc_final: 0.7046 (tp) REVERT: B 670 MET cc_start: 0.8379 (ppp) cc_final: 0.7872 (pmt) REVERT: B 694 ARG cc_start: 0.7909 (mpp80) cc_final: 0.7594 (tpp-160) REVERT: A 671 TRP cc_start: 0.8039 (t-100) cc_final: 0.7602 (t-100) REVERT: A 674 MET cc_start: 0.7466 (pmm) cc_final: 0.6592 (pmm) REVERT: A 704 LEU cc_start: 0.8040 (pp) cc_final: 0.7837 (pp) REVERT: A 767 TRP cc_start: 0.7075 (m-90) cc_final: 0.6665 (m-90) REVERT: D 467 LEU cc_start: 0.8565 (tm) cc_final: 0.8338 (pp) REVERT: D 496 MET cc_start: 0.8164 (ptp) cc_final: 0.7114 (mtm) REVERT: D 508 GLN cc_start: 0.8496 (mm110) cc_final: 0.8231 (mp10) REVERT: E 6 ARG cc_start: 0.8382 (mmm-85) cc_final: 0.7888 (mmm160) REVERT: E 206 LYS cc_start: 0.8151 (ptmt) cc_final: 0.7866 (ttmm) REVERT: G 5 ASP cc_start: 0.7456 (t70) cc_final: 0.7236 (t70) REVERT: G 41 LYS cc_start: 0.7320 (mmtt) cc_final: 0.6472 (tmmt) REVERT: G 59 THR cc_start: 0.6631 (p) cc_final: 0.6343 (t) REVERT: G 78 LYS cc_start: 0.7411 (OUTLIER) cc_final: 0.7154 (pttt) REVERT: G 117 MET cc_start: 0.8013 (mtm) cc_final: 0.7771 (tpt) REVERT: G 185 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.7132 (mm) outliers start: 48 outliers final: 35 residues processed: 327 average time/residue: 1.2529 time to fit residues: 461.7474 Evaluate side-chains 333 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 292 time to evaluate : 2.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 200 MET Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 204 ARG Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain D residue 740 SER Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 128 TYR Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain G residue 78 LYS Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain G residue 195 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 84 optimal weight: 9.9990 chunk 167 optimal weight: 0.5980 chunk 110 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 227 optimal weight: 6.9990 chunk 232 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 172 optimal weight: 0.0670 chunk 56 optimal weight: 1.9990 chunk 185 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 overall best weight: 1.2922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 149 ASN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 714 GLN ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4767 r_free = 0.4767 target = 0.221707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.160662 restraints weight = 57110.249| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 6.40 r_work: 0.3390 rms_B_bonded: 5.15 restraints_weight: 2.0000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3300 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18863 Z= 0.238 Angle : 0.676 15.587 25523 Z= 0.325 Chirality : 0.041 0.276 2883 Planarity : 0.004 0.057 3153 Dihedral : 3.748 32.794 2562 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.48 % Allowed : 33.45 % Favored : 64.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.49 (0.18), residues: 2343 helix: 2.34 (0.14), residues: 1353 sheet: -1.14 (0.39), residues: 162 loop : -0.88 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 671 HIS 0.007 0.001 HIS F 205 PHE 0.015 0.001 PHE C 584 TYR 0.022 0.001 TYR B 549 ARG 0.009 0.001 ARG A 660 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 309 time to evaluate : 2.