Starting phenix.real_space_refine on Sun Jul 5 12:14:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lgq_23328/07_2026/7lgq_23328_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lgq_23328/07_2026/7lgq_23328.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lgq_23328/07_2026/7lgq_23328_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lgq_23328/07_2026/7lgq_23328_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lgq_23328/07_2026/7lgq_23328.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lgq_23328/07_2026/7lgq_23328.map" } resolution = 2.7 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= 0.006 sd= 0.122 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: 7 Type Number sf(0) Gaussians P 24 5.49 5 Mg 8 5.21 5 S 96 5.16 5 C 17052 2.51 5 N 4816 2.21 5 O 5320 1.98 5 H 402 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27718 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 6636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 868, 6636 Classifications: {'peptide': 868} Link IDs: {'PTRANS': 40, 'TRANS': 827} Chain breaks: 1 Chain: "B" Number of atoms: 6636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 868, 6636 Classifications: {'peptide': 868} Link IDs: {'PTRANS': 40, 'TRANS': 827} Chain breaks: 1 Chain: "C" Number of atoms: 6636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 868, 6636 Classifications: {'peptide': 868} Link IDs: {'PTRANS': 40, 'TRANS': 827} Chain breaks: 1 Chain: "D" Number of atoms: 6636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 868, 6636 Classifications: {'peptide': 868} Link IDs: {'PTRANS': 40, 'TRANS': 827} Chain breaks: 1 Chain: "E" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 113 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'7ID:plan-1': 1, '7ID:plan-2': 1, '7ID:plan-3': 1, '7ID:plan-4': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 111 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'7ID:plan-1': 1, '7ID:plan-2': 1, '7ID:plan-3': 1, '7ID:plan-4': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "G" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 111 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'7ID:plan-1': 1, '7ID:plan-2': 1, '7ID:plan-3': 1, '7ID:plan-4': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "H" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 111 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'7ID:plan-1': 1, '7ID:plan-2': 1, '7ID:plan-3': 1, '7ID:plan-4': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "I" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'7ID:plan-4': 3} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'7ID:plan-4': 3} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'7ID:plan-4': 3} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'7ID:plan-4': 3} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 6.20, per 1000 atoms: 0.22 Number of scatterers: 27718 At special positions: 0 Unit cell: (135.945, 141.075, 147.915, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 96 16.00 P 24 15.00 Mg 8 11.99 O 5320 8.00 N 4816 7.00 C 17052 6.00 H 402 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.96 Conformation dependent library (CDL) restraints added in 1.1 seconds 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6368 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 28 sheets defined 38.5% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 44 through 51 Processing helix chain 'A' and resid 79 through 91 Processing helix chain 'A' and resid 118 through 136 Processing helix chain 'A' and resid 144 through 161 removed outlier: 4.358A pdb=" N ASP A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 177 Processing helix chain 'A' and resid 194 through 198 Processing helix chain 'A' and resid 210 through 217 Processing helix chain 'A' and resid 219 through 229 Processing helix chain 'A' and resid 245 through 254 removed outlier: 4.602A pdb=" N ASN A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASP A 252 " --> pdb=" O GLU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 289 Processing helix chain 'A' and resid 335 through 344 Processing helix chain 'A' and resid 363 through 372 Processing helix chain 'A' and resid 394 through 398 Processing helix chain 'A' and resid 405 through 408 removed outlier: 4.071A pdb=" N ILE A 408 " --> pdb=" O THR A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 408' Processing helix chain 'A' and resid 409 through 423 Processing helix chain 'A' and resid 440 through 445 Processing helix chain 'A' and resid 457 through 462 Processing helix chain 'A' and resid 472 through 480 removed outlier: 3.743A pdb=" N MET A 478 " --> pdb=" O PRO A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 511 Processing helix chain 'A' and resid 512 through 514 No H-bonds generated for 'chain 'A' and resid 512 through 514' Processing helix chain 'A' and resid 539 through 548 removed outlier: 3.842A pdb=" N VAL A 545 " --> pdb=" O GLN A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 568 Processing helix chain 'A' and resid 594 through 607 removed outlier: 3.651A pdb=" N LYS A 600 " --> pdb=" O GLU A 596 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL A 604 " --> pdb=" O LYS A 600 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ILE A 605 " --> pdb=" O VAL A 601 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA A 606 " --> pdb=" O LYS A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 626 removed outlier: 3.876A pdb=" N ALA A 626 " --> pdb=" O PRO A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 630 Processing helix chain 'A' and resid 644 through 652 Processing helix chain 'A' and resid 680 through 682 No H-bonds generated for 'chain 'A' and resid 680 through 682' Processing helix chain 'A' and resid 690 through 707 Processing helix chain 'A' and resid 710 through 721 Processing helix chain 'A' and resid 750 through 762 Processing helix chain 'A' and resid 781 through 791 removed outlier: 3.993A pdb=" N GLN A 791 " --> pdb=" O GLN A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 824 removed outlier: 3.810A pdb=" N GLU A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 866 Processing helix chain 'A' and resid 867 through 870 Processing helix chain 'B' and resid 44 through 51 Processing helix chain 'B' and resid 79 through 91 Processing helix chain 'B' and resid 118 through 136 Processing helix chain 'B' and resid 144 through 161 removed outlier: 4.358A pdb=" N ASP B 150 " --> pdb=" O GLU B 146 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER B 161 " --> pdb=" O LEU B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 177 Processing helix chain 'B' and resid 194 through 198 Processing helix chain 'B' and resid 210 through 217 Processing helix chain 'B' and resid 219 through 229 Processing helix chain 'B' and resid 245 through 254 removed outlier: 4.602A pdb=" N ASN B 251 " --> pdb=" O GLU B 247 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASP B 252 " --> pdb=" O GLU B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 289 Processing helix chain 'B' and resid 335 through 344 Processing helix chain 'B' and resid 363 through 372 Processing helix chain 'B' and resid 394 through 398 Processing helix chain 'B' and resid 405 through 408 removed outlier: 4.071A pdb=" N ILE B 408 " --> pdb=" O THR B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 409 through 423 Processing helix chain 'B' and resid 440 through 445 Processing helix chain 'B' and resid 457 through 462 Processing helix chain 'B' and resid 472 through 480 removed outlier: 3.743A pdb=" N MET B 478 " --> pdb=" O PRO B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 511 Processing helix chain 'B' and resid 512 through 514 No H-bonds generated for 'chain 'B' and resid 512 through 514' Processing helix chain 'B' and resid 539 through 548 removed outlier: 3.842A pdb=" N VAL B 545 " --> pdb=" O GLN B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 568 Processing helix chain 'B' and resid 594 through 607 removed outlier: 3.651A pdb=" N LYS B 600 " --> pdb=" O GLU B 596 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL B 604 " --> pdb=" O LYS B 600 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ILE B 605 " --> pdb=" O VAL B 601 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA B 606 " --> pdb=" O LYS B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 626 removed outlier: 3.876A pdb=" N ALA B 626 " --> pdb=" O PRO B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 630 Processing helix chain 'B' and resid 644 through 652 Processing helix chain 'B' and resid 680 through 682 No H-bonds generated for 'chain 'B' and resid 680 through 682' Processing helix chain 'B' and resid 690 through 707 Processing helix chain 'B' and resid 710 through 721 Processing helix chain 'B' and resid 750 through 762 Processing helix chain 'B' and resid 781 through 791 removed outlier: 3.994A pdb=" N GLN B 791 " --> pdb=" O GLN B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 810 through 824 removed outlier: 3.810A pdb=" N GLU B 823 " --> pdb=" O GLY B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 858 through 866 Processing helix chain 'B' and resid 867 through 870 Processing helix chain 'C' and resid 44 through 51 Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 118 through 136 Processing helix chain 'C' and resid 144 through 161 removed outlier: 4.358A pdb=" N ASP C 150 " --> pdb=" O GLU C 146 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER C 161 " --> pdb=" O LEU C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 177 Processing helix chain 'C' and resid 194 through 198 Processing helix chain 'C' and resid 210 through 217 Processing helix chain 'C' and resid 219 through 229 Processing helix chain 'C' and resid 245 through 254 removed outlier: 4.602A pdb=" N ASN C 251 " --> pdb=" O GLU C 247 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP C 252 " --> pdb=" O GLU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 289 Processing helix chain 'C' and resid 335 through 344 Processing helix chain 'C' and resid 363 through 372 Processing helix chain 'C' and resid 394 through 398 Processing helix chain 'C' and resid 405 through 408 removed