Starting phenix.real_space_refine on Thu Sep 18 16:55:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b61_44234/09_2025/9b61_44234.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b61_44234/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9b61_44234/09_2025/9b61_44234.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b61_44234/09_2025/9b61_44234.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b61_44234/09_2025/9b61_44234.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b61_44234/09_2025/9b61_44234.map" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ARG:plan': 5, 'PHE:plan': 1, 'ASP:plan': 1, 'GLU: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: {'ARG:plan': 5, 'PHE:plan': 1, 'ASP:plan': 1, 'GLU: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: {'ARG:plan': 4, 'PHE:plan': 1, '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: {'ARG:plan': 5, 'GLU:plan': 2, '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: {'ARG:plan': 5, 'GLU:plan': 2, '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: 5.41, per 1000 atoms: 0.29 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: 1.80 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.63 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: 3.16 Time building geometry restraints manager: 2.37 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: 3.400 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: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.030 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.310 ------------------------------------------------------------------------------- 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 : 11.06 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.021 0.001 ARG C 819 TYR 0.022 0.001 TYR B 673 PHE 0.022 0.001 PHE E 73 TRP 0.042 0.002 TRP A 671 HIS 0.008 0.001 HIS F 132 Details of bonding type rmsd covalent geometry : bond 0.00511 (18863) covalent geometry : angle 0.80143 (25523) SS BOND : bond 0.00342 ( 12) SS BOND : angle 0.98902 ( 24) hydrogen bonds : bond 0.19805 ( 1132) hydrogen bonds : angle 6.16307 ( 3349) *********************** 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 : 0.696 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: 0.5421 time to fit residues: 219.6989 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 : 0.717 ------------------------------------------------------------------------------- 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 216 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.0050 chunk 103 optimal weight: 0.0010 chunk 200 optimal weight: 7.9990 overall best weight: 0.9804 ------------------------------------------------------------------------------- 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 = 0.4782 r_free = 0.4782 target = 0.223359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.165336 restraints weight = 59079.074| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 7.00 r_work: 0.3430 rms_B_bonded: 5.37 restraints_weight: 2.0000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3347 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3347 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18875 Z= 0.141 Angle : 0.600 10.602 25547 Z= 0.302 Chirality : 0.040 0.158 2883 Planarity : 0.004 0.051 3153 Dihedral : 5.853 59.796 2641 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.34 % Allowed : 29.99 % Favored : 65.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.18), residues: 2343 helix: 2.31 (0.14), residues: 1372 sheet: -1.54 (0.40), residues: 146 loop : -0.71 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 819 TYR 0.021 0.001 TYR C 424 PHE 0.015 0.001 PHE E 73 TRP 0.024 0.002 TRP D 766 HIS 0.003 0.001 HIS E 199 Details of bonding type rmsd covalent geometry : bond 0.00311 (18863) covalent geometry : angle 0.59940 (25523) SS BOND : bond 0.00858 ( 12) SS BOND : angle 1.17769 ( 24) hydrogen bonds : bond 0.04421 ( 1132) hydrogen bonds : angle 4.18134 ( 3349) *********************** 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 412 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 331 time to evaluate : 0.542 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: 0.7829 (mtp180) cc_final: 0.7590 (mtp180) REVERT: H 192 MET cc_start: 0.7552 (OUTLIER) cc_final: 0.7319 (mtt) REVERT: H 204 ARG cc_start: 0.7401 (mmp-170) cc_final: 0.7186 (mmp-170) REVERT: F 31 ASP cc_start: 0.8082 (m-30) cc_final: 0.7633 (m-30) REVERT: F 134 ILE cc_start: 0.7459 (pp) cc_final: 0.7243 (pt) REVERT: F 196 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8311 (tt) REVERT: F 204 ARG cc_start: 0.7489 (mmp-170) cc_final: 0.6968 (tpm170) REVERT: C 425 CYS cc_start: 0.8321 (p) cc_final: 0.8101 (p) REVERT: C 569 ASN cc_start: 0.7011 (p0) cc_final: 0.6649 (p0) REVERT: C 674 MET cc_start: 0.8128 (pmm) cc_final: 0.7921 (pmm) REVERT: C 694 ARG cc_start: 0.8624 (mtp85) cc_final: 0.8261 (mmt-90) REVERT: B 660 ARG cc_start: 0.7732 (mtt-85) cc_final: 0.7369 (mpt-90) REVERT: B 674 MET cc_start: 0.7950 (mpp) cc_final: 0.7621 (pmm) REVERT: B 694 ARG cc_start: 0.7918 (mpp80) cc_final: 0.7625 (ptt-90) REVERT: B 708 MET cc_start: 0.8334 (tpp) cc_final: 0.8127 (tpp) REVERT: D 496 MET cc_start: 0.8041 (ptp) cc_final: 0.7006 (mtm) REVERT: D 678 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7350 (mp0) REVERT: E 6 ARG cc_start: 0.8316 (mmm-85) cc_final: 0.7810 (mmm160) REVERT: E 129 LYS cc_start: 0.8311 (mmmm) cc_final: 0.8016 (mppt) REVERT: E 175 SER cc_start: 0.7464 (OUTLIER) cc_final: 0.7185 (t) REVERT: G 82 HIS cc_start: 0.6651 (p-80) cc_final: 0.6425 (m-70) outliers start: 81 outliers final: 28 residues processed: 382 average time/residue: 0.5883 time to fit residues: 250.3090 Evaluate side-chains 335 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 304 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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 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 703 LEU 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 740 SER Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 79 GLN 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 150 optimal weight: 8.9990 chunk 162 optimal weight: 20.0000 chunk 74 optimal weight: 0.9990 chunk 168 optimal weight: 6.9990 chunk 199 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 231 optimal weight: 0.9980 chunk 217 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 177 optimal weight: 2.9990 chunk 206 optimal weight: 8.