Starting phenix.real_space_refine on Mon Jun 16 09:40:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b61_44234/06_2025/9b61_44234.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b61_44234/06_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_44234/06_2025/9b61_44234.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b61_44234/06_2025/9b61_44234.map" model { file = "/net/cci-nas-00/data/ceres_data/9b61_44234/06_2025/9b61_44234.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b61_44234/06_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 14.91, per 1000 atoms: 0.81 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: 4.46 Conformation dependent library (CDL) restraints added in 3.6 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: 1.86 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: 6.81 Time building geometry restraints manager: 5.24 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: 3.660 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: 0.680 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 47.730 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:17.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.260 ------------------------------------------------------------------------------- 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 18875 Z= 0.167 Angle : 0.802 60.254 25547 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 Details of bonding type rmsd hydrogen bonds : bond 0.19805 ( 1132) hydrogen bonds : angle 6.16307 ( 3349) SS BOND : bond 0.00342 ( 12) SS BOND : angle 0.98902 ( 24) covalent geometry : bond 0.00511 (18863) covalent geometry : angle 0.80143 (25523) *********************** 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 : 3.232 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: 1.2585 time to fit residues: 511.8216 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 : 2.147 ------------------------------------------------------------------------------- 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: 0.3412 rms_B_bonded: 5.47 restraints_weight: 2.0000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3373 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3373 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 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 18875 Z= 0.144 Angle : 0.605 10.579 25547 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 Details of bonding type rmsd hydrogen bonds : bond 0.04618 ( 1132) hydrogen bonds : angle 4.22142 ( 3349) SS BOND : bond 0.00518 ( 12) SS BOND : angle 1.17343 ( 24) covalent geometry : bond 0.00329 (18863) covalent geometry : angle 0.60381 (25523) *********************** 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 : 2.788 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: 0.7819 (mtp180) cc_final: 0.7574 (mtp180) REVERT: H 160 ASN cc_start: 0.7550 (m-40) cc_final: 0.7346 (m-40) REVERT: H 192 MET cc_start: 0.7592 (OUTLIER) cc_final: 0.7360 (mtt) REVERT: H 200 MET cc_start: 0.8390 (tpp) cc_final: 0.7796 (mtp) REVERT: H 204 ARG cc_start: 0.7414 (mmp-170) cc_final: 0.7201 (mmp-170) REVERT: F 31 ASP cc_start: 0.8106 (m-30) cc_final: 0.7709 (m-30) REVERT: F 134 ILE cc_start: 0.7439 (pp) cc_final: 0.7227 (pt) REVERT: F 196 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8333 (tt) REVERT: F 204 ARG cc_start: 0.7503 (mmp-170) cc_final: 0.6978 (tpm170) REVERT: C 627 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7961 (mp0) REVERT: C 694 ARG cc_start: 0.8616 (mtp85) cc_final: 0.8250 (mmt-90) REVERT: B 694 ARG cc_start: 0.7871 (mpp80) cc_final: 0.7565 (ptt-90) REVERT: A 671 TRP cc_start: 0.7674 (t60) cc_final: 0.7443 (t60) REVERT: D 496 MET cc_start: 0.8058 (ptp) cc_final: 0.6978 (mtm) REVERT: D 678 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7341 (mp0) REVERT: E 6 ARG cc_start: 0.8343 (mmm-85) cc_final: 0.7803 (mmm160) REVERT: E 129 LYS cc_start: 0.8346 (mmmm) cc_final: 0.8045 (mppt) outliers start: 80 outliers final: 29 residues processed: 378 average time/residue: 1.8027 time to fit residues: 768.4635 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 : 2.266 ------------------------------------------------------------------------------- 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: 10.0000 chunk 81 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 202 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 218 optimal weight: 5.9990 chunk 208 optimal weight: 5.9990 chunk 217 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 193 optimal weight: 9.9990 chunk 111 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 726 ASN A 714 GLN ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.219130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.163230 restraints weight = 64825.433| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 8.35 r_work: 0.3304 rms_B_bonded: 5.79 restraints_weight: 2.0000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 18875 Z= 0.232 Angle : 0.641 10.778 25547 Z= 0.325 Chirality : 0.042 0.166 2883 Planarity : 0.004 0.071 3153 Dihedral : 4.996 57.334 2578 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.55 % Allowed : 29.89 % Favored : 65.56 % 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: 1.21 (0.18), residues: 2343 helix: 2.00 (0.14), residues: 1377 sheet: -1.42 (0.40), residues: 150 loop : -0.85 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 766 HIS 0.009 0.001 HIS G 82 PHE 0.020 0.002 PHE C 584 TYR 0.015 0.001 TYR C 424 ARG 0.011 0.001 ARG C 819 Details of bonding type rmsd hydrogen bonds : bond 0.05072 ( 1132) hydrogen bonds : angle 4.24341 ( 3349) SS BOND : bond 0.00370 ( 12) SS BOND : angle 1.12629 ( 24) covalent geometry : bond 0.00556 (18863) covalent geometry : angle 0.64085 (25523) *********************** 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 404 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 318 time to evaluate : 2.