outlier: 4.071A pdb=" N ILE C 408 " --> pdb=" O THR C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 405 through 408' Processing helix chain 'C' and resid 409 through 423 Processing helix chain 'C' and resid 440 through 445 Processing helix chain 'C' and resid 457 through 462 Processing helix chain 'C' and resid 472 through 480 removed outlier: 3.743A pdb=" N MET C 478 " --> pdb=" O PRO C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 511 Processing helix chain 'C' and resid 512 through 514 No H-bonds generated for 'chain 'C' and resid 512 through 514' Processing helix chain 'C' and resid 539 through 548 removed outlier: 3.842A pdb=" N VAL C 545 " --> pdb=" O GLN C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 568 Processing helix chain 'C' and resid 594 through 607 removed outlier: 3.651A pdb=" N LYS C 600 " --> pdb=" O GLU C 596 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL C 604 " --> pdb=" O LYS C 600 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ILE C 605 " --> pdb=" O VAL C 601 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA C 606 " --> pdb=" O LYS C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 626 removed outlier: 3.876A pdb=" N ALA C 626 " --> pdb=" O PRO C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 630 Processing helix chain 'C' and resid 644 through 652 Processing helix chain 'C' and resid 680 through 682 No H-bonds generated for 'chain 'C' and resid 680 through 682' Processing helix chain 'C' and resid 690 through 707 Processing helix chain 'C' and resid 710 through 721 Processing helix chain 'C' and resid 750 through 762 Processing helix chain 'C' and resid 781 through 791 removed outlier: 3.994A pdb=" N GLN C 791 " --> pdb=" O GLN C 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 810 through 824 removed outlier: 3.810A pdb=" N GLU C 823 " --> pdb=" O GLY C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 858 through 866 Processing helix chain 'C' and resid 867 through 870 Processing helix chain 'D' and resid 44 through 51 Processing helix chain 'D' and resid 79 through 91 Processing helix chain 'D' and resid 118 through 136 Processing helix chain 'D' and resid 144 through 161 removed outlier: 4.358A pdb=" N ASP D 150 " --> pdb=" O GLU D 146 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER D 161 " --> pdb=" O LEU D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 177 Processing helix chain 'D' and resid 194 through 198 Processing helix chain 'D' and resid 210 through 217 Processing helix chain 'D' and resid 219 through 229 Processing helix chain 'D' and resid 245 through 254 removed outlier: 4.602A pdb=" N ASN D 251 " --> pdb=" O GLU D 247 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP D 252 " --> pdb=" O GLU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 289 Processing helix chain 'D' and resid 335 through 344 Processing helix chain 'D' and resid 363 through 372 Processing helix chain 'D' and resid 394 through 398 Processing helix chain 'D' and resid 405 through 408 removed outlier: 4.071A pdb=" N ILE D 408 " --> pdb=" O THR D 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 405 through 408' Processing helix chain 'D' and resid 409 through 423 Processing helix chain 'D' and resid 440 through 445 Processing helix chain 'D' and resid 457 through 462 Processing helix chain 'D' and resid 472 through 480 removed outlier: 3.743A pdb=" N MET D 478 " --> pdb=" O PRO D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 511 Processing helix chain 'D' and resid 512 through 514 No H-bonds generated for 'chain 'D' and resid 512 through 514' Processing helix chain 'D' and resid 539 through 548 removed outlier: 3.842A pdb=" N VAL D 545 " --> pdb=" O GLN D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 568 Processing helix chain 'D' and resid 594 through 607 removed outlier: 3.651A pdb=" N LYS D 600 " --> pdb=" O GLU D 596 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL D 604 " --> pdb=" O LYS D 600 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ILE D 605 " --> pdb=" O VAL D 601 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA D 606 " --> pdb=" O LYS D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 626 removed outlier: 3.876A pdb=" N ALA D 626 " --> pdb=" O PRO D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 630 Processing helix chain 'D' and resid 644 through 652 Processing helix chain 'D' and resid 680 through 682 No H-bonds generated for 'chain 'D' and resid 680 through 682' Processing helix chain 'D' and resid 690 through 707 Processing helix chain 'D' and resid 710 through 721 Processing helix chain 'D' and resid 750 through 762 Processing helix chain 'D' and resid 781 through 791 removed outlier: 3.994A pdb=" N GLN D 791 " --> pdb=" O GLN D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 810 through 824 removed outlier: 3.810A pdb=" N GLU D 823 " --> pdb=" O GLY D 819 " (cutoff:3.500A) Processing helix chain 'D' and resid 858 through 866 Processing helix chain 'D' and resid 867 through 870 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 10 removed outlier: 6.710A pdb=" N ARG A 26 " --> pdb=" O LEU A 4 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N THR A 6 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL A 24 " --> pdb=" O THR A 6 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N THR A 8 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU A 22 " --> pdb=" O THR A 8 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL A 109 " --> pdb=" O THR A 104 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA3, first strand: chain 'A' and resid 272 through 275 removed outlier: 5.291A pdb=" N ILE A 273 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ILE A 260 " --> pdb=" O ILE A 273 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 400 through 403 removed outlier: 4.193A pdb=" N ASP A 307 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL A 433 " --> pdb=" O ILE A 448 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ILE A 448 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 327 through 329 Processing sheet with id=AA6, first strand: chain 'A' and resid 530 through 534 removed outlier: 6.601A pdb=" N ILE A 525 " --> pdb=" O VAL A 532 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE A 490 " --> pdb=" O CYS A 574 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ASP A 575 " --> pdb=" O TYR A 614 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N VAL A 616 " --> pdb=" O ASP A 575 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLY A 577 " --> pdb=" O VAL A 616 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N ASN A 618 " --> pdb=" O GLY A 577 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N VAL A 579 " --> pdb=" O ASN A 618 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N VAL A 635 " --> pdb=" O ILE A 656 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N ALA A 658 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N TYR A 637 " --> pdb=" O ALA A 658 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N TYR A 660 " --> pdb=" O TYR A 637 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N SER A 639 " --> pdb=" O TYR A 660 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU A 677 " --> pdb=" O LEU A 665 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE A 667 " --> pdb=" O ARG A 675 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ARG A 675 " --> pdb=" O ILE A 667 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLU A 669 " --> pdb=" O THR A 673 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N THR A 673 " --> pdb=" O GLU A 669 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 733 through 736 removed outlier: 6.864A pdb=" N GLY A 769 " --> pdb=" O VAL A 853 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 2 through 10 removed outlier: 6.710A pdb=" N ARG B 26 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N THR B 6 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL B 24 " --> pdb=" O THR B 6 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N THR B 8 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU B 22 " --> pdb=" O THR B 8 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL B 109 " --> pdb=" O THR B 104 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AB1, first strand: chain 'B' and resid 272 through 275 removed outlier: 5.292A pdb=" N ILE B 273 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ILE B 260 " --> pdb=" O ILE B 273 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 400 through 403 removed outlier: 4.193A pdb=" N ASP B 307 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL B 433 " --> pdb=" O ILE B 448 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ILE B 448 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 327 through 329 Processing sheet with id=AB4, first strand: chain 'B' and resid 530 through 534 removed outlier: 6.601A pdb=" N ILE B 525 " --> pdb=" O VAL B 532 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE B 490 " --> pdb=" O CYS B 574 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ASP B 575 " --> pdb=" O TYR B 614 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL B 616 " --> pdb=" O ASP B 575 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLY B 577 " --> pdb=" O VAL B 616 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N ASN B 618 " --> pdb=" O GLY B 577 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N VAL B 579 " --> pdb=" O ASN B 618 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N VAL B 635 " --> pdb=" O ILE B 656 " (cutoff:3.500A) removed outlier: 9.074A pdb=" N ALA B 658 " --> pdb=" O VAL B 635 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N TYR B 637 " --> pdb=" O ALA B 658 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N TYR B 660 " --> pdb=" O TYR B 637 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N SER B 639 " --> pdb=" O TYR B 660 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU B 677 " --> pdb=" O LEU B 665 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE B 667 " --> pdb=" O ARG B 675 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ARG B 675 " --> pdb=" O ILE B 667 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLU B 669 " --> pdb=" O THR B 673 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N THR B 673 " --> pdb=" O GLU B 669 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 733 through 736 removed outlier: 6.863A pdb=" N GLY B 769 " --> pdb=" O VAL B 853 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 2 through 10 removed outlier: 6.710A pdb=" N ARG C 26 " --> pdb=" O LEU C 4 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N THR C 6 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL C 24 " --> pdb=" O THR C 6 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N THR C 8 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU C 22 " --> pdb=" O THR C 8 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL C 109 " --> pdb=" O THR C 104 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AB8, first strand: chain 'C' and resid 272 through 275 removed outlier: 5.291A pdb=" N ILE C 273 " --> pdb=" O ILE C 260 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ILE C 260 " --> pdb=" O ILE C 273 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 400 through 403 removed outlier: 4.192A pdb=" N ASP C 307 " --> pdb=" O ARG C 323 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL C 433 " --> pdb=" O ILE C 448 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ILE C 448 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 327 through 329 Processing sheet with id=AC2, first strand: chain 'C' and resid 530 through 534 removed outlier: 6.601A pdb=" N ILE C 525 " --> pdb=" O VAL C 532 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE C 490 " --> pdb=" O CYS C 574 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ASP C 575 " --> pdb=" O TYR C 614 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N VAL C 616 " --> pdb=" O ASP C 575 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLY C 577 " --> pdb=" O VAL C 616 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N ASN C 618 " --> pdb=" O GLY C 577 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N VAL C 579 " --> pdb=" O ASN C 618 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N VAL C 635 " --> pdb=" O ILE C 656 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N ALA C 658 " --> pdb=" O VAL C 635 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N TYR C 637 " --> pdb=" O ALA C 658 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N TYR C 660 " --> pdb=" O TYR C 637 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N SER C 639 " --> pdb=" O TYR C 660 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU C 677 " --> pdb=" O LEU C 665 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE C 667 " --> pdb=" O ARG C 675 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ARG C 675 " --> pdb=" O ILE C 667 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLU C 669 " --> pdb=" O THR C 673 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N THR C 673 " --> pdb=" O GLU C 669 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 733 through 736 removed outlier: 6.863A pdb=" N GLY C 769 " --> pdb=" O VAL C 853 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 2 through 10 removed outlier: 6.710A pdb=" N ARG D 26 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N THR D 6 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL D 24 " --> pdb=" O THR D 6 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N THR D 8 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU D 22 " --> pdb=" O THR D 8 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL D 109 " --> pdb=" O THR D 104 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 181 through 183 Processing sheet with id=AC6, first strand: chain 'D' and resid 272 through 275 removed outlier: 5.292A pdb=" N ILE D 273 " --> pdb=" O ILE D 260 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ILE D 260 " --> pdb=" O ILE D 273 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 400 through 403 removed outlier: 4.193A pdb=" N ASP D 307 " --> pdb=" O ARG D 323 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL D 433 " --> pdb=" O ILE D 448 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ILE D 448 " --> pdb=" O VAL D 433 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 327 through 329 Processing sheet with id=AC9, first strand: chain 'D' and resid 530 through 534 removed outlier: 6.601A pdb=" N ILE D 525 " --> pdb=" O VAL D 532 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE D 490 " --> pdb=" O CYS D 574 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ASP D 575 " --> pdb=" O TYR D 614 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N VAL D 616 " --> pdb=" O ASP D 575 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLY D 577 " --> pdb=" O VAL D 616 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N ASN D 618 " --> pdb=" O GLY D 577 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N VAL D 579 " --> pdb=" O ASN D 618 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N VAL D 635 " --> pdb=" O ILE D 656 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N ALA D 658 " --> pdb=" O VAL D 635 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N TYR D 637 " --> pdb=" O ALA D 658 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N TYR D 660 " --> pdb=" O TYR D 637 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N SER D 639 " --> pdb=" O TYR D 660 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU D 677 " --> pdb=" O LEU D 665 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE D 667 " --> pdb=" O ARG D 675 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ARG D 675 " --> pdb=" O ILE D 667 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLU D 669 " --> pdb=" O THR D 673 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N THR D 673 " --> pdb=" O GLU D 669 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 733 through 736 removed outlier: 6.864A pdb=" N GLY D 769 " --> pdb=" O VAL D 853 " (cutoff:3.500A) 1124 hydrogen bonds defined for protein. 3132 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.08 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.05: 402 1.05 - 1.24: 4407 1.24 - 1.43: 7031 1.43 - 1.63: 16158 1.63 - 1.82: 172 Bond restraints: 28170 Sorted by residual: bond pdb=" C 7ID G 5 " pdb=" N 7ID G 6 " ideal model delta sigma weight residual 1.329 1.518 -0.189 1.40e-02 5.10e+03 1.82e+02 bond pdb=" C 7ID H 5 " pdb=" N 7ID H 6 " ideal model delta sigma weight residual 1.329 1.518 -0.189 1.40e-02 5.10e+03 1.82e+02 bond pdb=" C 7ID F 5 " pdb=" N 7ID F 6 " ideal model delta sigma weight residual 1.329 1.518 -0.189 1.40e-02 5.10e+03 1.82e+02 bond pdb=" C 7ID E 5 " pdb=" N 7ID E 6 " ideal model delta sigma weight residual 1.329 1.518 -0.189 1.40e-02 5.10e+03 1.82e+02 bond pdb=" C 7ID E 6 " pdb=" N 7ID E 7 " ideal model delta sigma weight residual 1.329 1.479 -0.150 1.40e-02 5.10e+03 1.15e+02 ... (remaining 28165 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.50: 37832 5.50 - 11.00: 760 11.00 - 16.50: 52 16.50 - 22.00: 4 22.00 - 27.50: 12 Bond angle restraints: 38660 Sorted by residual: angle pdb=" PB ATP C 902 " pdb=" O3B ATP C 902 " pdb=" PG ATP C 902 " ideal model delta sigma weight residual 139.87 129.17 10.70 1.00e+00 1.00e+00 1.15e+02 angle pdb=" PB ATP D 902 " pdb=" O3B ATP D 902 " pdb=" PG ATP D 902 " ideal model delta sigma weight residual 139.87 129.17 10.70 1.00e+00 1.00e+00 1.15e+02 angle pdb=" PB ATP A 902 " pdb=" O3B ATP A 902 " pdb=" PG ATP A 902 " ideal model delta sigma weight residual 139.87 129.20 10.67 1.00e+00 1.00e+00 1.14e+02 angle pdb=" PB ATP B 902 " pdb=" O3B ATP B 902 " pdb=" PG ATP B 902 " ideal model delta sigma weight residual 139.87 129.22 10.65 1.00e+00 1.00e+00 1.14e+02 angle pdb=" C GLY C 773 " pdb=" N PRO C 774 " pdb=" CA PRO C 774 " ideal model delta sigma weight residual 119.92 130.40 -10.48 1.07e+00 8.73e-01 9.58e+01 ... (remaining 38655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.31: 16671 35.31 - 70.62: 483 70.62 - 105.93: 116 105.93 - 141.24: 76 141.24 - 176.55: 32 Dihedral angle restraints: 17378 sinusoidal: 7406 harmonic: 9972 Sorted by residual: dihedral pdb=" C ALA C 790 " pdb=" N ALA C 790 " pdb=" CA ALA C 790 " pdb=" CB ALA C 790 " ideal model delta harmonic sigma weight residual -122.60 -154.45 31.85 0 2.50e+00 1.60e-01 1.62e+02 dihedral pdb=" C ALA D 790 " pdb=" N ALA D 790 " pdb=" CA ALA D 790 " pdb=" CB ALA D 790 " ideal model delta harmonic sigma weight residual -122.60 -154.45 31.85 0 2.50e+00 1.60e-01 1.62e+02 dihedral pdb=" C ALA B 790 " pdb=" N ALA B 790 " pdb=" CA ALA B 790 " pdb=" CB ALA B 790 " ideal model delta harmonic sigma weight residual -122.60 -154.44 31.84 0 2.50e+00 1.60e-01 1.62e+02 ... (remaining 17375 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.265: 4280 0.265 - 0.530: 60 0.530 - 0.795: 0 0.795 - 1.059: 0 1.059 - 1.324: 8 Chirality restraints: 4348 Sorted by residual: chirality pdb=" CA ALA C 790 " pdb=" N ALA C 790 " pdb=" C ALA C 790 " pdb=" CB ALA C 790 " both_signs ideal model delta sigma weight residual False 2.48 1.16 1.32 2.00e-01 2.50e+01 4.38e+01 chirality pdb=" CA ALA B 790 " pdb=" N ALA B 790 " pdb=" C ALA B 790 " pdb=" CB ALA B 790 " both_signs ideal model delta sigma weight residual False 2.48 1.16 1.32 2.00e-01 2.50e+01 4.38e+01 chirality pdb=" CA ALA D 790 " pdb=" N ALA D 790 " pdb=" C ALA D 790 " pdb=" CB ALA D 790 " both_signs ideal model delta sigma weight residual False 2.48 1.16 1.32 2.00e-01 2.50e+01 4.38e+01 ... (remaining 4345 not shown) Planarity restraints: 4952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 747 " -0.018 2.00e-02 2.50e+03 3.61e-02 1.30e+01 pdb=" C ALA C 747 " 0.062 2.00e-02 2.50e+03 pdb=" O ALA C 747 " -0.023 2.00e-02 2.50e+03 pdb=" N HIS C 748 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 747 " 0.018 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C ALA D 747 " -0.062 2.00e-02 2.50e+03 pdb=" O ALA D 747 " 0.023 2.00e-02 2.50e+03 pdb=" N HIS D 748 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 747 " 0.018 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C ALA A 747 " -0.062 2.00e-02 2.50e+03 pdb=" O ALA A 747 " 0.023 2.00e-02 2.50e+03 pdb=" N HIS A 748 " 0.021 2.00e-02 2.50e+03 ... (remaining 4949 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 109 2.22 - 2.82: 8579 2.82 - 3.41: 30580 3.41 - 4.01: 53427 4.01 - 4.60: 77478 Nonbonded interactions: 170173 Sorted by model distance: nonbonded pdb=" HA2 7ID L 8 " pdb=" HBB 7ID L 8 " model vdw 1.630 1.952 nonbonded pdb=" HA2 7ID I 8 " pdb=" HBB 7ID I 8 " model vdw 1.630 1.952 nonbonded pdb=" HA2 7ID J 8 " pdb=" HBB 7ID J 8 " model vdw 1.630 1.952 nonbonded pdb=" HA2 7ID K 8 " pdb=" HBB 7ID K 8 " model vdw 1.630 1.952 nonbonded pdb=" OE2 GLU A 558 " pdb="MG MG A 903 " model vdw 1.806 2.050 ... (remaining 170168 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and ((resid 5 and (name N or name CA or name C or name O or name CB o \ r name H or name HA or name HB2)) or resid 6 through 9)) selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.310 Extract box with map and model: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 24.590 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 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:6.