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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** 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 = 0.221719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.165623 restraints weight = 57996.368| |-----------------------------------------------------------------------------| r_work (start): 0.4123 rms_B_bonded: 7.10 r_work: 0.3388 rms_B_bonded: 5.49 restraints_weight: 2.0000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3335 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3335 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18875 Z= 0.152 Angle : 0.592 10.510 25547 Z= 0.296 Chirality : 0.040 0.158 2883 Planarity : 0.004 0.044 3153 Dihedral : 4.448 58.024 2575 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.77 % Allowed : 30.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.18), residues: 2343 helix: 2.29 (0.14), residues: 1375 sheet: -1.36 (0.38), residues: 155 loop : -0.79 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 660 TYR 0.017 0.001 TYR C 424 PHE 0.017 0.001 PHE C 584 TRP 0.021 0.002 TRP C 671 HIS 0.004 0.001 HIS E 205 Details of bonding type rmsd covalent geometry : bond 0.00356 (18863) covalent geometry : angle 0.59053 (25523) SS BOND : bond 0.00395 ( 12) SS BOND : angle 1.56729 ( 24) hydrogen bonds : bond 0.04370 ( 1132) hydrogen bonds : angle 4.06473 ( 3349) *********************** 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 399 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 328 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 192 MET cc_start: 0.7602 (OUTLIER) cc_final: 0.7366 (mtt) REVERT: H 204 ARG cc_start: 0.7350 (mmp-170) cc_final: 0.7131 (mmp-170) REVERT: F 31 ASP cc_start: 0.8081 (m-30) cc_final: 0.7763 (m-30) REVERT: F 149 ASN cc_start: 0.8374 (t0) cc_final: 0.8171 (t0) REVERT: F 196 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8324 (tt) REVERT: F 204 ARG cc_start: 0.7526 (mmp-170) cc_final: 0.7009 (tpm170) REVERT: C 408 MET cc_start: 0.6341 (tpt) cc_final: 0.5810 (tpp) REVERT: C 425 CYS cc_start: 0.8253 (p) cc_final: 0.8016 (p) REVERT: C 569 ASN cc_start: 0.7039 (p0) cc_final: 0.6702 (p0) REVERT: C 627 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7996 (mp0) REVERT: B 671 TRP cc_start: 0.8224 (t-100) cc_final: 0.7999 (t-100) REVERT: B 694 ARG cc_start: 0.7886 (mpp80) cc_final: 0.7566 (ptt-90) REVERT: B 708 MET cc_start: 0.8494 (tpp) cc_final: 0.8284 (tpp) REVERT: B 714 GLN cc_start: 0.6938 (OUTLIER) cc_final: 0.6696 (mm-40) REVERT: A 713 GLU cc_start: 0.8712 (pp20) cc_final: 0.8488 (pp20) REVERT: A 767 TRP cc_start: 0.7184 (m-90) cc_final: 0.6868 (m-90) REVERT: D 545 ARG cc_start: 0.8739 (mtt180) cc_final: 0.8412 (mmt90) REVERT: E 6 ARG cc_start: 0.8340 (mmm-85) cc_final: 0.7839 (mmm160) REVERT: E 129 LYS cc_start: 0.8268 (mmmm) cc_final: 0.7989 (mppt) REVERT: G 11 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8019 (tm) REVERT: G 78 LYS cc_start: 0.7442 (ttpt) cc_final: 0.7185 (ptpt) REVERT: G 206 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7636 (ttpp) outliers start: 71 outliers final: 40 residues processed: 371 average time/residue: 0.5532 time to fit residues: 230.3181 Evaluate side-chains 353 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 307 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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 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 86 ASP Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 714 GLN Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain A residue 435 HIS Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain G residue 206 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 232 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 173 optimal weight: 0.6980 chunk 90 optimal weight: 0.4980 chunk 153 optimal weight: 5.9990 chunk 129 optimal weight: 0.6980 chunk 157 optimal weight: 30.0000 chunk 48 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 8 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 726 ASN A 709 ASN A 714 GLN D 764 ASN A ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.223123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.165045 restraints weight = 68230.185| |-----------------------------------------------------------------------------| r_work (start): 0.4104 rms_B_bonded: 7.94 r_work: 0.3420 rms_B_bonded: 5.58 restraints_weight: 2.0000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3365 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3365 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18875 Z= 0.118 Angle : 0.572 10.842 25547 Z= 0.283 Chirality : 0.039 0.153 2883 Planarity : 0.003 0.048 3153 Dihedral : 4.121 57.355 2569 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 4.08 % Allowed : 30.82 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.18), residues: 2343 helix: 2.43 (0.14), residues: 