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 66 THR cc_start: 0.8590 (p) cc_final: 0.8088 (t) REVERT: H 192 MET cc_start: 0.7668 (OUTLIER) cc_final: 0.7430 (mtt) REVERT: F 31 ASP cc_start: 0.8120 (m-30) cc_final: 0.7823 (m-30) REVERT: F 196 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8381 (tt) REVERT: F 204 ARG cc_start: 0.7494 (mmp-170) cc_final: 0.7009 (tpm170) REVERT: C 408 MET cc_start: 0.6482 (tpt) cc_final: 0.5937 (tpp) REVERT: C 673 TYR cc_start: 0.8006 (t80) cc_final: 0.7783 (t80) REVERT: B 670 MET cc_start: 0.8464 (ppp) cc_final: 0.7856 (ppp) REVERT: B 694 ARG cc_start: 0.7998 (mpp80) cc_final: 0.7656 (ptt-90) REVERT: B 708 MET cc_start: 0.8478 (tpp) cc_final: 0.8075 (tpp) REVERT: B 765 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7465 (tmtm) REVERT: B 782 GLU cc_start: 0.6338 (pp20) cc_final: 0.5888 (pm20) REVERT: B 783 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.6921 (tptm) REVERT: A 420 ARG cc_start: 0.8067 (mtm110) cc_final: 0.7821 (mtm110) REVERT: A 713 GLU cc_start: 0.8740 (pp20) cc_final: 0.8492 (pp20) REVERT: A 721 MET cc_start: 0.7988 (ppp) cc_final: 0.7760 (ppp) REVERT: D 594 ARG cc_start: 0.9199 (OUTLIER) cc_final: 0.8918 (mtp85) REVERT: D 782 GLU cc_start: 0.7324 (mp0) cc_final: 0.7031 (mp0) REVERT: E 6 ARG cc_start: 0.8386 (mmm-85) cc_final: 0.7832 (mmm160) REVERT: E 37 ARG cc_start: 0.7570 (mtp85) cc_final: 0.7270 (mtp85) REVERT: E 129 LYS cc_start: 0.8252 (mmmm) cc_final: 0.7977 (mppt) REVERT: G 78 LYS cc_start: 0.7384 (ttpt) cc_final: 0.7132 (ptpt) REVERT: G 206 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7555 (ttpp) outliers start: 86 outliers final: 43 residues processed: 370 average time/residue: 1.2395 time to fit residues: 514.5622 Evaluate side-chains 348 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 299 time to evaluate : 1.831 ------------------------------------------------------------------------------- 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 150 ILE 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 502 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 765 LYS 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 809 VAL Chi-restraints excluded: chain A residue 811 LEU 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 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 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 34 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 196 LEU 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: 0.7980 chunk 174 optimal weight: 0.5980 chunk 127 optimal weight: 0.4980 chunk 30 optimal weight: 3.9990 chunk 133 optimal weight: 0.8980 chunk 107 optimal weight: 20.0000 chunk 52 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 187 optimal weight: 1.9990 chunk 121 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 D 764 ASN A ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 82 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.222737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.164792 restraints weight = 62560.202| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 7.29 r_work: 0.3421 rms_B_bonded: 5.46 restraints_weight: 2.0000 r_work (final): 0.3421 ------------------------------------------------------------------------------- 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 = 0.30 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 = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3362 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18875 Z= 0.119 Angle : 0.584 10.245 25547 Z= 0.289 Chirality : 0.039 0.149 2883 Planarity : 0.004 0.049 3153 Dihedral : 4.368 56.695 2573 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.88 % Allowed : 30.35 % Favored : 65.77 % 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: 1.64 (0.18), residues: 2343 helix: 2.44 (0.14), residues: 1363 sheet: -1.32 (0.40), residues: 148 loop : -0.79 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 671 HIS 0.009 0.001 HIS G 82 PHE 0.011 0.001 PHE H 107 TYR 0.014 0.001 TYR C 424 ARG 0.012 0.001 ARG D 660 Details of bonding type rmsd hydrogen bonds : bond 0.03804 ( 1132) hydrogen bonds : angle 3.92113 ( 3349) SS BOND : bond 0.00292 ( 12) SS BOND : angle 1.17911 ( 24) covalent geometry : bond 0.00265 (18863) covalent geometry : angle 0.58320 (25523) *********************** 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 397 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 325 time to evaluate : 1.