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 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 : 0.022 0.189 27768 Z= 1.152 Angle : 1.935 19.815 37764 Z= 1.255 Chirality : 0.110 1.324 4348 Planarity : 0.009 0.036 4928 Dihedral : 17.838 174.765 10724 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 1.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.28 % Allowed : 0.56 % Favored : 99.16 % Cbeta Deviations : 0.75 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.63 (0.13), residues: 3456 helix: -1.07 (0.13), residues: 1256 sheet: 1.22 (0.21), residues: 584 loop : -0.35 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 177 TYR 0.043 0.007 TYR B 829 PHE 0.028 0.005 PHE D 58 TRP 0.015 0.005 TRP C 181 HIS 0.019 0.004 HIS D 586 Details of bonding type rmsd/Z covalent geometry : bond 0.02155 / 1.15 (27768) covalent geometry : angle 1.93512 / 1.25 (37764) hydrogen bonds : bond 0.21422 / 14.54 ( 1124) hydrogen bonds : angle 7.07155 / 4.97 ( 3132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 382 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.7417 (mtt180) cc_final: 0.6574 (pmt170) REVERT: A 316 LYS cc_start: 0.8739 (tttt) cc_final: 0.8075 (mtmm) REVERT: A 342 LYS cc_start: 0.7020 (tttm) cc_final: 0.6553 (mttm) REVERT: A 445 ASN cc_start: 0.8029 (t0) cc_final: 0.7735 (t160) REVERT: A 534 LYS cc_start: 0.7740 (mttt) cc_final: 0.7420 (mttt) REVERT: A 589 LEU cc_start: 0.6020 (mt) cc_final: 0.5760 (mp) REVERT: A 600 LYS cc_start: 0.7375 (mttt) cc_final: 0.7135 (mmtm) REVERT: A 630 LYS cc_start: 0.7105 (mmtt) cc_final: 0.6684 (mtpt) REVERT: A 661 GLU cc_start: 0.7724 (pt0) cc_final: 0.7004 (pp20) REVERT: A 712 GLU cc_start: 0.7161 (tp30) cc_final: 0.6708 (mp0) REVERT: B 18 ARG cc_start: 0.7387 (mtt180) cc_final: 0.6510 (pmt170) REVERT: B 316 LYS cc_start: 0.8738 (tttt) cc_final: 0.8074 (mtmm) REVERT: B 342 LYS cc_start: 0.6977 (tttm) cc_final: 0.6551 (mttm) REVERT: B 442 ARG cc_start: 0.8312 (ptt-90) cc_final: 0.8106 (ttp-110) REVERT: B 445 ASN cc_start: 0.8005 (t0) cc_final: 0.7690 (t160) REVERT: B 534 LYS cc_start: 0.7752 (mttt) cc_final: 0.7428 (mttt) REVERT: B 600 LYS cc_start: 0.7494 (mttt) cc_final: 0.7223 (mmtm) REVERT: B 630 LYS cc_start: 0.7173 (mmtt) cc_final: 0.6781 (mtpt) REVERT: B 661 GLU cc_start: 0.7770 (pt0) cc_final: 0.7094 (pp20) REVERT: B 669 GLU cc_start: 0.7768 (tt0) cc_final: 0.7374 (tp30) REVERT: C 18 ARG cc_start: 0.7454 (mtt180) cc_final: 0.6616 (pmt170) REVERT: C 316 LYS cc_start: 0.8711 (tttt) cc_final: 0.7990 (mtmm) REVERT: C 342 LYS cc_start: 0.7056 (tttm) cc_final: 0.6628 (mttm) REVERT: C 372 ARG cc_start: 0.5702 (mtt90) cc_final: 0.5266 (ttt180) REVERT: C 445 ASN cc_start: 0.7982 (t0) cc_final: 0.7672 (t160) REVERT: C 534 LYS cc_start: 0.7803 (mttt) cc_final: 0.7474 (mttt) REVERT: C 600 LYS cc_start: 0.7450 (mttt) cc_final: 0.7200 (mmtm) REVERT: C 630 LYS cc_start: 0.7093 (mmtt) cc_final: 0.6727 (mtpt) REVERT: C 661 GLU cc_start: 0.7750 (pt0) cc_final: 0.7008 (pp20) REVERT: D 18 ARG cc_start: 0.7471 (mtt180) cc_final: 0.6609 (pmt170) REVERT: D 316 LYS cc_start: 0.8719 (tttt) cc_final: 0.8056 (mtmm) REVERT: D 342 LYS cc_start: 0.7053 (tttm) cc_final: 0.6627 (mttm) REVERT: D 371 GLU cc_start: 0.7010 (mt-10) cc_final: 0.6784 (tp30) REVERT: D 372 ARG cc_start: 0.5716 (mtt90) cc_final: 0.5259 (ttt180) REVERT: D 445 ASN cc_start: 0.7997 (t0) cc_final: 0.7716 (t160) REVERT: D 534 LYS cc_start: 0.7715 (mttt) cc_final: 0.7384 (mttt) REVERT: D 600 LYS cc_start: 0.7417 (mttt) cc_final: 0.7141 (mmtm) REVERT: D 630 LYS cc_start: 0.7152 (mmtt) cc_final: 0.6776 (mtpt) REVERT: D 661 GLU cc_start: 0.7792 (pt0) cc_final: 0.7055 (pp20) REVERT: D 712 GLU cc_start: 0.7147 (tp30) cc_final: 0.6642 (mp0) outliers start: 8 outliers final: 0 residues processed: 390 average time/residue: 0.7837 time to fit residues: 347.8073 Evaluate side-chains 257 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 202 GLN A 748 HIS B 202 GLN B 748 HIS C 202 GLN C 541 GLN C 748 HIS D 202 GLN D 541 GLN D 748 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.200378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.130561 restraints weight = 32866.349| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.63 r_work: 0.3387 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 27768 Z= 0.133 Angle : 0.636 10.326 37764 Z= 0.333 Chirality : 0.064 1.570 4348 Planarity : 0.004 0.034 4928 Dihedral : 21.693 146.068 4504 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.76 % Allowed : 4.78 % Favored : 93.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.11 (0.14), residues: 3456 helix: 0.19 (0.14), residues: 1316 sheet: 0.68 (0.22), residues: 592 loop : -0.50 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 70 TYR 0.013 0.002 TYR A 14 PHE 0.009 0.001 PHE A 58 TRP 0.024 0.002 TRP C 278 HIS 0.006 0.001 HIS A 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (27768) covalent geometry : angle 0.63629 / 0.33 (37764) hydrogen bonds : bond 0.05570 / 3.77 ( 1124) hydrogen bonds : angle 5.02831 / 3.53 ( 3132) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 287 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8135 (tttt) cc_final: 0.7898 (ttmm) REVERT: A 18 ARG cc_start: 0.8066 (mtt180) cc_final: 0.7298 (pmt170) REVERT: A 35 ARG cc_start: 0.6536 (mtm180) cc_final: 0.6179 (mtp-110) REVERT: A 316 LYS cc_start: 0.8624 (tttt) cc_final: 0.8108 (mtmm) REVERT: A 342 LYS cc_start: 0.7605 (tttm) cc_final: 0.6787 (mttm) REVERT: A 589 LEU cc_start: 0.7605 (mt) cc_final: 0.7331 (mp) REVERT: A 630 LYS cc_start: 0.7513 (mmtt) cc_final: 0.7159 (mtpt) REVERT: A 661 GLU cc_start: 0.7948 (pt0) cc_final: 0.7325 (pp20) REVERT: A 680 LYS cc_start: 0.8462 (pttt) cc_final: 0.8233 (ptpp) REVERT: B 18 ARG cc_start: 0.8089 (mtt180) cc_final: 0.7314 (pmt170) REVERT: B 316 LYS cc_start: 0.8574 (tttt) cc_final: 0.8107 (mtmm) REVERT: B 342 LYS cc_start: 0.7589 (tttm) cc_final: 0.6737 (mttm) REVERT: B 630 LYS cc_start: 0.7492 (mmtt) cc_final: 0.7150 (mtpt) REVERT: B 661 GLU cc_start: 0.7924 (pt0) cc_final: 0.7341 (pp20) REVERT: B 836 THR cc_start: 0.2720 (OUTLIER) cc_final: 0.2481 (m) REVERT: C 18 ARG cc_start: 0.8049 (mtt180) cc_final: 0.7282 (pmt170) REVERT: C 316 LYS cc_start: 0.8559 (tttt) cc_final: 0.8078 (mtmm) REVERT: C 342 LYS cc_start: 0.7657 (tttm) cc_final: 0.6925 (mttm) REVERT: C 534 LYS cc_start: 0.8455 (mttt) cc_final: 0.8248 (mttt) REVERT: C 630 LYS cc_start: 0.7488 (mmtt) cc_final: 0.7174 (mtpt) REVERT: C 661 GLU cc_start: 0.7921 (pt0) cc_final: 0.7295 (pp20) REVERT: C 836 THR cc_start: 0.2710 (OUTLIER) cc_final: 0.2121 (m) REVERT: D 18 ARG cc_start: 0.8101 (mtt180) cc_final: 0.7323 (pmt170) REVERT: D 35 ARG cc_start: 0.6326 (mtm180) cc_final: 0.5941 (mtp-110) REVERT: D 316 LYS cc_start: 0.8600 (tttt) cc_final: 0.8102 (mtmm) REVERT: D 342 LYS cc_start: 0.7667 (tttm) cc_final: 0.6906 (mttm) REVERT: D 630 LYS cc_start: 0.7506 (mmtt) cc_final: 0.7194 (mtpt) REVERT: D 661 GLU cc_start: 0.7946 (pt0) cc_final: 0.7329 (pp20) REVERT: D 836 THR cc_start: 0.2715 (OUTLIER) cc_final: 0.2126 (m) outliers start: 50 outliers final: 15 residues processed: 327 average time/residue: 0.7618 time to fit residues: 285.1440 Evaluate side-chains 246 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 228 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 632 LYS Chi-restraints excluded: chain B residue 835 GLU Chi-restraints excluded: chain B residue 836 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 836 THR Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 836 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 224 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 133 optimal weight: 0.5980 chunk 334 optimal weight: 0.8980 chunk 311 optimal weight: 6.9990 chunk 147 optimal weight: 0.0770 chunk 72 optimal weight: 0.7980 chunk 101 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 308 optimal weight: 3.9990 overall best weight: 1.2740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 445 ASN A 740 HIS B 445 ASN B 740 HIS C 445 ASN C 740 HIS D 445 ASN D 740 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.197218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.125842 restraints weight = 32737.250| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.67 r_work: 0.3330 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27768 Z= 0.125 Angle : 0.548 9.410 37764 Z= 0.283 Chirality : 0.064 1.573 4348 Planarity : 0.004 0.033 4928 Dihedral : 19.679 146.256 4504 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.51 % Allowed : 7.35 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.15 (0.15), residues: 3456 helix: 0.83 (0.15), residues: 1316 sheet: 0.67 (0.22), residues: 568 loop : -0.70 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 511 TYR 0.021 0.002 TYR D 116 PHE 0.011 0.001 PHE D 457 TRP 0.037 0.002 TRP D 278 HIS 0.006 0.001 HIS D 586 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (27768) covalent geometry : angle 0.54815 / 0.28 (37764) hydrogen bonds : bond 0.04646 / 3.13 ( 1124) hydrogen bonds : angle 4.51561 / 3.17 ( 3132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 270 time to evaluate : 0.941 Fit side-chains REVERT: A 5 LYS cc_start: 0.8119 (tttt) cc_final: 0.7739 (ttpp) REVERT: A 18 ARG cc_start: 0.8072 (mtt180) cc_final: 0.7302 (pmt170) REVERT: A 35 ARG cc_start: 0.6458 (mtm180) cc_final: 0.6071 (mtp-110) REVERT: A 43 PHE cc_start: 0.7426 (t80) cc_final: 0.6921 (t80) REVERT: A 304 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8090 (mm-30) REVERT: A 316 LYS cc_start: 0.8661 (tttt) cc_final: 0.8124 (mtmm) REVERT: A 589 LEU cc_start: 0.7743 (mt) cc_final: 0.7530 (mp) REVERT: A 630 LYS cc_start: 0.7466 (mmtt) cc_final: 0.7108 (mtpt) REVERT: A 654 ASN cc_start: 0.7263 (m-40) cc_final: 0.7011 (m110) REVERT: A 661 GLU cc_start: 0.7910 (pt0) cc_final: 0.7102 (pp20) REVERT: B 5 LYS cc_start: 0.8064 (tttt) cc_final: 0.7682 (ttpp) REVERT: B 18 ARG cc_start: 0.8089 (mtt180) cc_final: 0.7278 (pmt170) REVERT: B 38 ASN cc_start: 0.5391 (m110) cc_final: 0.3906 (p0) REVERT: B 43 PHE cc_start: 0.7347 (t80) cc_final: 0.6788 (t80) REVERT: B 134 ARG cc_start: 0.6689 (OUTLIER) cc_final: 0.5758 (ttt90) REVERT: B 304 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8112 (mm-30) REVERT: B 316 LYS cc_start: 0.8665 (tttt) cc_final: 0.8115 (mtmm) REVERT: B 630 LYS cc_start: 0.7488 (mmtt) cc_final: 0.7169 (mtpt) REVERT: B 654 ASN cc_start: 0.7232 (m-40) cc_final: 0.6968 (m110) REVERT: B 661 GLU cc_start: 0.7913 (pt0) cc_final: 0.7067 (pp20) REVERT: B 836 THR cc_start: 0.2624 (OUTLIER) cc_final: 0.2385 (m) REVERT: C 5 LYS cc_start: 0.8035 (tttt) cc_final: 0.7653 (ttpp) REVERT: C 18 ARG cc_start: 0.8086 (mtt180) cc_final: 0.7284 (pmt170) REVERT: C 43 PHE cc_start: 0.7383 (t80) cc_final: 0.6866 (t80) REVERT: C 304 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8087 (mm-30) REVERT: C 316 LYS cc_start: 0.8648 (tttt) cc_final: 0.8111 (mtmm) REVERT: C 534 LYS cc_start: 0.8573 (mttt) cc_final: 0.8347 (mttt) REVERT: C 630 LYS cc_start: 0.7487 (mmtt) cc_final: 0.7149 (mtmt) REVERT: C 654 ASN cc_start: 0.7259 (m-40) cc_final: 0.7023 (m110) REVERT: C 661 GLU cc_start: 0.7915 (pt0) cc_final: 0.7099 (pp20) REVERT: C 836 THR cc_start: 0.2230 (OUTLIER) cc_final: 0.1943 (m) REVERT: D 5 LYS cc_start: 0.8058 (tttt) cc_final: 0.7666 (ttpp) REVERT: D 18 ARG cc_start: 0.8075 (mtt180) cc_final: 0.7295 (pmt170) REVERT: D 35 ARG cc_start: 0.6445 (mtm180) cc_final: 0.6040 (mtp-110) REVERT: D 43 PHE cc_start: 0.7435 (t80) cc_final: 0.6898 (t80) REVERT: D 304 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8089 (mm-30) REVERT: D 316 LYS cc_start: 0.8652 (tttt) cc_final: 0.8120 (mtmm) REVERT: D 630 LYS cc_start: 0.7480 (mmtt) cc_final: 0.7138 (mtmt) REVERT: D 654 ASN cc_start: 0.7199 (m-40) cc_final: 0.6961 (m110) REVERT: D 661 GLU cc_start: 0.7956 (pt0) cc_final: 0.7086 (pp20) REVERT: D 836 THR cc_start: 0.2310 (OUTLIER) cc_final: 0.2021 (m) outliers start: 43 outliers final: 21 residues processed: 299 average time/residue: 0.7050 time to fit residues: 242.9471 Evaluate side-chains 262 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 237 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 836 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 836 THR Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 632 LYS Chi-restraints excluded: chain D residue 732 MET Chi-restraints excluded: chain D residue 836 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 23 optimal weight: 0.4980 chunk 79 optimal weight: 8.9990 chunk 165 optimal weight: 9.9990 chunk 73 optimal weight: 20.0000 chunk 146 optimal weight: 4.9990 chunk 139 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 279 optimal weight: 3.9990 chunk 280 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 185 optimal weight: 8.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 355 ASN B 355 ASN C 355 ASN D 355 ASN D 445 ASN I 9 ASN J 9 ASN K 9 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.193243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.122262 restraints weight = 32619.092| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.63 r_work: 0.3232 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 27768 Z= 0.237 Angle : 0.641 10.248 37764 Z= 0.333 Chirality : 0.066 1.541 4348 Planarity : 0.004 0.038 4928 Dihedral : 19.061 148.434 4504 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.57 % Allowed : 7.49 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.33 (0.14), residues: 3456 helix: 0.23 (0.14), residues: 1368 sheet: 0.51 (0.22), residues: 564 loop : -0.83 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 715 TYR 0.021 0.002 TYR A 829 PHE 0.017 0.002 PHE A 58 TRP 0.011 0.002 TRP A 181 HIS 0.009 0.002 HIS D 586 Details of bonding type rmsd/Z covalent geometry : bond 0.00591 / 0.24 (27768) covalent geometry : angle 0.64147 / 0.33 (37764) hydrogen bonds : bond 0.06243 / 4.23 ( 1124) hydrogen bonds : angle 4.81877 / 3.39 ( 3132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 233 time to evaluate : 1.098 Fit side-chains REVERT: A 5 LYS cc_start: 0.8221 (tttt) cc_final: 0.7830 (ttpp) REVERT: A 18 ARG cc_start: 0.8199 (mtt180) cc_final: 0.7441 (pmt170) REVERT: A 49 LYS cc_start: 0.6621 (OUTLIER) cc_final: 0.6384 (ptmt) REVERT: A 304 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8174 (mm-30) REVERT: A 316 LYS cc_start: 0.8781 (tttt) cc_final: 0.8240 (mtmm) REVERT: A 558 GLU cc_start: 0.9387 (OUTLIER) cc_final: 0.8358 (pt0) REVERT: A 589 LEU cc_start: 0.7834 (mt) cc_final: 0.7602 (mp) REVERT: A 630 LYS cc_start: 0.7621 (mmtt) cc_final: 0.7263 (mtpt) REVERT: A 654 ASN cc_start: 0.7249 (m-40) cc_final: 0.6941 (m110) REVERT: A 661 GLU cc_start: 0.8110 (pt0) cc_final: 0.7172 (pp20) REVERT: B 5 LYS cc_start: 0.8189 (tttt) cc_final: 0.7796 (ttpp) REVERT: B 18 ARG cc_start: 0.8223 (mtt180) cc_final: 0.7412 (pmt170) REVERT: B 134 ARG cc_start: 0.6659 (OUTLIER) cc_final: 0.5903 (ttt90) REVERT: B 304 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8185 (mm-30) REVERT: B 316 LYS cc_start: 0.8779 (tttt) cc_final: 0.8239 (mtmm) REVERT: B 558 GLU cc_start: 0.9387 (OUTLIER) cc_final: 0.8362 (pt0) REVERT: B 630 LYS cc_start: 0.7597 (mmtt) cc_final: 0.7256 (mtpt) REVERT: B 654 ASN cc_start: 0.7234 (m-40) cc_final: 0.6926 (m110) REVERT: B 661 GLU cc_start: 0.8108 (pt0) cc_final: 0.7181 (pp20) REVERT: C 5 LYS cc_start: 0.8207 (tttt) cc_final: 0.7792 (ttpp) REVERT: C 18 ARG cc_start: 0.8176 (mtt180) cc_final: 0.7395 (pmt170) REVERT: C 49 LYS cc_start: 0.6573 (OUTLIER) cc_final: 0.6327 (ptmt) REVERT: C 304 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8157 (mm-30) REVERT: C 316 LYS cc_start: 0.8765 (tttt) cc_final: 0.8220 (mtmm) REVERT: C 534 LYS cc_start: 0.8672 (mttt) cc_final: 0.8429 (mttt) REVERT: C 558 GLU cc_start: 0.9390 (OUTLIER) cc_final: 0.8367 (pt0) REVERT: C 630 LYS cc_start: 0.7620 (mmtt) cc_final: 0.7278 (mtpt) REVERT: C 654 ASN cc_start: 0.7258 (m-40) cc_final: 0.6958 (m110) REVERT: C 661 GLU cc_start: 0.8114 (pt0) cc_final: 0.7176 (pp20) REVERT: D 5 LYS cc_start: 0.8179 (tttt) cc_final: 0.7784 (ttpp) REVERT: D 18 ARG cc_start: 0.8188 (mtt180) cc_final: 0.7410 (pmt170) REVERT: D 49 LYS cc_start: 0.6578 (OUTLIER) cc_final: 0.6346 (ptmt) REVERT: D 94 MET cc_start: 0.7247 (mtt) cc_final: 0.7036 (mtp) REVERT: D 304 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8173 (mm-30) REVERT: D 316 LYS cc_start: 0.8790 (tttt) cc_final: 0.8259 (mtmm) REVERT: D 558 GLU cc_start: 0.9400 (OUTLIER) cc_final: 0.8296 (pt0) REVERT: D 630 LYS cc_start: 0.7615 (mmtt) cc_final: 0.7269 (mtpt) REVERT: D 654 ASN cc_start: 0.7250 (m-40) cc_final: 0.6964 (m110) REVERT: D 661 GLU cc_start: 0.8080 (pt0) cc_final: 0.7158 (pp20) outliers start: 73 outliers final: 31 residues processed: 285 average time/residue: 0.7562 time to fit residues: 246.9284 Evaluate side-chains 276 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 237 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 632 LYS Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 732 MET Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 632 LYS Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 49 LYS Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 558 GLU Chi-restraints excluded: chain D residue 632 LYS Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain D residue 732 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 0 optimal weight: 6.9990 chunk 93 optimal weight: 8.9990 chunk 287 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 105 optimal weight: 0.8980 chunk 260 optimal weight: 3.9990 chunk 249 optimal weight: 0.6980 chunk 172 optimal weight: 6.9990 chunk 198 optimal weight: 8.9990 chunk 183 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 HIS B 327 HIS C 327 HIS D 327 HIS I 9 ASN J 9 ASN K 9 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.194397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.125419 restraints weight = 32456.355| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.54 r_work: 0.3264 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 27768 Z= 0.143 Angle : 0.545 9.637 37764 Z= 0.280 Chirality : 0.064 1.565 4348 Planarity : 0.004 0.037 4928 Dihedral : 18.077 150.744 4504 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.04 % Allowed : 7.88 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.30 (0.14), residues: 3456 helix: 0.42 (0.14), residues: 1372 sheet: 0.34 (0.21), residues: 612 loop : -0.95 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 715 TYR 0.018 0.002 TYR A 829 PHE 0.013 0.001 PHE B 638 TRP 0.012 0.001 TRP C 278 HIS 0.005 0.001 HIS B 586 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (27768) covalent geometry : angle 0.54478 / 0.28 (37764) hydrogen bonds : bond 0.04777 / 3.22 ( 1124) hydrogen bonds : angle 4.57164 / 3.22 ( 3132) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 250 time to evaluate : 1.106 Fit side-chains REVERT: A 5 LYS cc_start: 0.8193 (tttt) cc_final: 0.7846 (ttpp) REVERT: A 18 ARG cc_start: 0.8196 (mtt180) cc_final: 0.7411 (pmt170) REVERT: A 35 ARG cc_start: 0.6234 (mtp-110) cc_final: 0.5830 (mtp-110) REVERT: A 43 PHE cc_start: 0.7268 (t80) cc_final: 0.6749 (t80) REVERT: A 79 HIS cc_start: 0.5419 (OUTLIER) cc_final: 0.4685 (m170) REVERT: A 304 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8167 (mm-30) REVERT: A 316 LYS cc_start: 0.8729 (tttt) cc_final: 0.8216 (mtmm) REVERT: A 558 GLU cc_start: 0.9348 (OUTLIER) cc_final: 0.8315 (pt0) REVERT: A 589 LEU cc_start: 0.7813 (mt) cc_final: 0.7574 (mp) REVERT: A 630 LYS cc_start: 0.7614 (mmtt) cc_final: 0.7221 (mtpt) REVERT: A 654 ASN cc_start: 0.7298 (m-40) cc_final: 0.6984 (m110) REVERT: A 661 GLU cc_start: 0.8068 (pt0) cc_final: 0.7130 (pp20) REVERT: B 5 LYS cc_start: 0.8190 (tttt) cc_final: 0.7841 (ttpp) REVERT: B 18 ARG cc_start: 0.8199 (mtt180) cc_final: 0.7387 (pmt170) REVERT: B 35 ARG cc_start: 0.6699 (mtm180) cc_final: 0.6288 (mtp-110) REVERT: B 79 HIS cc_start: 0.5417 (OUTLIER) cc_final: 0.4703 (m170) REVERT: B 134 ARG cc_start: 0.6594 (OUTLIER) cc_final: 0.5724 (ttt90) REVERT: B 304 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8180 (mm-30) REVERT: B 316 LYS cc_start: 0.8742 (tttt) cc_final: 0.8235 (mtmm) REVERT: B 355 ASN cc_start: 0.6898 (m-40) cc_final: 0.6468 (t0) REVERT: B 558 GLU cc_start: 0.9342 (OUTLIER) cc_final: 0.8256 (pt0) REVERT: B 630 LYS cc_start: 0.7622 (mmtt) cc_final: 0.7233 (mtpt) REVERT: B 654 ASN cc_start: 0.7279 (m-40) cc_final: 0.6970 (m110) REVERT: B 661 GLU cc_start: 0.8074 (pt0) cc_final: 0.7140 (pp20) REVERT: B 836 THR cc_start: 0.2559 (OUTLIER) cc_final: 0.2319 (m) REVERT: C 5 LYS cc_start: 0.8189 (tttt) cc_final: 0.7820 (ttpp) REVERT: C 18 ARG cc_start: 0.8176 (mtt180) cc_final: 0.7387 (pmt170) REVERT: C 43 PHE cc_start: 0.7199 (t80) cc_final: 0.6651 (t80) REVERT: C 304 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8152 (mm-30) REVERT: C 316 LYS cc_start: 0.8720 (tttt) cc_final: 0.8196 (mtmm) REVERT: C 416 MET cc_start: 0.8827 (mmt) cc_final: 0.8307 (mmt) REVERT: C 534 LYS cc_start: 0.8657 (mttt) cc_final: 0.8407 (mttt) REVERT: C 558 GLU cc_start: 0.9352 (OUTLIER) cc_final: 0.8262 (pt0) REVERT: C 630 LYS cc_start: 0.7640 (mmtt) cc_final: 0.7251 (mtpt) REVERT: C 654 ASN cc_start: 0.7317 (m-40) cc_final: 0.7017 (m110) REVERT: C 661 GLU cc_start: 0.8070 (pt0) cc_final: 0.7123 (pp20) REVERT: C 836 THR cc_start: 0.2495 (OUTLIER) cc_final: 0.2137 (m) REVERT: D 5 LYS cc_start: 0.8183 (tttt) cc_final: 0.7824 (ttpp) REVERT: D 18 ARG cc_start: 0.8195 (mtt180) cc_final: 0.7396 (pmt170) REVERT: D 43 PHE cc_start: 0.7199 (t80) cc_final: 0.6642 (t80) REVERT: D 304 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8176 (mm-30) REVERT: D 316 LYS cc_start: 0.8732 (tttt) cc_final: 0.8227 (mtmm) REVERT: D 416 MET cc_start: 0.8826 (mmt) cc_final: 0.8322 (mmt) REVERT: D 558 GLU cc_start: 0.9359 (OUTLIER) cc_final: 0.8330 (pt0) REVERT: D 630 LYS cc_start: 0.7624 (mmtt) cc_final: 0.7236 (mtpt) REVERT: D 654 ASN cc_start: 0.7299 (m-40) cc_final: 0.6992 (m110) REVERT: D 661 GLU cc_start: 0.8045 (pt0) cc_final: 0.7132 (pp20) REVERT: D 836 THR cc_start: 0.2428 (OUTLIER) cc_final: 0.2057 (m) outliers start: 58 outliers final: 37 residues processed: 288 average time/residue: 0.7765 time to fit residues: 256.6262 Evaluate side-chains 288 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 241 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 HIS Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain B residue 79 HIS Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 632 LYS Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain B residue 732 MET Chi-restraints excluded: chain B residue 836 THR Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 621 ASP Chi-restraints excluded: chain C residue 632 LYS Chi-restraints excluded: chain C residue 677 GLU Chi-restraints excluded: chain C residue 836 THR Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 478 MET Chi-restraints excluded: chain D residue 558 GLU Chi-restraints excluded: chain D residue 621 ASP Chi-restraints excluded: chain D residue 632 LYS Chi-restraints excluded: chain D residue 677 GLU Chi-restraints excluded: chain D residue 732 MET Chi-restraints excluded: chain D residue 836 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 250 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 115 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 117 optimal weight: 0.5980 chunk 268 optimal weight: 0.0070 chunk 43 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 110 optimal weight: 10.0000 chunk 102 optimal weight: 0.8980 overall best weight: 1.7002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 191 GLN B 191 GLN B 541 GLN I 9 ASN J 9 ASN K 9 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.194176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.124265 restraints weight = 32673.710| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.68 r_work: 0.3299 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 27768 Z= 0.138 Angle : 0.540 9.687 37764 Z= 0.275 Chirality : 0.064 1.569 4348 Planarity : 0.003 0.036 4928 Dihedral : 17.398 151.417 4504 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.04 % Allowed : 8.44 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.26 (0.14), residues: 3456 helix: 0.56 (0.15), residues: 1372 sheet: 0.27 (0.20), residues: 616 loop : -1.00 (0.16), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 715 TYR 0.016 0.001 TYR A 829 PHE 0.012 0.001 PHE B 638 TRP 0.012 0.001 TRP C 278 HIS 0.005 0.001 HIS A 586 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (27768) covalent geometry : angle 0.54011 / 0.28 (37764) hydrogen bonds : bond 0.04717 / 3.18 ( 1124) hydrogen bonds : angle 4.50391 / 3.17 ( 3132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 242 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8120 (tttt) cc_final: 0.7839 (ttpp) REVERT: A 18 ARG cc_start: 0.8234 (mtt180) cc_final: 0.7476 (pmt170) REVERT: A 35 ARG cc_start: 0.6272 (mtp-110) cc_final: 0.5850 (mtp-110) REVERT: A 103 GLU cc_start: 0.7736 (pm20) cc_final: 0.7529 (tp30) REVERT: A 304 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8171 (mm-30) REVERT: A 316 LYS cc_start: 0.8749 (tttt) cc_final: 0.8271 (mtmm) REVERT: A 558 GLU cc_start: 0.9341 (OUTLIER) cc_final: 0.8329 (pt0) REVERT: A 589 LEU cc_start: 0.7827 (mt) cc_final: 0.7596 (mp) REVERT: A 630 LYS cc_start: 0.7657 (mmtt) cc_final: 0.7229 (mtmt) REVERT: A 654 ASN cc_start: 0.7275 (m-40) cc_final: 0.6983 (m110) REVERT: A 661 GLU cc_start: 0.8088 (pt0) cc_final: 0.7180 (pp20) REVERT: B 5 LYS cc_start: 0.8127 (tttt) cc_final: 0.7817 (ttpp) REVERT: B 18 ARG cc_start: 0.8241 (mtt180) cc_final: 0.7443 (pmt170) REVERT: B 79 HIS cc_start: 0.5189 (OUTLIER) cc_final: 0.4411 (m170) REVERT: B 134 ARG cc_start: 0.6609 (OUTLIER) cc_final: 0.5630 (ttt90) REVERT: B 304 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8166 (mm-30) REVERT: B 316 LYS cc_start: 0.8734 (tttt) cc_final: 0.8251 (mtmm) REVERT: B 355 ASN cc_start: 0.6948 (m-40) cc_final: 0.6631 (t0) REVERT: B 558 GLU cc_start: 0.9336 (OUTLIER) cc_final: 0.8307 (pt0) REVERT: B 630 LYS cc_start: 0.7670 (mmtt) cc_final: 0.7241 (mtmt) REVERT: B 654 ASN cc_start: 0.7241 (m-40) cc_final: 0.6960 (m110) REVERT: B 661 GLU cc_start: 0.8098 (pt0) cc_final: 0.7198 (pp20) REVERT: C 5 LYS cc_start: 0.8138 (tttt) cc_final: 0.7822 (ttpp) REVERT: C 18 ARG cc_start: 0.8220 (mtt180) cc_final: 0.7481 (pmt170) REVERT: C 79 HIS cc_start: 0.5074 (OUTLIER) cc_final: 0.4036 (m170) REVERT: C 304 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8201 (mm-30) REVERT: C 316 LYS cc_start: 0.8739 (tttt) cc_final: 0.8230 (mtmm) REVERT: C 416 MET cc_start: 0.8855 (mmt) cc_final: 0.8370 (mmt) REVERT: C 534 LYS cc_start: 0.8647 (mttt) cc_final: 0.8429 (mttt) REVERT: C 558 GLU cc_start: 0.9351 (OUTLIER) cc_final: 0.8335 (pt0) REVERT: C 630 LYS cc_start: 0.7653 (mmtt) cc_final: 0.7232 (mtmt) REVERT: C 654 ASN cc_start: 0.7281 (m-40) cc_final: 0.6989 (m110) REVERT: C 661 GLU cc_start: 0.8108 (pt0) cc_final: 0.7207 (pp20) REVERT: D 5 LYS cc_start: 0.8123 (tttt) cc_final: 0.7807 (ttpp) REVERT: D 18 ARG cc_start: 0.8254 (mtt180) cc_final: 0.7453 (pmt170) REVERT: D 35 ARG cc_start: 0.6550 (mtp-110) cc_final: 0.6199 (mtp-110) REVERT: D 79 HIS cc_start: 0.5025 (OUTLIER) cc_final: 0.4012 (m170) REVERT: D 304 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8202 (mm-30) REVERT: D 316 LYS cc_start: 0.8738 (tttt) cc_final: 0.8252 (mtmm) REVERT: D 416 MET cc_start: 0.8864 (mmt) cc_final: 0.8382 (mmt) REVERT: D 558 GLU cc_start: 0.9348 (OUTLIER) cc_final: 0.8323 (pt0) REVERT: D 630 LYS cc_start: 0.7690 (mmtt) cc_final: 0.7269 (mtmt) REVERT: D 654 ASN cc_start: 0.7261 (m-40) cc_final: 0.6966 (m110) REVERT: D 661 GLU cc_start: 0.8072 (pt0) cc_final: 0.7174 (pp20) outliers start: 58 outliers final: 42 residues processed: 281 average time/residue: 0.7571 time to fit residues: 243.4198 Evaluate side-chains 281 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 231 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 621 ASP Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain B residue 79 HIS Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain B residue 732 MET Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain C residue 79 HIS Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 621 ASP Chi-restraints excluded: chain C residue 632 LYS Chi-restraints excluded: chain C residue 677 GLU Chi-restraints excluded: chain C residue 820 ILE Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 478 MET Chi-restraints excluded: chain D residue 558 GLU Chi-restraints excluded: chain D residue 621 ASP Chi-restraints excluded: chain D residue 677 GLU Chi-restraints excluded: chain D residue 820 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 268 optimal weight: 1.9990 chunk 164 optimal weight: 9.9990 chunk 104 optimal weight: 3.9990 chunk 299 optimal weight: 0.9990 chunk 231 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 187 optimal weight: 9.