1372 sheet: -1.28 (0.38), residues: 153 loop : -0.77 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 660 TYR 0.016 0.001 TYR C 424 PHE 0.016 0.001 PHE E 73 TRP 0.023 0.001 TRP C 671 HIS 0.007 0.001 HIS F 205 Details of bonding type rmsd covalent geometry : bond 0.00267 (18863) covalent geometry : angle 0.57208 (25523) SS BOND : bond 0.00271 ( 12) SS BOND : angle 0.91424 ( 24) hydrogen bonds : bond 0.03793 ( 1132) hydrogen bonds : angle 3.88104 ( 3349) *********************** 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 403 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 327 time to evaluate : 0.647 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: 0.1659 (OUTLIER) cc_final: 0.1257 (p0) REVERT: H 192 MET cc_start: 0.7537 (OUTLIER) cc_final: 0.7310 (mtt) REVERT: H 204 ARG cc_start: 0.7345 (mmp-170) cc_final: 0.7101 (mmp-170) REVERT: F 31 ASP cc_start: 0.8181 (m-30) cc_final: 0.7804 (m-30) REVERT: F 65 ARG cc_start: 0.7575 (pmt170) cc_final: 0.7268 (ptt-90) REVERT: F 78 LYS cc_start: 0.8544 (ptmt) cc_final: 0.7860 (pttm) REVERT: F 149 ASN cc_start: 0.8388 (t0) cc_final: 0.8182 (t0) REVERT: F 196 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8273 (tt) REVERT: F 204 ARG cc_start: 0.7503 (mmp-170) cc_final: 0.6904 (tpm170) REVERT: C 408 MET cc_start: 0.6243 (tpt) cc_final: 0.5587 (tpp) REVERT: C 627 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.8006 (mp0) REVERT: B 694 ARG cc_start: 0.7967 (mpp80) cc_final: 0.7599 (ptt-90) REVERT: B 708 MET cc_start: 0.8526 (tpp) cc_final: 0.8187 (tpp) REVERT: A 713 GLU cc_start: 0.8781 (pp20) cc_final: 0.8497 (pp20) REVERT: A 767 TRP cc_start: 0.7126 (m-90) cc_final: 0.6736 (m-90) REVERT: D 496 MET cc_start: 0.8100 (ptp) cc_final: 0.7102 (mtm) REVERT: D 545 ARG cc_start: 0.8773 (mtt180) cc_final: 0.8442 (mmt90) REVERT: D 660 ARG cc_start: 0.7967 (ttm110) cc_final: 0.7579 (mtm-85) REVERT: D 678 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7448 (mp0) REVERT: E 6 ARG cc_start: 0.8184 (mmm-85) cc_final: 0.7852 (mmm160) REVERT: E 129 LYS cc_start: 0.8336 (mmmm) cc_final: 0.8066 (mppt) REVERT: E 196 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8406 (tt) REVERT: G 5 ASP cc_start: 0.7410 (t70) cc_final: 0.7206 (t70) REVERT: G 11 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8009 (tm) REVERT: G 156 TYR cc_start: 0.8791 (t80) cc_final: 0.8417 (t80) outliers start: 76 outliers final: 35 residues processed: 375 average time/residue: 0.5504 time to fit residues: 231.7479 Evaluate side-chains 344 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 303 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 200 MET Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain A residue 435 HIS Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain D residue 740 SER Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 28 VAL 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 192 MET Chi-restraints excluded: chain G residue 195 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 57 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 204 optimal weight: 5.9990 chunk 133 optimal weight: 0.8980 chunk 125 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 107 optimal weight: 20.0000 chunk 94 optimal weight: 0.4980 chunk 8 optimal weight: 10.0000 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 709 ASN B 726 ASN A 709 ASN A 714 GLN ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4761 r_free = 0.4761 target = 0.220975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.161009 restraints weight = 63726.452| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 7.76 r_work: 0.3379 rms_B_bonded: 5.44 restraints_weight: 2.0000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3320 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3320 r_free = 0.3320 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3320 r_free = 0.3320 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3320 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18875 Z= 0.157 Angle : 0.609 11.199 25547 Z= 0.301 Chirality : 0.040 0.155 2883 Planarity : 0.004 0.051 3153 Dihedral : 3.842 55.847 2564 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.19 % Allowed : 31.18 % Favored : 64.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.18), residues: 2343 helix: 2.34 (0.14), residues: 1365 sheet: -1.23 (0.37), residues: 164 loop : -0.79 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 660 TYR 0.017 0.001 TYR B 549 PHE 0.018 0.001 PHE C 584 TRP 0.024 0.002 TRP C 671 HIS 0.008 0.001 HIS F 205 Details of bonding type rmsd covalent geometry : bond 0.00373 (18863) covalent geometry : angle 0.60704 (25523) SS BOND : bond 0.00585 ( 12) SS BOND : angle 1.82869 ( 24) hydrogen bonds : bond 0.04155 ( 1132) hydrogen bonds : angle 3.94642 ( 3349) *********************** 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 395 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 317 time to evaluate : 0.660 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: 0.1756 (OUTLIER) cc_final: 0.1340 (p0) REVERT: H 192 MET cc_start: 0.7599 (OUTLIER) cc_final: 0.7376 (mtt) REVERT: H 204 ARG cc_start: 0.7384 (mmp-170) cc_final: 0.7131 (mmp-170) REVERT: F 31 ASP cc_start: 0.8181 (m-30) cc_final: 0.7811 (m-30) REVERT: F 65 ARG cc_start: 0.7629 (pmt170) cc_final: 0.7267 (ptt-90) REVERT: F 78 LYS cc_start: 0.8579 (ptmt) cc_final: 0.7834 (pttm) REVERT: F 196 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8273 (tt) REVERT: F 204 ARG cc_start: 0.7463 (mmp-170) cc_final: 0.6852 (tpm170) REVERT: C 408 MET cc_start: 0.6378 (tpt) cc_final: 0.5741 (tpp) REVERT: C 627 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.8029 (mp0) REVERT: B 