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 66 THR cc_start: 0.8574 (p) cc_final: 0.8022 (t) REVERT: H 86 ASP cc_start: 0.1751 (OUTLIER) cc_final: 0.1331 (p0) REVERT: H 192 MET cc_start: 0.7532 (OUTLIER) cc_final: 0.7287 (mtt) REVERT: F 31 ASP cc_start: 0.8202 (m-30) cc_final: 0.7754 (m-30) REVERT: F 78 LYS cc_start: 0.8560 (ptmt) cc_final: 0.7925 (pttm) REVERT: F 196 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8291 (tt) REVERT: F 204 ARG cc_start: 0.7508 (mmp-170) cc_final: 0.6925 (tpm170) REVERT: C 408 MET cc_start: 0.6411 (tpt) cc_final: 0.5751 (tpp) REVERT: C 627 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8090 (mp0) REVERT: C 673 TYR cc_start: 0.7972 (t80) cc_final: 0.7692 (t80) REVERT: B 694 ARG cc_start: 0.7987 (mpp80) cc_final: 0.7737 (mpt-90) REVERT: B 708 MET cc_start: 0.8556 (tpp) cc_final: 0.8069 (tpp) REVERT: A 721 MET cc_start: 0.8005 (ppp) cc_final: 0.7699 (ppp) REVERT: A 767 TRP cc_start: 0.7170 (m-90) cc_final: 0.6793 (m-90) REVERT: D 496 MET cc_start: 0.8064 (ptp) cc_final: 0.7048 (mtm) REVERT: D 678 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7553 (mp0) REVERT: D 782 GLU cc_start: 0.7171 (mp0) cc_final: 0.6958 (mp0) REVERT: E 6 ARG cc_start: 0.8253 (mmm-85) cc_final: 0.7819 (mmm160) REVERT: E 10 MET cc_start: 0.8249 (tpt) cc_final: 0.8010 (tpt) REVERT: E 129 LYS cc_start: 0.8311 (mmmm) cc_final: 0.8048 (mppt) REVERT: G 185 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.7153 (mm) REVERT: G 207 GLN cc_start: 0.7486 (OUTLIER) cc_final: 0.7220 (pt0) outliers start: 72 outliers final: 35 residues processed: 367 average time/residue: 1.2673 time to fit residues: 522.1722 Evaluate side-chains 341 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 300 time to evaluate : 2.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 105 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 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 812 ILE Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 811 LEU 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 E residue 203 ASP Chi-restraints excluded: chain G residue 34 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 195 VAL Chi-restraints excluded: chain G residue 200 MET Chi-restraints excluded: chain G residue 207 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 208 optimal weight: 2.9990 chunk 228 optimal weight: 0.7980 chunk 204 optimal weight: 0.0030 chunk 173 optimal weight: 3.9990 chunk 148 optimal weight: 8.9990 chunk 105 optimal weight: 9.9990 chunk 195 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.2994 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4762 r_free = 0.4762 target = 0.221059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.162306 restraints weight = 61276.295| |-----------------------------------------------------------------------------| r_work (start): 0.4098 rms_B_bonded: 7.13 r_work: 0.3382 rms_B_bonded: 5.40 restraints_weight: 2.0000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3335 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3335 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18875 Z= 0.146 Angle : 0.603 10.772 25547 Z= 0.298 Chirality : 0.040 0.153 2883 Planarity : 0.004 0.052 3153 Dihedral : 4.333 54.865 2571 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.19 % Allowed : 30.71 % Favored : 65.10 % 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: 1.55 (0.18), residues: 2343 helix: 2.32 (0.14), residues: 1377 sheet: -1.41 (0.37), residues: 170 loop : -0.73 (0.22), residues: 796 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 0.016 0.001 PHE E 73 TYR 0.015 0.001 TYR G 156 ARG 0.010 0.001 ARG A 660 Details of bonding type rmsd hydrogen bonds : bond 0.04065 ( 1132) hydrogen bonds : angle 3.94955 ( 3349) SS BOND : bond 0.00407 ( 12) SS BOND : angle 1.47172 ( 24) covalent geometry : bond 0.00345 (18863) covalent geometry : angle 0.60153 (25523) *********************** 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 393 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 315 time to evaluate : 2.142 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: 0.2010 (OUTLIER) cc_final: 0.1579 (p0) REVERT: H 192 MET cc_start: 0.7555 (OUTLIER) cc_final: 0.7318 (mtt) REVERT: F 31 ASP cc_start: 0.8212 (m-30) cc_final: 0.7896 (m-30) REVERT: F 78 LYS cc_start: 0.8550 (ptmt) cc_final: 0.7813 (pttm) REVERT: F 204 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.6894 (tpm170) REVERT: F 206 LYS cc_start: 0.6453 (tmmt) cc_final: 0.5891 (mtpp) REVERT: C 408 MET cc_start: 0.6476 (tpt) cc_final: 0.5797 (tpp) REVERT: C 673 TYR cc_start: 0.8034 (t80) cc_final: 0.7700 (t80) REVERT: C 674 MET cc_start: 0.8115 (pmm) cc_final: 0.7802 (pmm) REVERT: B 407 MET cc_start: 0.7098 (pmm) cc_final: 0.6867 (pmm) REVERT: B 497 SER cc_start: 0.8722 (m) cc_final: 0.8513 (t) REVERT: B 670 MET cc_start: 0.8311 (ppp) cc_final: 0.7909 (pmm) REVERT: B 674 MET cc_start: 0.7811 (pmm) cc_final: 0.7555 (pmm) REVERT: B 708 MET cc_start: 0.8614 (tpp) cc_final: 0.8099 (tpp) REVERT: B 782 GLU cc_start: 0.6215 (pp20) cc_final: 0.5821 (pm20) REVERT: A 721 MET cc_start: 0.8053 (ppp) cc_final: 0.7789 (ppp) REVERT: A 767 TRP cc_start: 0.7178 (m-90) cc_final: 0.6773 (m-90) REVERT: D 496 MET cc_start: 0.7983 (ptp) cc_final: 0.7025 (mtm) REVERT: D 660 ARG cc_start: 0.8052 (ttm-80) cc_final: 0.7827 (mtm-85) REVERT: D 694 ARG cc_start: 0.8135 (mmm-85) cc_final: 0.7907 (mpt-90) REVERT: D 782 GLU cc_start: 0.7230 (mp0) cc_final: 0.7010 (mp0) REVERT: E 6 ARG cc_start: 