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 79 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7390 (tm-30) REVERT: H 86 ASP cc_start: 0.2397 (OUTLIER) cc_final: 0.1939 (p0) REVERT: H 192 MET cc_start: 0.7480 (OUTLIER) cc_final: 0.7248 (mtt) REVERT: H 204 ARG cc_start: 0.7282 (mmp-170) cc_final: 0.6985 (mmp-170) REVERT: F 31 ASP cc_start: 0.8051 (m-30) cc_final: 0.7787 (m-30) REVERT: F 78 LYS cc_start: 0.8481 (ptmt) cc_final: 0.7758 (pttm) REVERT: F 204 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.6936 (tpm170) REVERT: F 206 LYS cc_start: 0.6645 (tmmt) cc_final: 0.6126 (mtpp) REVERT: C 463 MET cc_start: 0.8693 (tpt) cc_final: 0.8486 (mmm) REVERT: C 673 TYR cc_start: 0.8097 (t80) cc_final: 0.7704 (t80) REVERT: C 819 ARG cc_start: 0.6940 (ttp80) cc_final: 0.6469 (tpp80) REVERT: B 407 MET cc_start: 0.7252 (pmm) cc_final: 0.6296 (pmm) REVERT: B 439 LYS cc_start: 0.7925 (pmtt) cc_final: 0.7664 (pmmt) REVERT: B 500 ILE cc_start: 0.7669 (OUTLIER) cc_final: 0.7001 (tp) REVERT: B 670 MET cc_start: 0.8276 (ppp) cc_final: 0.7739 (pmt) REVERT: B 674 MET cc_start: 0.7552 (pmm) cc_final: 0.7335 (pmm) REVERT: B 694 ARG cc_start: 0.7900 (mpp80) cc_final: 0.7561 (tpp-160) REVERT: B 708 MET cc_start: 0.8680 (tpp) cc_final: 0.8275 (tpp) REVERT: A 767 TRP cc_start: 0.7086 (m-90) cc_final: 0.6656 (m-90) REVERT: D 467 LEU cc_start: 0.8581 (tm) cc_final: 0.8347 (pp) REVERT: D 678 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7739 (mp0) REVERT: E 6 ARG cc_start: 0.8387 (mmm-85) cc_final: 0.7863 (mmm160) REVERT: E 206 LYS cc_start: 0.8123 (ptmt) cc_final: 0.7871 (ttmm) REVERT: G 5 ASP cc_start: 0.7360 (t70) cc_final: 0.7145 (t70) REVERT: G 59 THR cc_start: 0.6372 (p) cc_final: 0.5639 (t) REVERT: G 69 LEU cc_start: 0.7510 (mt) cc_final: 0.7307 (mp) REVERT: G 117 MET cc_start: 0.7959 (mtm) cc_final: 0.7723 (tpt) REVERT: G 185 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.7165 (mm) outliers start: 45 outliers final: 34 residues processed: 331 average time/residue: 1.2559 time to fit residues: 470.8297 Evaluate side-chains 339 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 299 time to evaluate : 2.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 200 MET Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 204 ARG Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 740 SER Chi-restraints excluded: chain D residue 753 LEU Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain G residue 195 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 166 optimal weight: 0.9990 chunk 199 optimal weight: 0.9980 chunk 125 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 173 optimal weight: 0.0470 chunk 26 optimal weight: 7.9990 chunk 139 optimal weight: 0.2980 chunk 96 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 201 optimal weight: 6.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- 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 ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.223277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.146148 restraints weight = 63928.569| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 5.91 r_work: 0.3393 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3379 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3379 r_free = 0.3379 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3379 r_free = 0.3379 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3379 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18863 Z= 0.184 Angle : 0.661 12.365 25523 Z= 0.319 Chirality : 0.040 0.259 2883 Planarity : 0.004 0.057 3153 Dihedral : 3.739 32.048 2562 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.38 % Allowed : 33.71 % Favored : 63.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.60 (0.18), residues: 2343 helix: 2.45 (0.14), residues: 1351 sheet: -1.21 (0.39), residues: 166 loop : -0.83 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP A 671 HIS 0.007 0.001 HIS F 205 PHE 0.012 0.001 PHE H 107 TYR 0.022 0.001 TYR B 549 ARG 0.008 0.001 ARG A 660 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18796.06 seconds wall clock time: 339 minutes 23.69 seconds (20363.69 seconds total)