407 MET cc_start: 0.7177 (pmm) cc_final: 0.6947 (pmm) REVERT: B 708 MET cc_start: 0.8621 (tpp) cc_final: 0.8200 (tpp) REVERT: B 782 GLU cc_start: 0.6113 (pp20) cc_final: 0.5752 (pm20) REVERT: A 713 GLU cc_start: 0.8821 (pp20) cc_final: 0.8558 (pp20) REVERT: A 764 ASN cc_start: 0.8559 (p0) cc_final: 0.8357 (p0) REVERT: A 767 TRP cc_start: 0.7150 (m-90) cc_final: 0.6768 (m-90) REVERT: D 407 MET cc_start: 0.6888 (mmt) cc_final: 0.6488 (mpm) REVERT: D 496 MET cc_start: 0.7969 (ptp) cc_final: 0.7021 (mtm) REVERT: D 545 ARG cc_start: 0.8752 (mtt180) cc_final: 0.8551 (mmt90) REVERT: D 629 MET cc_start: 0.6876 (tpt) cc_final: 0.6665 (tpt) REVERT: D 660 ARG cc_start: 0.8014 (ttm110) cc_final: 0.7791 (ttm110) REVERT: E 6 ARG cc_start: 0.8293 (mmm-85) cc_final: 0.7873 (mmm160) REVERT: E 129 LYS cc_start: 0.8299 (mmmm) cc_final: 0.8040 (mppt) REVERT: E 196 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8415 (tt) REVERT: G 5 ASP cc_start: 0.7381 (t70) cc_final: 0.7160 (t70) REVERT: G 11 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8010 (tm) REVERT: G 117 MET cc_start: 0.7674 (mmp) cc_final: 0.7416 (mtm) REVERT: G 156 TYR cc_start: 0.8760 (t80) cc_final: 0.8439 (t80) REVERT: G 207 GLN cc_start: 0.7478 (OUTLIER) cc_final: 0.7135 (pt0) outliers start: 78 outliers final: 51 residues processed: 363 average time/residue: 0.5886 time to fit residues: 239.4925 Evaluate side-chains 367 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 309 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 200 MET Chi-restraints excluded: chain 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 80 ILE Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 186 SER 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 435 HIS Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 740 SER Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 24 MET 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 67 CYS Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 200 MET Chi-restraints excluded: chain G residue 207 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 221 optimal weight: 7.9990 chunk 12 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 173 optimal weight: 0.9980 chunk 40 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 158 optimal weight: 9.9990 chunk 191 optimal weight: 4.9990 chunk 210 optimal weight: 0.6980 chunk 230 optimal weight: 0.6980 chunk 84 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 149 ASN B 726 ASN A 709 ASN A 714 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4772 r_free = 0.4772 target = 0.222383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.162170 restraints weight = 57629.894| |-----------------------------------------------------------------------------| r_work (start): 0.4098 rms_B_bonded: 7.10 r_work: 0.3417 rms_B_bonded: 5.24 restraints_weight: 2.0000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3369 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3369 r_free = 0.3369 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3369 r_free = 0.3369 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3369 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1950 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= 0.122 Angle : 0.590 11.142 25547 Z= 0.289 Chirality : 0.039 0.155 2883 Planarity : 0.004 0.067 3153 Dihedral : 3.731 54.868 2563 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.67 % Allowed : 31.90 % Favored : 64.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.18), residues: 2343 helix: 2.39 (0.14), residues: 1377 sheet: -1.29 (0.36), residues: 174 loop : -0.75 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 819 TYR 0.014 0.001 TYR B 549 PHE 0.011 0.001 PHE C 584 TRP 0.027 0.001 TRP C 671 HIS 0.007 0.001 HIS F 205 Details of bonding type rmsd covalent geometry : bond 0.00280 (18863) covalent geometry : angle 0.58891 (25523) SS BOND : bond 0.00302 ( 12) SS BOND : angle 1.08346 ( 24) hydrogen bonds : bond 0.03727 ( 1132) hydrogen bonds : angle 3.83995 ( 3349) *********************** 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: 68 poor density : 316 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 ASP cc_start: 0.1902 (OUTLIER) cc_final: 0.1481 (p0) REVERT: H 192 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.7275 (mtt) REVERT: H 204 ARG cc_start: 0.7378 (mmp-170) cc_final: 0.7094 (mmp-170) REVERT: F 31 ASP cc_start: 0.8117 (m-30) cc_final: 0.7907 (m-30) REVERT: F 78 LYS cc_start: 0.8490 (ptmt) cc_final: 0.7759 (pttm) REVERT: F 196 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8268 (tt) REVERT: F 204 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.6837 (tpm170) REVERT: F 206 LYS cc_start: 0.6467 (tmmt) cc_final: 0.5921 (mtpp) REVERT: C 408 MET cc_start: 0.6378 (tpt) cc_final: 0.5572 (tpp) REVERT: C 627 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7956 (mp0) REVERT: C 673 TYR cc_start: 0.8036 (t80) cc_final: 0.7771 (t80) REVERT: C 674 MET cc_start: 0.8068 (pmm) cc_final: 0.7821 (pmm) REVERT: B 694 ARG cc_start: 0.7684 (mpp80) cc_final: 0.7092 (tpp-160) REVERT: B 708 MET cc_start: 0.8650 (tpp) cc_final: 0.8212 (tpp) REVERT: B 782 GLU cc_start: 0.6057 (pp20) cc_final: 0.5755 (pm20) REVERT: A 713 GLU cc_start: 0.8813 (pp20) cc_final: 0.8471 (pp20) REVERT: A 767 TRP cc_start: 0.7145 (m-90) cc_final: 0.6721 (m-90) REVERT: D 496 MET cc_start: 0.8000 (ptp) cc_final: 0.7005 (mtm) REVERT: D 594 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.8750 (mtp85) REVERT: D 629 MET cc_start: 0.6893 (tpt) cc_final: 0.6657 (tpt) REVERT: D 660 ARG cc_start: 0.8052 (ttm110) cc_final: 0.7810 (ttm110) REVERT: D 678 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7596 (mp0) REVERT: E 6 ARG cc_start: 0.8288 (mmm-85) cc_final: 0.7862 (mmm160) REVERT: E 129 LYS cc_start: 0.8279 (mmmm) cc_final: 0.8048 (mppt) REVERT: E 196 LEU cc_start: 0.8579 (tp) cc_final: 0.8345 (tt) REVERT: G 5 ASP cc_start: 0.7384 (t70) cc_final: 0.7155 (t70) REVERT: G 11 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7992 (tm) REVERT: G 156 TYR cc_start: 0.8684 (t80) cc_final: 0.8466 (t80) REVERT: G 185 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7174 (mm) REVERT: G 207 GLN cc_start: 0.7489 (OUTLIER) cc_final: 0.7058 (pt0) outliers start: 68 outliers final: 44 residues processed: 357 average time/residue: 0.5745 time to fit residues: 230.3970 Evaluate side-chains 353 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 300 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 200 MET Chi-restraints excluded: chain 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 66 THR Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 204 ARG Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 783 LYS 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 811 LEU Chi-restraints excluded: chain D residue 594 ARG Chi-restraints excluded: chain D residue 740 SER Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 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 11 LEU Chi-restraints excluded: chain G residue 28 VAL 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 Chi-restraints excluded: chain G residue 207 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 109 optimal weight: 0.9990 chunk 142 optimal weight: 10.0000 chunk 76 optimal weight: 20.0000 chunk 21 optimal weight: 0.5980 chunk 157 optimal weight: 30.0000 chunk 13 optimal weight: 1.9990 chunk 192 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 77 optimal weight: 0.0870 chunk 56 optimal weight: 0.8980 chunk 191 optimal weight: 3.9990 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 709 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 = 0.4775 r_free = 0.4775 target = 0.222535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.148854 restraints weight = 73594.087| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 5.82 r_work: 0.3434 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3404 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3404 r_free = 0.3404 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3404 r_free = 0.3404 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3404 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18875 Z= 0.127 Angle : 0.607 10.909 25547 Z= 0.296 Chirality : 0.040 0.238 2883 Planarity : 0.004 0.071 3153 Dihedral : 3.769 54.050 2563 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.98 % Allowed : 31.59 % Favored : 64.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.18), residues: 2343 helix: 2.45 (0.14), residues: 1365 sheet: -1.24 (0.37), residues: 174 loop : -0.76 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 819 TYR 0.014 0.001 TYR D 673 PHE 0.012 0.001 PHE C 584 TRP 0.032 0.001 TRP A 671 HIS 0.007 0.001 HIS F 205 Details of bonding type rmsd covalent geometry : bond 0.00294 (18863) covalent geometry : angle 0.60546 (25523) SS BOND : bond 0.00322 ( 12) SS BOND : angle 1.45615 ( 24) hydrogen bonds : bond 0.03736 ( 1132) hydrogen bonds : angle 3.83236 ( 3349) *********************** 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 382 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 308 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 ASP cc_start: 0.1974 (OUTLIER) cc_final: 0.1547 (p0) REVERT: H 192 MET cc_start: 0.7409 (OUTLIER) cc_final: 0.7177 (mtt) REVERT: H 204 ARG cc_start: 0.7333 (mmp-170) cc_final: 0.7009 (mmp-170) REVERT: F 31 ASP cc_start: 0.8002 (m-30) cc_final: 0.7801 (m-30) REVERT: F 78 LYS cc_start: 0.8537 (ptmt) cc_final: 0.7794 (pttm) REVERT: F 204 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.6878 (tpm170) REVERT: C 408 MET cc_start: 0.6399 (tpt) cc_final: 0.5569 (tpp) REVERT: C 463 MET cc_start: 0.8514 (tpt) cc_final: 0.8285 (mmm) REVERT: C 627 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7860 (mp0) REVERT: C 673 TYR cc_start: 0.8025 (t80) cc_final: 0.7741 (t80) REVERT: B 497 SER cc_start: 0.8827 (m) cc_final: 0.8602 (t) REVERT: B 674 MET cc_start: 0.7285 (pmm) cc_final: 0.7002 (pmm) REVERT: B 694 ARG cc_start: 0.7724 (mpp80) cc_final: 0.7159 (tpp-160) REVERT: B 782 GLU cc_start: 0.5960 (pp20) cc_final: 0.5725 (pm20) REVERT: A 674 MET cc_start: 0.7457 (pmm) cc_final: 0.6606 (pmm) REVERT: A 713 GLU cc_start: 0.8810 (pp20) cc_final: 0.8467 (pp20) REVERT: A 767 TRP cc_start: 0.7048 (m-90) cc_final: 0.6592 (m-90) REVERT: D 496 MET cc_start: 0.8051 (ptp) cc_final: 0.6949 (mtm) REVERT: D 594 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.8720 (mtp85) REVERT: D 660 ARG cc_start: 0.8148 (ttm110) cc_final: 0.7828 (mtm-85) REVERT: D 678 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7434 (mp0) REVERT: E 6 ARG cc_start: 0.8359 (mmm-85) cc_final: 0.7929 (mmm160) REVERT: E 196 LEU cc_start: 0.8422 (tp) cc_final: 0.8180 (tt) REVERT: E 200 MET cc_start: 0.7438 (mtm) cc_final: 0.7156 (mtp) REVERT: E 206 LYS cc_start: 0.8054 (ptmt) cc_final: 0.7810 (ttmm) REVERT: G 5 ASP cc_start: 0.7422 (t70) cc_final: 0.7196 (t70) REVERT: G 11 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7996 (tm) REVERT: G 78 LYS cc_start: 0.7289 (ptpt) cc_final: 0.7042 (pttt) REVERT: G 156 TYR cc_start: 0.8651 (t80) cc_final: 0.8404 (t80) REVERT: G 185 LEU cc_start: 0.7262 (OUTLIER) cc_final: 0.7044 (mm) REVERT: G 207 GLN cc_start: 0.7479 (OUTLIER) cc_final: 0.7057 (pt0) outliers start: 74 outliers final: 44 residues processed: 355 average time/residue: 0.5550 time to fit residues: 221.7433 Evaluate side-chains 