0.8375 (mmm-85) cc_final: 0.7878 (mmm160) REVERT: E 117 MET cc_start: 0.6232 (tpt) cc_final: 0.6026 (tpt) REVERT: E 129 LYS cc_start: 0.8279 (mmmm) cc_final: 0.8038 (mppt) REVERT: G 59 THR cc_start: 0.6723 (p) cc_final: 0.6232 (t) REVERT: G 207 GLN cc_start: 0.7454 (OUTLIER) cc_final: 0.7094 (pt0) outliers start: 78 outliers final: 50 residues processed: 360 average time/residue: 1.2474 time to fit residues: 505.4706 Evaluate side-chains 357 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 303 time to evaluate : 2.081 ------------------------------------------------------------------------------- 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 98 LEU Chi-restraints excluded: chain H residue 105 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 204 ARG 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 443 THR 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 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 28 VAL 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 E residue 112 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 34 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 207 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 165 optimal weight: 8.9990 chunk 207 optimal weight: 0.8980 chunk 211 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 130 optimal weight: 0.2980 chunk 197 optimal weight: 0.9980 chunk 46 optimal weight: 8.9990 chunk 229 optimal weight: 0.9990 chunk 203 optimal weight: 10.0000 chunk 185 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 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 709 ASN A 714 GLN ** G 79 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 = 0.4775 r_free = 0.4775 target = 0.222531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.149325 restraints weight = 64107.148| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 5.10 r_work: 0.3392 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3367 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3367 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18875 Z= 0.125 Angle : 0.598 11.402 25547 Z= 0.295 Chirality : 0.040 0.175 2883 Planarity : 0.004 0.052 3153 Dihedral : 4.111 46.382 2569 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.83 % Allowed : 31.18 % Favored : 64.99 % 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: 1.63 (0.18), residues: 2343 helix: 2.39 (0.14), residues: 1377 sheet: -1.35 (0.37), residues: 176 loop : -0.72 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 671 HIS 0.008 0.001 HIS F 205 PHE 0.012 0.001 PHE C 584 TYR 0.020 0.001 TYR B 549 ARG 0.008 0.001 ARG G 204 Details of bonding type rmsd hydrogen bonds : bond 0.03776 ( 1132) hydrogen bonds : angle 3.89436 ( 3349) SS BOND : bond 0.00303 ( 12) SS BOND : angle 1.29929 ( 24) covalent geometry : bond 0.00288 (18863) covalent geometry : angle 0.59710 (25523) *********************** 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 384 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 313 time to evaluate : 1.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 ASP cc_start: 0.2006 (OUTLIER) cc_final: 0.1564 (p0) REVERT: H 192 MET cc_start: 0.7477 (OUTLIER) cc_final: 0.7238 (mtt) REVERT: H 204 ARG cc_start: 0.7679 (mmm160) cc_final: 0.7257 (mmp-170) REVERT: F 31 ASP cc_start: 0.8044 (m-30) cc_final: 0.7608 (m-30) REVERT: F 78 LYS cc_start: 0.8503 (ptmt) cc_final: 0.7767 (pttm) REVERT: F 204 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.6919 (tpm170) REVERT: C 408 MET cc_start: 0.6390 (tpt) cc_final: 0.5717 (tpp) REVERT: C 673 TYR cc_start: 0.7914 (t80) cc_final: 0.7561 (t80) REVERT: C 674 MET cc_start: 0.8145 (pmm) cc_final: 0.7887 (pmm) REVERT: C 819 ARG cc_start: 0.6955 (ttp80) cc_final: 0.6689 (ttp80) REVERT: B 670 MET cc_start: 0.8364 (ppp) cc_final: 0.7947 (pmm) REVERT: B 674 MET cc_start: 0.7816 (pmm) cc_final: 0.7554 (pmm) REVERT: B 694 ARG cc_start: 0.7705 (mpp80) cc_final: 0.7489 (mpp80) REVERT: B 708 MET cc_start: 0.8671 (tpp) cc_final: 0.8328 (tpp) REVERT: B 782 GLU cc_start: 0.6100 (pp20) cc_final: 0.5827 (pm20) REVERT: A 674 MET cc_start: 0.7525 (pmm) cc_final: 0.6420 (pmm) REVERT: A 721 MET cc_start: 0.8092 (ppp) cc_final: 0.7822 (ppp) REVERT: A 767 TRP cc_start: 0.7103 (m-90) cc_final: 0.6679 (m-90) REVERT: D 496 MET cc_start: 0.8047 (ptp) cc_final: 0.6930 (mtm) REVERT: D 678 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7534 (mp0) REVERT: D 694 ARG cc_start: 0.8162 (mmm-85) cc_final: 0.7927 (mpt-90) REVERT: D 782 GLU cc_start: 0.7112 (mp0) cc_final: 0.6819 (mp0) REVERT: E 6 ARG cc_start: 0.8348 (mmm-85) cc_final: 0.7873 (mmm160) REVERT: E 203 ASP cc_start: 0.8237 (t0) cc_final: 0.7945 (m-30) REVERT: G 59 THR cc_start: 0.6597 (p) cc_final: 0.6013 (t) REVERT: G 185 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.7097 (mm) outliers start: 71 outliers final: 43 residues processed: 355 average time/residue: 1.2238 time to fit residues: 490.7228 Evaluate side-chains 346 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 299 time to evaluate : 2.039 ------------------------------------------------------------------------------- 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 105 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 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 592 SER Chi-restraints