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 541 GLN I 9 ASN J 9 ASN K 9 ASN L 9 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.193794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.124058 restraints weight = 32526.481| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.66 r_work: 0.3285 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 27768 Z= 0.142 Angle : 0.543 9.725 37764 Z= 0.276 Chirality : 0.064 1.572 4348 Planarity : 0.003 0.035 4928 Dihedral : 17.089 152.171 4504 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.04 % Allowed : 8.33 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.29 (0.15), residues: 3456 helix: 0.51 (0.14), residues: 1396 sheet: 0.16 (0.20), residues: 624 loop : -0.97 (0.17), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 715 TYR 0.017 0.002 TYR A 829 PHE 0.013 0.001 PHE A 58 TRP 0.015 0.002 TRP A 278 HIS 0.005 0.001 HIS D 586 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (27768) covalent geometry : angle 0.54314 / 0.28 (37764) hydrogen bonds : bond 0.04734 / 3.19 ( 1124) hydrogen bonds : angle 4.50274 / 3.17 ( 3132) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 242 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8073 (tttt) cc_final: 0.7799 (ttpp) REVERT: A 18 ARG cc_start: 0.8247 (mtt180) cc_final: 0.7502 (pmt170) REVERT: A 35 ARG cc_start: 0.6325 (mtp-110) cc_final: 0.5904 (mtp-110) REVERT: A 79 HIS cc_start: 0.4977 (OUTLIER) cc_final: 0.3858 (m170) REVERT: A 304 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8188 (mm-30) REVERT: A 316 LYS cc_start: 0.8723 (tttt) cc_final: 0.8266 (mtmm) REVERT: A 558 GLU cc_start: 0.9347 (OUTLIER) cc_final: 0.8326 (pt0) REVERT: A 589 LEU cc_start: 0.7837 (mt) cc_final: 0.7595 (mp) REVERT: A 630 LYS cc_start: 0.7659 (mmtt) cc_final: 0.7244 (mtmt) REVERT: A 654 ASN cc_start: 0.7273 (m-40) cc_final: 0.6986 (m110) REVERT: A 661 GLU cc_start: 0.8096 (pt0) cc_final: 0.7211 (pp20) REVERT: B 5 LYS cc_start: 0.8060 (tttt) cc_final: 0.7791 (ttpp) REVERT: B 18 ARG cc_start: 0.8241 (mtt180) cc_final: 0.7496 (pmt170) REVERT: B 35 ARG cc_start: 0.6668 (mtm180) cc_final: 0.6455 (mtp-110) REVERT: B 79 HIS cc_start: 0.4914 (OUTLIER) cc_final: 0.4107 (m170) REVERT: B 134 ARG cc_start: 0.6590 (OUTLIER) cc_final: 0.5680 (ttt90) REVERT: B 304 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8162 (mm-30) REVERT: B 316 LYS cc_start: 0.8712 (tttt) cc_final: 0.8254 (mtmm) REVERT: B 355 ASN cc_start: 0.6977 (m-40) cc_final: 0.6679 (t0) REVERT: B 558 GLU cc_start: 0.9334 (OUTLIER) cc_final: 0.8304 (pt0) REVERT: B 630 LYS cc_start: 0.7676 (mmtt) cc_final: 0.7250 (mtmt) REVERT: B 654 ASN cc_start: 0.7288 (m-40) cc_final: 0.6999 (m110) REVERT: B 661 GLU cc_start: 0.8122 (pt0) cc_final: 0.7251 (pp20) REVERT: C 5 LYS cc_start: 0.8079 (tttt) cc_final: 0.7798 (ttpp) REVERT: C 18 ARG cc_start: 0.8248 (mtt180) cc_final: 0.7511 (pmt170) REVERT: C 79 HIS cc_start: 0.4888 (OUTLIER) cc_final: 0.3889 (m170) REVERT: C 304 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8159 (mm-30) REVERT: C 316 LYS cc_start: 0.8712 (tttt) cc_final: 0.8249 (mtmm) REVERT: C 534 LYS cc_start: 0.8664 (mttt) cc_final: 0.8397 (mttt) REVERT: C 558 GLU cc_start: 0.9347 (OUTLIER) cc_final: 0.8352 (pt0) REVERT: C 630 LYS cc_start: 0.7684 (mmtt) cc_final: 0.7259 (mtmt) REVERT: C 654 ASN cc_start: 0.7300 (m-40) cc_final: 0.7008 (m110) REVERT: C 661 GLU cc_start: 0.8120 (pt0) cc_final: 0.7236 (pp20) REVERT: D 5 LYS cc_start: 0.8049 (tttt) cc_final: 0.7763 (ttpp) REVERT: D 18 ARG cc_start: 0.8269 (mtt180) cc_final: 0.7506 (pmt170) REVERT: D 35 ARG cc_start: 0.6482 (mtp-110) cc_final: 0.6067 (mtp-110) REVERT: D 79 HIS cc_start: 0.4905 (OUTLIER) cc_final: 0.3883 (m170) REVERT: D 304 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8141 (mm-30) REVERT: D 316 LYS cc_start: 0.8718 (tttt) cc_final: 0.8249 (mtmm) REVERT: D 558 GLU cc_start: 0.9348 (OUTLIER) cc_final: 0.8317 (pt0) REVERT: D 630 LYS cc_start: 0.7695 (mmtt) cc_final: 0.7279 (mtmt) REVERT: D 654 ASN cc_start: 0.7262 (m-40) cc_final: 0.6979 (m110) REVERT: D 661 GLU cc_start: 0.8117 (pt0) cc_final: 0.7233 (pp20) outliers start: 58 outliers final: 42 residues processed: 279 average time/residue: 0.7366 time to fit residues: 235.2472 Evaluate side-chains 283 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 232 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 HIS Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 621 ASP Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain B residue 79 HIS Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 632 LYS Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain B residue 732 MET Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain C residue 79 HIS Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 621 ASP Chi-restraints excluded: chain C residue 677 GLU Chi-restraints excluded: chain C residue 820 ILE Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 478 MET Chi-restraints excluded: chain D residue 558 GLU Chi-restraints excluded: chain D residue 621 ASP Chi-restraints excluded: chain D residue 632 LYS Chi-restraints excluded: chain D residue 677 GLU Chi-restraints excluded: chain D residue 732 MET Chi-restraints excluded: chain D residue 820 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 139 optimal weight: 3.9990 chunk 123 optimal weight: 0.0870 chunk 125 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 262 optimal weight: 2.9990 chunk 270 optimal weight: 9.9990 chunk 225 optimal weight: 2.9990 chunk 314 optimal weight: 0.0370 chunk 305 optimal weight: 0.0000 chunk 233 optimal weight: 0.2980 overall best weight: 0.2640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 9 ASN J 9 ASN K 9 ASN L 9 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.197085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.128269 restraints weight = 32736.974| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.50 r_work: 0.3371 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.032 27768 Z= 0.070 Angle : 0.470 9.359 37764 Z= 0.233 Chirality : 0.063 1.594 4348 Planarity : 0.003 0.032 4928 Dihedral : 16.588 151.687 4504 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.09 % Allowed : 9.49 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.12 (0.15), residues: 3456 helix: 1.01 (0.15), residues: 1400 sheet: 0.26 (0.21), residues: 628 loop : -0.89 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 511 TYR 0.016 0.001 TYR D 116 PHE 0.010 0.001 PHE B 638 TRP 0.017 0.001 TRP B 278 HIS 0.002 0.000 HIS B 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00139 / 0.07 (27768) covalent geometry : angle 0.46960 / 0.23 (37764) hydrogen bonds : bond 0.02927 / 1.95 ( 1124) hydrogen bonds : angle 4.20656 / 2.96 ( 3132) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 262 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8013 (tttt) cc_final: 0.7808 (ttpp) REVERT: A 18 ARG cc_start: 0.8263 (mtt180) cc_final: 0.7541 (pmt170) REVERT: A 35 ARG cc_start: 0.6346 (mtp-110) cc_final: 0.5939 (mtp-110) REVERT: A 79 HIS cc_start: 0.4859 (OUTLIER) cc_final: 0.3863 (m170) REVERT: A 103 GLU cc_start: 0.7792 (pm20) cc_final: 0.7585 (tp30) REVERT: A 304 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8175 (mm-30) REVERT: A 316 LYS cc_start: 0.8766 (tttt) cc_final: 0.8367 (mtmm) REVERT: A 558 GLU cc_start: 0.9257 (OUTLIER) cc_final: 0.8078 (pt0) REVERT: A 589 LEU cc_start: 0.7879 (mt) cc_final: 0.7639 (mp) REVERT: A 630 LYS cc_start: 0.7688 (mmtt) cc_final: 0.7307 (mtmt) REVERT: A 654 ASN cc_start: 0.7147 (m-40) cc_final: 0.6930 (m110) REVERT: A 661 GLU cc_start: 0.8004 (pt0) cc_final: 0.7192 (pp20) REVERT: B 5 LYS cc_start: 0.8018 (tttt) cc_final: 0.7809 (ttpp) REVERT: B 18 ARG cc_start: 0.8281 (mtt180) cc_final: 0.7569 (pmt170) REVERT: B 79 HIS cc_start: 0.4964 (m170) cc_final: 0.4184 (m170) REVERT: B 304 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8161 (mm-30) REVERT: B 316 LYS cc_start: 0.8719 (tttt) cc_final: 0.8302 (mtmm) REVERT: B 355 ASN cc_start: 0.7015 (m-40) cc_final: 0.6742 (t0) REVERT: B 558 GLU cc_start: 0.9260 (OUTLIER) cc_final: 0.8226 (pt0) REVERT: B 630 LYS cc_start: 0.7708 (mmtt) cc_final: 0.7314 (mtmt) REVERT: B 654 ASN cc_start: 0.7147 (m-40) cc_final: 0.6929 (m110) REVERT: B 661 GLU cc_start: 0.8060 (pt0) cc_final: 0.7274 (pp20) REVERT: C 5 LYS cc_start: 0.8008 (tttt) cc_final: 0.7788 (ttpp) REVERT: C 18 ARG cc_start: 0.8256 (mtt180) cc_final: 0.7538 (pmt170) REVERT: C 79 HIS cc_start: 0.4915 (OUTLIER) cc_final: 0.3851 (m170) REVERT: C 250 ILE cc_start: 0.5333 (mp) cc_final: 0.5129 (mp) REVERT: C 304 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8145 (mm-30) REVERT: C 316 LYS cc_start: 0.8715 (tttt) cc_final: 0.8289 (mtmm) REVERT: C 534 LYS cc_start: 0.8668 (mttt) cc_final: 0.8442 (mttt) REVERT: C 558 GLU cc_start: 0.9264 (OUTLIER) cc_final: 0.8224 (pt0) REVERT: C 630 LYS cc_start: 0.7690 (mmtt) cc_final: 0.7313 (mtmt) REVERT: C 654 ASN cc_start: 0.7195 (m-40) cc_final: 0.6979 (m110) REVERT: C 661 GLU cc_start: 0.8054 (pt0) cc_final: 0.7258 (pp20) REVERT: D 5 LYS cc_start: 0.7999 (tttt) cc_final: 0.7790 (ttpp) REVERT: D 18 ARG cc_start: 0.8305 (mtt180) cc_final: 0.7569 (pmt170) REVERT: D 79 HIS cc_start: 0.4847 (OUTLIER) cc_final: 0.3839 (m170) REVERT: D 304 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8127 (mm-30) REVERT: D 316 LYS cc_start: 0.8723 (tttt) cc_final: 0.8297 (mtmm) REVERT: D 558 GLU cc_start: 0.9255 (OUTLIER) cc_final: 0.8053 (pt0) REVERT: D 630 LYS cc_start: 0.7711 (mmtt) cc_final: 0.7339 (mtmt) REVERT: D 654 ASN cc_start: 0.7166 (m-40) cc_final: 0.6946 (m110) REVERT: D 661 GLU cc_start: 0.8041 (pt0) cc_final: 0.7242 (pp20) outliers start: 31 outliers final: 9 residues processed: 281 average time/residue: 0.6971 time to fit residues: 226.8381 Evaluate side-chains 254 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 238 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 HIS Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 621 ASP Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 732 MET Chi-restraints excluded: chain C residue 79 HIS Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 621 ASP Chi-restraints excluded: chain C residue 677 GLU Chi-restraints excluded: chain C residue 820 ILE Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain D residue 558 GLU Chi-restraints excluded: chain D residue 621 ASP Chi-restraints excluded: chain D residue 677 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 41 optimal weight: 4.9990 chunk 77 optimal weight: 20.0000 chunk 164 optimal weight: 10.0000 chunk 113 optimal weight: 0.0770 chunk 103 optimal weight: 2.9990 chunk 280 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 211 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 308 optimal weight: 3.9990 chunk 177 optimal weight: 4.9990 overall best weight: 1.