352 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 300 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 200 MET Chi-restraints excluded: chain 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 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 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 195 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 28 VAL 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 Chi-restraints excluded: chain G residue 207 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 133 optimal weight: 0.7980 chunk 183 optimal weight: 0.6980 chunk 203 optimal weight: 10.0000 chunk 127 optimal weight: 0.2980 chunk 6 optimal weight: 0.0060 chunk 164 optimal weight: 0.9990 chunk 54 optimal weight: 0.3980 chunk 168 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 172 optimal weight: 0.1980 chunk 55 optimal weight: 0.6980 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 709 ASN C 747 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.224819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.166700 restraints weight = 59594.487| |-----------------------------------------------------------------------------| r_work (start): 0.4095 rms_B_bonded: 7.02 r_work: 0.3404 rms_B_bonded: 5.46 restraints_weight: 2.0000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3410 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3410 r_free = 0.3410 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3410 r_free = 0.3410 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3410 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18875 Z= 0.111 Angle : 0.615 11.395 25547 Z= 0.296 Chirality : 0.039 0.149 2883 Planarity : 0.004 0.070 3153 Dihedral : 3.525 32.413 2561 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.84 % Allowed : 32.89 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.18), residues: 2343 helix: 2.59 (0.14), residues: 1367 sheet: -1.23 (0.37), residues: 174 loop : -0.72 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 819 TYR 0.019 0.001 TYR B 549 PHE 0.010 0.001 PHE H 107 TRP 0.037 0.001 TRP A 671 HIS 0.007 0.001 HIS F 205 Details of bonding type rmsd covalent geometry : bond 0.00249 (18863) covalent geometry : angle 0.61433 (25523) SS BOND : bond 0.00241 ( 12) SS BOND : angle 0.91375 ( 24) hydrogen bonds : bond 0.03334 ( 1132) hydrogen bonds : angle 3.75125 ( 3349) *********************** 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 366 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 314 time to evaluate : 0.641 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 79 GLN cc_start: 0.7719 (pp30) cc_final: 0.7028 (mt0) REVERT: H 86 ASP cc_start: 0.2058 (OUTLIER) cc_final: 0.1646 (p0) REVERT: H 192 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.7185 (mtt) REVERT: H 204 ARG cc_start: 0.7342 (mmp-170) cc_final: 0.6997 (mmp-170) REVERT: F 78 LYS cc_start: 0.8568 (ptmt) cc_final: 0.7822 (pttm) REVERT: F 149 ASN cc_start: 0.8202 (t0) cc_final: 0.7698 (t0) REVERT: F 204 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.6817 (tpm170) REVERT: F 206 LYS cc_start: 0.6491 (tmmt) cc_final: 0.5959 (mtpp) REVERT: C 673 TYR cc_start: 0.7967 (t80) cc_final: 0.7571 (t80) REVERT: C 819 ARG cc_start: 0.6968 (ttp80) cc_final: 0.6424 (tpp80) REVERT: B 463 MET cc_start: 0.7576 (tpt) cc_final: 0.7284 (tpt) REVERT: B 497 SER cc_start: 0.8854 (m) cc_final: 0.8652 (t) REVERT: B 670 MET cc_start: 0.8260 (ppp) cc_final: 0.8053 (pmm) REVERT: B 674 MET cc_start: 0.7438 (pmm) cc_final: 0.7231 (pmm) REVERT: B 694 ARG cc_start: 0.7831 (mpp80) cc_final: 0.7429 (tpp-160) REVERT: B 708 MET cc_start: 0.8638 (tpp) cc_final: 0.8188 (tpp) REVERT: A 671 TRP cc_start: 0.8351 (t-100) cc_final: 0.8018 (t60) REVERT: A 713 GLU cc_start: 0.8846 (pp20) cc_final: 0.8493 (pp20) REVERT: A 767 TRP cc_start: 0.6861 (m-90) cc_final: 0.6438 (m-90) REVERT: D 420 ARG cc_start: 0.8874 (pmm-80) cc_final: 0.8648 (pmm-80) REVERT: D 496 MET cc_start: 0.8041 (ptp) cc_final: 0.7004 (mtm) REVERT: E 6 ARG cc_start: 0.8295 (mmm-85) cc_final: 0.7928 (mmm160) REVERT: E 30 THR cc_start: 0.6580 (m) cc_final: 0.6284 (p) REVERT: E 99 ARG cc_start: 0.7090 (mpp80) cc_final: 0.6359 (ptm160) REVERT: E 196 LEU cc_start: 0.8534 (tp) cc_final: 0.8323 (tt) REVERT: E 203 ASP cc_start: 0.8279 (t0) cc_final: 0.7985 (m-30) REVERT: E 206 LYS cc_start: 0.8023 (ptmt) cc_final: 0.7757 (ttpt) REVERT: G 5 ASP cc_start: 0.7484 (t70) cc_final: 0.7228 (t70) REVERT: G 11 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7933 (tm) REVERT: G 37 ARG cc_start: 0.7905 (mtt-85) cc_final: 0.7676 (mtp-110) REVERT: G 156 TYR cc_start: 0.8646 (t80) cc_final: 0.8441 (t80) REVERT: G 207 GLN cc_start: 0.7409 (OUTLIER) cc_final: 0.6987 (pt0) outliers start: 52 outliers final: 29 residues processed: 345 average time/residue: 0.5452 time to fit residues: 211.6029 Evaluate side-chains 336 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 302 time to evaluate : 0.599 ------------------------------------------------------------------------------- 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 130 THR Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 205 HIS 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 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 B residue 592 SER Chi-restraints excluded: chain B residue 812 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 746 VAL Chi-restraints excluded: chain D residue 592 SER 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 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain G residue 11 LEU 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 195 VAL Chi-restraints excluded: chain G residue 200 MET Chi-restraints