excluded: chain B residue 812 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 D residue 643 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 76 LEU Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain G residue 34 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 195 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 188 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 174 optimal weight: 0.8980 chunk 221 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 169 optimal weight: 0.0370 chunk 90 optimal weight: 0.8980 chunk 180 optimal weight: 30.0000 overall best weight: 0.7460 ------------------------------------------------------------------------------- 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 709 ASN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.222733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.165586 restraints weight = 61427.038| |-----------------------------------------------------------------------------| r_work (start): 0.4137 rms_B_bonded: 7.25 r_work: 0.3418 rms_B_bonded: 5.52 restraints_weight: 2.0000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3351 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3351 r_free = 0.3351 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3351 r_free = 0.3351 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3351 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18875 Z= 0.122 Angle : 0.622 12.819 25547 Z= 0.303 Chirality : 0.040 0.261 2883 Planarity : 0.004 0.055 3153 Dihedral : 3.755 36.233 2564 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.83 % Allowed : 31.44 % Favored : 64.74 % 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: 1.68 (0.18), residues: 2343 helix: 2.44 (0.14), residues: 1375 sheet: -1.25 (0.37), residues: 174 loop : -0.73 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 671 HIS 0.007 0.001 HIS F 205 PHE 0.011 0.001 PHE C 584 TYR 0.016 0.001 TYR D 421 ARG 0.009 0.001 ARG G 204 Details of bonding type rmsd hydrogen bonds : bond 0.03654 ( 1132) hydrogen bonds : angle 3.85405 ( 3349) SS BOND : bond 0.00506 ( 12) SS BOND : angle 1.96113 ( 24) covalent geometry : bond 0.00282 (18863) covalent geometry : angle 0.61935 (25523) *********************** 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 385 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 314 time to evaluate : 2.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 ASP cc_start: 0.2014 (OUTLIER) cc_final: 0.1586 (p0) REVERT: H 192 MET cc_start: 0.7516 (OUTLIER) cc_final: 0.7287 (mtt) REVERT: F 31 ASP cc_start: 0.8103 (m-30) cc_final: 0.7708 (m-30) REVERT: F 78 LYS cc_start: 0.8574 (ptmt) cc_final: 0.7814 (pttm) REVERT: F 204 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.6933 (tpm170) REVERT: F 206 LYS cc_start: 0.6595 (tmmt) cc_final: 0.5982 (mtpp) REVERT: C 408 MET cc_start: 0.6403 (tpt) cc_final: 0.5734 (tpp) REVERT: C 627 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7953 (mp0) REVERT: C 673 TYR cc_start: 0.7965 (t80) cc_final: 0.7644 (t80) REVERT: C 674 MET cc_start: 0.8116 (pmm) cc_final: 0.7899 (pmm) REVERT: B 670 MET cc_start: 0.8416 (ppp) cc_final: 0.7782 (pmt) REVERT: B 674 MET cc_start: 0.7864 (pmm) cc_final: 0.7633 (pmm) REVERT: B 694 ARG cc_start: 0.7742 (mpp80) cc_final: 0.7235 (tpp-160) REVERT: B 708 MET cc_start: 0.8711 (tpp) cc_final: 0.8282 (tpp) REVERT: B 782 GLU cc_start: 0.6187 (pp20) cc_final: 0.5885 (pm20) REVERT: A 671 TRP cc_start: 0.8295 (t-100) cc_final: 0.8045 (t-100) REVERT: A 721 MET cc_start: 0.8146 (OUTLIER) cc_final: 0.7848 (ppp) REVERT: A 767 TRP cc_start: 0.7115 (m-90) cc_final: 0.6661 (m-90) REVERT: D 496 MET cc_start: 0.8089 (ptp) cc_final: 0.7000 (mtm) REVERT: D 694 ARG cc_start: 0.8161 (mmm-85) cc_final: 0.7815 (mtt90) REVERT: D 782 GLU cc_start: 0.7223 (mp0) cc_final: 0.6935 (mp0) REVERT: E 6 ARG cc_start: 0.8389 (mmm-85) cc_final: 0.7860 (mmm160) REVERT: E 203 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.8019 (OUTLIER) REVERT: G 59 THR cc_start: 0.6500 (p) cc_final: 0.5824 (t) REVERT: G 185 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.7163 (mm) outliers start: 71 outliers final: 46 residues processed: 354 average time/residue: 1.2569 time to fit residues: 506.5680 Evaluate side-chains 354 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 302 time to evaluate : 1.888 ------------------------------------------------------------------------------- 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 105 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 H residue 205 HIS 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 195 VAL 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 443 THR 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 A residue 709 ASN Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 643 THR 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 E residue 179 SER Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 40 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 192 MET Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 200 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 182 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 136 optimal weight: 0.7980 chunk 185 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 133 optimal weight: 0.9990 chunk 163 optimal weight: 9.9990 chunk 152 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 149 ASN B 726 ASN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 ASN A 714 GLN ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 HIS G 207 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.221836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.161452 restraints weight = 55374.433| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 6.37 r_work: 0.3420 rms_B_bonded: 5.10 restraints_weight: 2.0000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3357 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3357 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18875 Z= 0.138 Angle : 0.625 11.461 25547 Z= 0.306 Chirality : 0.040 0.180 2883 Planarity : 0.004 0.057 3153 Dihedral : 3.681 32.940 2562 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.19 % Allowed : 31.54 % Favored : 64.27 % 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: 2.42 (0.14), residues: 1353 sheet: -1.18 (0.37), residues: 174 loop : -0.79 (0.21), residues: 816 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 0.017 0.001 TYR D 421 ARG 0.013 0.001 ARG C 819 Details of bonding type rmsd hydrogen bonds : bond 0.03826 ( 1132) hydrogen bonds : angle 3.89353 ( 3349) SS BOND : bond 0.00346 ( 12) SS BOND : angle 1.24204 ( 24) covalent geometry : bond 0.00326 (18863) covalent geometry : angle 0.62456 (25523) *********************** 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 391 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 313 time to evaluate : 1.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 ASP cc_start: 0.2111 (OUTLIER) cc_final: 0.1673 (p0) REVERT: H 192 MET cc_start: 0.7529 (OUTLIER) cc_final: 0.7284 (mtt) REVERT: F 31 ASP cc_start: 0.7988 (m-30) cc_final: 0.7686 (m-30) REVERT: F 78 LYS cc_start: 0.8523 (ptmt) cc_final: 0.7761 (pttm) REVERT: F 204 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.6922 (tpm170) REVERT: F 206 LYS cc_start: 0.6580 (tmmt) cc_final: 0.5978 (mtpp) REVERT: C 408 MET cc_start: 0.6463 (tpt) cc_final: 0.5773 (tpp) REVERT: C 627 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7954 (mp0) REVERT: C 673 TYR cc_start: 0.7983 (t80) cc_final: 0.7577 (t80) REVERT: C 674 MET cc_start: 0.8097 (pmm) cc_final: 0.7778 (pmm) REVERT: B 670 MET cc_start: 0.8413 (ppp) cc_final: 0.7860 (pmt) REVERT: B 674 MET cc_start: 0.7887 (pmm) cc_final: 0.7658 (pmm) REVERT: B 694 ARG cc_start: 0.7845 (mpp80) cc_final: 0.7403 (tpp-160) REVERT: B 708 MET cc_start: 0.8716 (tpp) cc_final: 0.8279 (tpp) REVERT: A 713 GLU cc_start: 0.8821 (pp20) cc_final: 0.8490 (pp20) REVERT: A 721 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7834 (ppp) REVERT: A 767 TRP cc_start: 0.7129 (m-90) cc_final: 0.6663 (m-90) REVERT: D 678 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7672 (mp0) REVERT: D 694 ARG cc_start: 0.8160 (mmm-85) cc_final: 0.7813 (mtt90) REVERT: D 782 GLU cc_start: 0.7219 (mp0) cc_final: 0.6964 (mp0) REVERT: E 6 ARG cc_start: 0.8357 (mmm-85) cc_final: 0.7846 (mmm160) REVERT: G 5 ASP cc_start: 0.7462 (t70) cc_final: 0.7254 (t70) REVERT: G 185 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.7166 (mm) outliers start: 78 outliers final: 55 residues processed: 355 average time/residue: 1.4629 time to fit residues: 587.7579 Evaluate side-chains 359 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 298 time to evaluate : 1.766 ------------------------------------------------------------------------------- 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 105 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 H residue 205 HIS 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 195 VAL 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 663 LYS Chi-restraints excluded: chain C residue 795 VAL 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 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 721 MET 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 D residue 643 THR Chi-restraints excluded: chain D residue 740 SER Chi-restraints excluded: chain D residue 753 LEU 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 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 E residue 155 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 192 MET 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 34 LEU Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 66 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 5 optimal weight: 10.0000 chunk 172 optimal weight: 0.0030 chunk 192 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 220 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 232 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 overall best weight: 1.1996 ------------------------------------------------------------------------------- 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 709 ASN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.221567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.163977 restraints weight = 60352.877| |-----------------------------------------------------------------------------| r_work (start): 0.4109 rms_B_bonded: 7.46 r_work: 0.3395 rms_B_bonded: 5.46 restraints_weight: 2.0000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3338 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3338 