excluded: chain G residue 207 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 65 optimal weight: 9.9990 chunk 166 optimal weight: 6.9990 chunk 229 optimal weight: 0.6980 chunk 81 optimal weight: 20.0000 chunk 74 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 190 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 29 optimal weight: 0.2980 chunk 71 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 726 ASN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 ASN A 714 GLN ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4780 r_free = 0.4780 target = 0.223441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.148971 restraints weight = 68826.966| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 5.69 r_work: 0.3453 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3441 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3441 r_free = 0.3441 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3441 r_free = 0.3441 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3441 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2310 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= 0.124 Angle : 0.643 13.625 25547 Z= 0.306 Chirality : 0.040 0.247 2883 Planarity : 0.004 0.070 3153 Dihedral : 3.547 32.229 2561 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.53 % Allowed : 33.71 % Favored : 63.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.18), residues: 2343 helix: 2.53 (0.14), residues: 1367 sheet: -1.20 (0.37), residues: 174 loop : -0.72 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 819 TYR 0.019 0.001 TYR B 549 PHE 0.011 0.001 PHE G 97 TRP 0.030 0.001 TRP A 671 HIS 0.007 0.001 HIS F 205 Details of bonding type rmsd covalent geometry : bond 0.00287 (18863) covalent geometry : angle 0.64243 (25523) SS BOND : bond 0.00263 ( 12) SS BOND : angle 0.87912 ( 24) hydrogen bonds : bond 0.03564 ( 1132) hydrogen bonds : angle 3.77710 ( 3349) *********************** 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 350 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 304 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 ASP cc_start: 0.1985 (OUTLIER) cc_final: 0.1571 (p0) REVERT: H 192 MET cc_start: 0.7363 (OUTLIER) cc_final: 0.7140 (mtt) REVERT: H 204 ARG cc_start: 0.7312 (mmp-170) cc_final: 0.6969 (mmp-170) REVERT: F 65 ARG cc_start: 0.7190 (OUTLIER) cc_final: 0.6966 (pmt170) REVERT: F 78 LYS cc_start: 0.8544 (ptmt) cc_final: 0.7786 (pttm) REVERT: F 149 ASN cc_start: 0.8173 (t0) cc_final: 0.7706 (t0) REVERT: F 204 ARG cc_start: 0.7436 (OUTLIER) cc_final: 0.6881 (tpm170) REVERT: F 206 LYS cc_start: 0.6571 (tmmt) cc_final: 0.5975 (mtpp) REVERT: C 673 TYR cc_start: 0.7998 (t80) cc_final: 0.7618 (t80) REVERT: C 819 ARG cc_start: 0.6988 (ttp80) cc_final: 0.6449 (tpp80) REVERT: B 407 MET cc_start: 0.7112 (pmm) cc_final: 0.6747 (pmm) REVERT: B 463 MET cc_start: 0.7544 (tpt) cc_final: 0.7303 (tpt) REVERT: B 497 SER cc_start: 0.8886 (m) cc_final: 0.8679 (t) REVERT: B 670 MET cc_start: 0.8198 (ppp) cc_final: 0.7962 (pmm) REVERT: B 674 MET cc_start: 0.7538 (pmm) cc_final: 0.7334 (pmm) REVERT: B 694 ARG cc_start: 0.7830 (mpp80) cc_final: 0.7456 (tpp-160) REVERT: B 704 LEU cc_start: 0.7655 (tp) cc_final: 0.7347 (mt) REVERT: B 708 MET cc_start: 0.8667 (tpp) cc_final: 0.8318 (tpp) REVERT: B 783 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7507 (tptp) REVERT: A 713 GLU cc_start: 0.8849 (pp20) cc_final: 0.8471 (pp20) REVERT: A 767 TRP cc_start: 0.6911 (m-90) cc_final: 0.6494 (m-90) REVERT: D 420 ARG cc_start: 0.8834 (pmm-80) cc_final: 0.8622 (pmm-80) REVERT: D 441 LYS cc_start: 0.8726 (tmmm) cc_final: 0.8518 (tmmm) REVERT: D 508 GLN cc_start: 0.8645 (mp-120) cc_final: 0.8423 (mp10) REVERT: D 660 ARG cc_start: 0.8108 (ttm110) cc_final: 0.7548 (mtm-85) REVERT: E 6 ARG cc_start: 0.8310 (mmm-85) cc_final: 0.7958 (mmm160) REVERT: E 196 LEU cc_start: 0.8458 (tp) cc_final: 0.8240 (tt) REVERT: E 203 ASP cc_start: 0.8281 (t0) cc_final: 0.8020 (m-30) REVERT: G 5 ASP cc_start: 0.7480 (t70) cc_final: 0.7229 (t70) REVERT: G 11 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7969 (tm) REVERT: G 37 ARG cc_start: 0.7926 (mtt-85) cc_final: 0.7568 (mtp-110) REVERT: G 156 TYR cc_start: 0.8646 (t80) cc_final: 0.8388 (t80) outliers start: 46 outliers final: 30 residues processed: 332 average time/residue: 0.5796 time to fit residues: 215.7729 Evaluate side-chains 334 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 298 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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 130 THR Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 205 HIS Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 65 ARG Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 86 ASP 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 B residue 592 SER Chi-restraints excluded: chain B residue 783 LYS Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 740 SER Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain G residue 11 LEU 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 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 127 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 189 optimal weight: 5.9990 chunk 204 optimal weight: 30.0000 chunk 61 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 199 optimal weight: 0.7980 chunk 85 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 726 ASN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 ASN A 714 GLN ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 207 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.220367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.157178 restraints weight = 48856.820| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 5.57 r_work: 0.3344 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3305 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3305 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 18875 Z= 0.203 Angle : 0.688 12.448 25547 Z= 0.337 Chirality : 0.042 0.196 2883 Planarity : 0.004 0.073 3153 Dihedral : 3.773 33.889 2561 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.79 % Allowed : 33.66 % Favored : 63.