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18875 Z= 0.146 Angle : 0.656 12.126 25547 Z= 0.321 Chirality : 0.040 0.177 2883 Planarity : 0.004 0.099 3153 Dihedral : 3.757 33.219 2562 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.72 % Allowed : 32.21 % 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: 1.56 (0.18), residues: 2343 helix: 2.38 (0.14), residues: 1353 sheet: -1.09 (0.38), residues: 174 loop : -0.81 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 671 HIS 0.007 0.001 HIS F 205 PHE 0.032 0.001 PHE E 73 TYR 0.018 0.001 TYR B 700 ARG 0.019 0.001 ARG C 819 Details of bonding type rmsd hydrogen bonds : bond 0.03896 ( 1132) hydrogen bonds : angle 3.91352 ( 3349) SS BOND : bond 0.00323 ( 12) SS BOND : angle 1.33831 ( 24) covalent geometry : bond 0.00348 (18863) covalent geometry : angle 0.65494 (25523) *********************** 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 372 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 303 time to evaluate : 1.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 79 GLN cc_start: 0.7829 (pp30) cc_final: 0.7100 (mt0) REVERT: H 86 ASP cc_start: 0.2113 (OUTLIER) cc_final: 0.1675 (p0) REVERT: H 192 MET cc_start: 0.7568 (OUTLIER) cc_final: 0.7328 (mtt) REVERT: F 31 ASP cc_start: 0.8029 (m-30) cc_final: 0.7663 (m-30) REVERT: F 78 LYS cc_start: 0.8586 (ptmt) cc_final: 0.7836 (pttm) REVERT: F 204 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.6949 (tpm170) REVERT: F 206 LYS cc_start: 0.6712 (tmmt) cc_final: 0.6114 (mtpp) REVERT: C 408 MET cc_start: 0.6426 (tpt) cc_final: 0.5726 (tpp) REVERT: C 627 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7996 (mp0) REVERT: C 673 TYR cc_start: 0.7948 (t80) cc_final: 0.7606 (t80) REVERT: C 674 MET cc_start: 0.8117 (pmm) cc_final: 0.7792 (pmm) REVERT: C 819 ARG cc_start: 0.7039 (ttp80) cc_final: 0.6481 (tpp80) REVERT: B 407 MET cc_start: 0.7211 (pmm) cc_final: 0.6853 (pmm) REVERT: B 463 MET cc_start: 0.7618 (tpt) cc_final: 0.7288 (tpt) REVERT: B 670 MET cc_start: 0.8379 (ppp) cc_final: 0.7865 (pmt) REVERT: B 674 MET cc_start: 0.7919 (pmm) cc_final: 0.7699 (pmm) REVERT: B 708 MET cc_start: 0.8749 (tpp) cc_final: 0.8546 (tpp) REVERT: B 782 GLU cc_start: 0.6293 (pp20) cc_final: 0.5890 (pm20) REVERT: A 721 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7831 (ppp) REVERT: A 767 TRP cc_start: 0.7162 (m-90) cc_final: 0.6691 (m-90) REVERT: D 420 ARG cc_start: 0.7857 (pmm-80) cc_final: 0.7646 (pmm-80) REVERT: D 496 MET cc_start: 0.8078 (ptp) cc_final: 0.7105 (mtm) REVERT: D 678 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7595 (mp0) REVERT: D 782 GLU cc_start: 0.7283 (mp0) cc_final: 0.7060 (mp0) REVERT: E 6 ARG cc_start: 0.8354 (mmm-85) cc_final: 0.7841 (mmm160) REVERT: G 5 ASP cc_start: 0.7440 (t70) cc_final: 0.7226 (t70) REVERT: G 117 MET cc_start: 0.8032 (mtm) cc_final: 0.7771 (tpp) REVERT: G 185 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7243 (mm) outliers start: 69 outliers final: 52 residues processed: 341 average time/residue: 1.1959 time to fit residues: 462.2052 Evaluate side-chains 351 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 293 time to evaluate : 1.827 ------------------------------------------------------------------------------- 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 105 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 H residue 205 HIS 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 195 VAL 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 A residue 592 SER Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 721 MET 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 D residue 643 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 28 VAL 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 E residue 112 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 192 MET 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 34 LEU Chi-restraints excluded: chain G residue 66 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 84 optimal weight: 0.9990 chunk 167 optimal weight: 6.9990 chunk 110 optimal weight: 8.9990 chunk 22 optimal weight: 0.6980 chunk 227 optimal weight: 5.9990 chunk 232 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 172 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 185 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 709 ASN 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 = 0.4768 r_free = 0.4768 target = 0.221970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.160990 restraints weight = 57099.343| |-----------------------------------------------------------------------------| r_work (start): 0.4083 rms_B_bonded: 6.54 r_work: 0.3413 rms_B_bonded: 5.16 restraints_weight: 2.0000 r_work (final): 0.3413 ------------------------------------------------------------------------------- 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 = 0.29 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 = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3362 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18875 Z= 0.140 Angle : 0.674 12.986 25547 Z= 0.327 Chirality : 0.040 0.165 2883 Planarity : 0.004 0.091 3153 Dihedral : 3.804 32.838 2562 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.26 % Allowed : 32.73 % Favored : 64.01 % 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: 1.54 (0.18), residues: 2343 helix: 2.35 (0.14), residues: 1353 sheet: -1.07 (0.38), residues: 174 loop : -0.81 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 671 HIS 0.007 0.001 HIS F 205 PHE 0.026 0.001 PHE E 73 TYR 0.015 0.001 TYR D 421 ARG 0.019 0.001 ARG C 819 Details of bonding type rmsd hydrogen bonds : bond 0.03841 ( 1132) hydrogen bonds : angle 3.90536 ( 3349) SS BOND : bond 0.00399 ( 12) SS BOND : angle 1.78482 ( 24) covalent geometry : bond 0.00333 (18863) covalent geometry : angle 0.67179 (25523) ********************** 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 367 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 307 time to evaluate : 2.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 79 GLN cc_start: 0.7847 (pp30) cc_final: 0.7108 (mt0) REVERT: H 86 ASP cc_start: 0.2135 (OUTLIER) cc_final: 0.1690 (p0) REVERT: H 192 MET cc_start: 0.7506 (OUTLIER) cc_final: 0.7266 (mtt) REVERT: F 31 ASP cc_start: 0.7927 (m-30) cc_final: 0.7610 (m-30) REVERT: F 78 LYS cc_start: 0.8510 (ptmt) cc_final: 0.7759 (pttm) REVERT: F 149 ASN cc_start: 0.8223 (t0) cc_final: 0.7833 (t0) REVERT: F 204 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.7034 (tpm170) REVERT: F 206 LYS cc_start: 0.6707 (tmmt) cc_final: 0.6146 (mtpp) REVERT: C 627 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7911 (mp0) REVERT: C 673 TYR cc_start: 0.8014 (t80) cc_final: 0.7718 (t80) REVERT: C 819 ARG cc_start: 0.6990 (ttp80) cc_final: 0.6463 (tpp80) REVERT: B 407 MET cc_start: 0.7210 (pmm) cc_final: 0.6140 (pmm) REVERT: B 463 MET cc_start: 0.7648 (tpt) cc_final: 0.7315 (tpt) REVERT: B 670 MET cc_start: 0.8359 (ppp) cc_final: 0.7856 (pmt) REVERT: B 674 MET cc_start: 0.7918 (pmm) cc_final: 0.7706 (pmm) REVERT: B 782 GLU cc_start: 0.6213 (pp20) cc_final: 0.5862 (pm20) REVERT: A 721 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7812 (ppp) REVERT: A 767 TRP cc_start: 0.7090 (m-90) cc_final: 0.6653 (m-90) REVERT: D 420 ARG cc_start: 0.7871 (pmm-80) cc_final: 0.7663 (pmm-80) REVERT: D 496 MET cc_start: 0.8009 (ptp) cc_final: 0.7033 (mtm) REVERT: D 503 MET cc_start: 0.8416 (tpp) cc_final: 0.8031 (mmt) REVERT: D 678 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7601 (mp0) REVERT: D 782 GLU cc_start: 0.7253 (mp0) cc_final: 0.7019 (mp0) REVERT: E 6 ARG cc_start: 0.8305 (mmm-85) cc_final: 0.7844 (mmm160) REVERT: G 5 ASP cc_start: 0.7436 (t70) cc_final: 0.7198 (t70) REVERT: G 65 ARG cc_start: 0.6222 (OUTLIER) cc_final: 0.5944 (pmm-80) REVERT: G 117 MET cc_start: 0.7971 (mtm) cc_final: 0.7737 (tpt) REVERT: G 185 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.7174 (mm) outliers start: 60 outliers final: 46 residues processed: 340 average time/residue: 1.3435 time to fit residues: 525.0701 Evaluate side-chains 348 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 295 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 105 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 H residue 205 HIS 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 195 VAL 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 592 SER Chi-restraints excluded: chain A residue 721 MET 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 D residue 643 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 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 155 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 192 MET 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 34 LEU Chi-restraints excluded: chain G residue 65 ARG 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 166 optimal weight: 6.9990 chunk 199 optimal weight: 0.9990 chunk 125 optimal weight: 7.9990 chunk 4 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 173 optimal weight: 0.9980 chunk 26 optimal weight: 9.9990 chunk 139 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 201 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.222138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.147028 restraints weight = 62593.116| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 5.09 r_work: 0.3444 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3425 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3425 r_free = 0.3425 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3425 r_free = 0.3425 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3425 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18875 Z= 0.135 Angle : 0.665 12.481 25547 Z= 0.324 Chirality : 0.040 0.161 2883 Planarity : 0.004 0.077 3153 Dihedral : 3.776 32.391 2562 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.41 % Allowed : 32.73 % Favored : 63.86 % 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: 2.38 (0.14), residues: 1351 sheet: -1.10 (0.39), residues: 162 loop : -0.82 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 671 HIS 0.007 0.001 HIS F 205 PHE 0.025 0.001 PHE E 73 TYR 0.022 0.001 TYR B 700 ARG 0.018 0.001 ARG A 660 Details of bonding type rmsd hydrogen bonds : bond 0.03739 ( 1132) hydrogen bonds : angle 3.88942 ( 3349) SS BOND : bond 0.00350 ( 12) SS BOND : angle 1.25058 ( 24) covalent geometry : bond 0.00317 (18863) covalent geometry : angle 0.66452 (25523) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20065.75 seconds wall clock time: 348 minutes 18.52 seconds (20898.52 seconds total)