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.18), residues: 2343 helix: 2.21 (0.14), residues: 1367 sheet: -1.12 (0.38), residues: 174 loop : -0.76 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 819 TYR 0.023 0.001 TYR B 549 PHE 0.036 0.002 PHE E 73 TRP 0.050 0.002 TRP A 671 HIS 0.007 0.001 HIS F 205 Details of bonding type rmsd covalent geometry : bond 0.00488 (18863) covalent geometry : angle 0.68756 (25523) SS BOND : bond 0.00442 ( 12) SS BOND : angle 1.07452 ( 24) hydrogen bonds : bond 0.04436 ( 1132) hydrogen bonds : angle 3.98705 ( 3349) ********************** 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 357 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 306 time to evaluate : 0.610 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: 0.8542 (p) cc_final: 0.7990 (t) REVERT: H 86 ASP cc_start: 0.2153 (OUTLIER) cc_final: 0.1721 (p0) REVERT: H 192 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.7367 (mtt) REVERT: H 204 ARG cc_start: 0.7330 (mmp-170) cc_final: 0.7024 (mmp-170) REVERT: F 78 LYS cc_start: 0.8482 (ptmt) cc_final: 0.7719 (pttm) REVERT: F 204 ARG cc_start: 0.7451 (OUTLIER) cc_final: 0.6899 (tpm170) REVERT: F 206 LYS cc_start: 0.6617 (tmmt) cc_final: 0.6018 (mtpp) REVERT: C 673 TYR cc_start: 0.8040 (t80) cc_final: 0.7676 (t80) REVERT: C 747 ASN cc_start: 0.8044 (m-40) cc_final: 0.7737 (t0) REVERT: B 407 MET cc_start: 0.7222 (pmm) cc_final: 0.6076 (pmm) REVERT: B 463 MET cc_start: 0.7582 (tpt) cc_final: 0.7325 (tpt) REVERT: B 670 MET cc_start: 0.8250 (ppp) cc_final: 0.8002 (pmm) REVERT: B 694 ARG cc_start: 0.7894 (mpp80) cc_final: 0.7447 (tpp-160) REVERT: B 704 LEU cc_start: 0.7702 (tp) cc_final: 0.7398 (mt) REVERT: B 708 MET cc_start: 0.8702 (tpp) cc_final: 0.8418 (tpp) REVERT: A 713 GLU cc_start: 0.8792 (pp20) cc_final: 0.8444 (pp20) REVERT: A 767 TRP cc_start: 0.7055 (m-90) cc_final: 0.6610 (m-90) REVERT: D 496 MET cc_start: 0.7911 (ptp) cc_final: 0.6943 (mtm) REVERT: D 508 GLN cc_start: 0.8728 (mp-120) cc_final: 0.8487 (mp10) REVERT: D 660 ARG cc_start: 0.8119 (ttm110) cc_final: 0.7560 (mtm-85) REVERT: D 692 ARG cc_start: 0.7938 (ppp80) cc_final: 0.7735 (tmm-80) REVERT: D 694 ARG cc_start: 0.8043 (mmm-85) cc_final: 0.7798 (mtt90) REVERT: D 812 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.8073 (mt) REVERT: E 6 ARG cc_start: 0.8312 (mmm-85) cc_final: 0.7907 (mmm160) REVERT: G 5 ASP cc_start: 0.7364 (t70) cc_final: 0.7108 (t70) REVERT: G 11 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7985 (tm) REVERT: G 37 ARG cc_start: 0.7936 (mtt-85) cc_final: 0.7702 (mtp-110) outliers start: 51 outliers final: 31 residues processed: 336 average time/residue: 0.5948 time to fit residues: 223.3794 Evaluate side-chains 334 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 298 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 205 HIS 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 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 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 746 VAL Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 740 SER Chi-restraints excluded: chain D residue 812 ILE Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain G residue 11 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 185 LEU 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 163 optimal weight: 0.9980 chunk 160 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 197 optimal weight: 0.6980 chunk 181 optimal weight: 8.9990 chunk 114 optimal weight: 0.7980 chunk 26 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 229 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 146 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 149 ASN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 ASN A 714 GLN ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4767 r_free = 0.4767 target = 0.221806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.162007 restraints weight = 54257.694| |-----------------------------------------------------------------------------| r_work (start): 0.4077 rms_B_bonded: 6.33 r_work: 0.3428 rms_B_bonded: 5.10 restraints_weight: 2.0000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3370 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3371 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2402 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= 0.140 Angle : 0.674 12.463 25547 Z= 0.325 Chirality : 0.040 0.162 2883 Planarity : 0.004 0.090 3153 Dihedral : 3.707 33.321 2561 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.38 % Allowed : 34.28 % Favored : 63.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.18), residues: 2343 helix: 2.31 (0.14), residues: 1365 sheet: -1.15 (0.38), residues: 174 loop : -0.78 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 819 TYR 0.022 0.001 TYR B 549 PHE 0.025 0.001 PHE E 73 TRP 0.046 0.002 TRP A 671 HIS 0.007 0.001 HIS F 205 Details of bonding type rmsd covalent geometry : bond 0.00330 (18863) covalent geometry : angle 0.67405 (25523) SS BOND : bond 0.00318 ( 12) SS BOND : angle 0.98957 ( 24) hydrogen bonds : bond 0.03901 ( 1132) hydrogen bonds : angle 3.89301 ( 3349) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9207.79 seconds wall clock time: 156 minutes 49.91 seconds (9409.91 seconds total)