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 641 ASN C 641 ASN I 9 ASN J 9 ASN K 9 ASN L 9 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.193850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.126809 restraints weight = 32648.230| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.52 r_work: 0.3308 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 27768 Z= 0.146 Angle : 0.533 9.819 37764 Z= 0.270 Chirality : 0.065 1.606 4348 Planarity : 0.003 0.033 4928 Dihedral : 16.715 150.926 4504 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.13 % Allowed : 10.41 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.03 (0.15), residues: 3456 helix: 0.84 (0.15), residues: 1396 sheet: 0.30 (0.22), residues: 564 loop : -0.93 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 511 TYR 0.015 0.002 TYR A 829 PHE 0.009 0.001 PHE A 692 TRP 0.009 0.001 TRP B 181 HIS 0.004 0.001 HIS D 586 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (27768) covalent geometry : angle 0.53342 / 0.27 (37764) hydrogen bonds : bond 0.04615 / 3.11 ( 1124) hydrogen bonds : angle 4.35740 / 3.07 ( 3132) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 237 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8096 (tttt) cc_final: 0.7814 (ttpp) REVERT: A 18 ARG cc_start: 0.8292 (mtt180) cc_final: 0.7573 (pmt170) REVERT: A 35 ARG cc_start: 0.6369 (mtp-110) cc_final: 0.5942 (mtp-110) REVERT: A 79 HIS cc_start: 0.4783 (OUTLIER) cc_final: 0.3631 (m170) REVERT: A 304 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8195 (mm-30) REVERT: A 316 LYS cc_start: 0.8775 (tttt) cc_final: 0.8355 (mtmm) REVERT: A 526 TYR cc_start: 0.8943 (m-80) cc_final: 0.8738 (m-80) REVERT: A 558 GLU cc_start: 0.9327 (OUTLIER) cc_final: 0.8350 (pt0) REVERT: A 589 LEU cc_start: 0.7922 (mt) cc_final: 0.7685 (mp) REVERT: A 630 LYS cc_start: 0.7721 (mmtt) cc_final: 0.7342 (mtmt) REVERT: A 654 ASN cc_start: 0.7289 (m-40) cc_final: 0.7028 (m110) REVERT: A 661 GLU cc_start: 0.8136 (pt0) cc_final: 0.7288 (pp20) REVERT: B 5 LYS cc_start: 0.8074 (tttt) cc_final: 0.7789 (ttpp) REVERT: B 18 ARG cc_start: 0.8273 (mtt180) cc_final: 0.7585 (pmt170) REVERT: B 79 HIS cc_start: 0.4991 (OUTLIER) cc_final: 0.4151 (m170) REVERT: B 304 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8186 (mm-30) REVERT: B 316 LYS cc_start: 0.8774 (tttt) cc_final: 0.8347 (mtmm) REVERT: B 355 ASN cc_start: 0.6987 (m-40) cc_final: 0.6715 (t0) REVERT: B 558 GLU cc_start: 0.9331 (OUTLIER) cc_final: 0.8320 (pt0) REVERT: B 630 LYS cc_start: 0.7740 (mmtt) cc_final: 0.7358 (mtmt) REVERT: B 654 ASN cc_start: 0.7272 (m-40) cc_final: 0.7013 (m110) REVERT: B 661 GLU cc_start: 0.8152 (pt0) cc_final: 0.7333 (pp20) REVERT: C 5 LYS cc_start: 0.8078 (tttt) cc_final: 0.7784 (ttpp) REVERT: C 18 ARG cc_start: 0.8265 (mtt180) cc_final: 0.7576 (pmt170) REVERT: C 79 HIS cc_start: 0.4746 (OUTLIER) cc_final: 0.3722 (m170) REVERT: C 304 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8168 (mm-30) REVERT: C 316 LYS cc_start: 0.8776 (tttt) cc_final: 0.8342 (mtmm) REVERT: C 534 LYS cc_start: 0.8678 (mttt) cc_final: 0.8461 (mttt) REVERT: C 558 GLU cc_start: 0.9339 (OUTLIER) cc_final: 0.8347 (pt0) REVERT: C 630 LYS cc_start: 0.7736 (mmtt) cc_final: 0.7360 (mtmt) REVERT: C 654 ASN cc_start: 0.7292 (m-40) cc_final: 0.7020 (m110) REVERT: C 661 GLU cc_start: 0.8164 (pt0) cc_final: 0.7315 (pp20) REVERT: D 5 LYS cc_start: 0.8066 (tttt) cc_final: 0.7847 (ttpp) REVERT: D 18 ARG cc_start: 0.8284 (mtt180) cc_final: 0.7576 (pmt170) REVERT: D 35 ARG cc_start: 0.6521 (mtp-110) cc_final: 0.6249 (mtp180) REVERT: D 79 HIS cc_start: 0.4768 (OUTLIER) cc_final: 0.3745 (m170) REVERT: D 304 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8179 (mm-30) REVERT: D 316 LYS cc_start: 0.8774 (tttt) cc_final: 0.8336 (mtmm) REVERT: D 558 GLU cc_start: 0.9330 (OUTLIER) cc_final: 0.8322 (pt0) REVERT: D 630 LYS cc_start: 0.7754 (mmtt) cc_final: 0.7389 (mtmt) REVERT: D 654 ASN cc_start: 0.7272 (m-40) cc_final: 0.7004 (m110) REVERT: D 661 GLU cc_start: 0.8116 (pt0) cc_final: 0.7287 (pp20) outliers start: 32 outliers final: 22 residues processed: 261 average time/residue: 0.7787 time to fit residues: 232.8488 Evaluate side-chains 258 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 228 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 HIS Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 621 ASP Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain B residue 79 HIS Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain B residue 732 MET Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain C residue 79 HIS Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 621 ASP Chi-restraints excluded: chain C residue 677 GLU Chi-restraints excluded: chain C residue 820 ILE Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 558 GLU Chi-restraints excluded: chain D residue 621 ASP Chi-restraints excluded: chain D residue 677 GLU Chi-restraints excluded: chain D residue 732 MET Chi-restraints excluded: chain D residue 820 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 216 optimal weight: 5.9990 chunk 319 optimal weight: 0.0980 chunk 35 optimal weight: 9.9990 chunk 275 optimal weight: 5.9990 chunk 209 optimal weight: 0.1980 chunk 334 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 61 optimal weight: 0.0770 chunk 306 optimal weight: 2.9990 chunk 245 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.0742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 740 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 9 ASN J 9 ASN K 9 ASN L 9 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.195275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.128572 restraints weight = 32501.608| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.52 r_work: 0.3337 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 27768 Z= 0.098 Angle : 0.489 9.678 37764 Z= 0.245 Chirality : 0.064 1.604 4348 Planarity : 0.003 0.032 4928 Dihedral : 16.528 150.782 4504 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.09 % Allowed : 10.51 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.07 (0.15), residues: 3456 helix: 1.00 (0.15), residues: 1396 sheet: 0.30 (0.20), residues: 636 loop : -1.00 (0.17), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 715 TYR 0.013 0.001 TYR D 116 PHE 0.011 0.001 PHE B 638 TRP 0.024 0.001 TRP B 278 HIS 0.003 0.000 HIS C 650 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (27768) covalent geometry : angle 0.48905 / 0.24 (37764) hydrogen bonds : bond 0.03654 / 2.45 ( 1124) hydrogen bonds : angle 4.23953 / 2.99 ( 3132) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 232 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8036 (tttt) cc_final: 0.7765 (ttpp) REVERT: A 18 ARG cc_start: 0.8270 (mtt180) cc_final: 0.7512 (pmt170) REVERT: A 35 ARG cc_start: 0.6399 (mtp-110) cc_final: 0.5984 (mtp-110) REVERT: A 79 HIS cc_start: 0.4686 (OUTLIER) cc_final: 0.3601 (m170) REVERT: A 304 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8180 (mm-30) REVERT: A 316 LYS cc_start: 0.8743 (tttt) cc_final: 0.8307 (mtmm) REVERT: A 558 GLU cc_start: 0.9297 (OUTLIER) cc_final: 0.8297 (pt0) REVERT: A 589 LEU cc_start: 0.7858 (mt) cc_final: 0.7611 (mp) REVERT: A 630 LYS cc_start: 0.7710 (mmtt) cc_final: 0.7323 (mtmt) REVERT: A 654 ASN cc_start: 0.7211 (m-40) cc_final: 0.6939 (m110) REVERT: A 661 GLU cc_start: 0.8063 (pt0) cc_final: 0.7240 (pp20) REVERT: B 5 LYS cc_start: 0.8017 (tttt) cc_final: 0.7757 (ttpp) REVERT: B 18 ARG cc_start: 0.8238 (mtt180) cc_final: 0.7503 (pmt170) REVERT: B 79 HIS cc_start: 0.4939 (OUTLIER) cc_final: 0.4107 (m170) REVERT: B 304 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8154 (mm-30) REVERT: B 316 LYS cc_start: 0.8736 (tttt) cc_final: 0.8296 (mtmm) REVERT: B 355 ASN cc_start: 0.7024 (m-40) cc_final: 0.6759 (t0) REVERT: B 558 GLU cc_start: 0.9291 (OUTLIER) cc_final: 0.8257 (pt0) REVERT: B 630 LYS cc_start: 0.7720 (mmtt) cc_final: 0.7329 (mtmt) REVERT: B 654 ASN cc_start: 0.7199 (m-40) cc_final: 0.6927 (m110) REVERT: B 661 GLU cc_start: 0.8092 (pt0) cc_final: 0.7285 (pp20) REVERT: C 5 LYS cc_start: 0.8015 (tttt) cc_final: 0.7737 (ttpp) REVERT: C 18 ARG cc_start: 0.8265 (mtt180) cc_final: 0.7527 (pmt170) REVERT: C 79 HIS cc_start: 0.4631 (OUTLIER) cc_final: 0.3510 (m170) REVERT: C 304 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8139 (mm-30) REVERT: C 316 LYS cc_start: 0.8728 (tttt) cc_final: 0.8286 (mtmm) REVERT: C 534 LYS cc_start: 0.8674 (mttt) cc_final: 0.8449 (mttt) REVERT: C 558 GLU cc_start: 0.9295 (OUTLIER) cc_final: 0.8277 (pt0) REVERT: C 630 LYS cc_start: 0.7703 (mmtt) cc_final: 0.7329 (mtmt) REVERT: C 654 ASN cc_start: 0.7217 (m-40) cc_final: 0.6942 (m110) REVERT: C 661 GLU cc_start: 0.8086 (pt0) cc_final: 0.7277 (pp20) REVERT: D 5 LYS cc_start: 0.7958 (tttt) cc_final: 0.7723 (ttpp) REVERT: D 18 ARG cc_start: 0.8293 (mtt180) cc_final: 0.7543 (pmt170) REVERT: D 79 HIS cc_start: 0.4689 (OUTLIER) cc_final: 0.3706 (m170) REVERT: D 304 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8145 (mm-30) REVERT: D 316 LYS cc_start: 0.8735 (tttt) cc_final: 0.8282 (mtmm) REVERT: D 558 GLU cc_start: 0.9287 (OUTLIER) cc_final: 0.8253 (pt0) REVERT: D 630 LYS cc_start: 0.7694 (mmtt) cc_final: 0.7344 (mtmt) REVERT: D 654 ASN cc_start: 0.7183 (m-40) cc_final: 0.6916 (m110) REVERT: D 661 GLU cc_start: 0.8122 (pt0) cc_final: 0.7292 (pp20) outliers start: 31 outliers final: 18 residues processed: 255 average time/residue: 0.7351 time to fit residues: 214.9389 Evaluate side-chains 256 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 230 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 HIS Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 621 ASP Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain B residue 79 HIS Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 632 LYS Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain B residue 732 MET Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain C residue 79 HIS Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 621 ASP Chi-restraints excluded: chain C residue 677 GLU Chi-restraints excluded: chain C residue 820 ILE Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 558 GLU Chi-restraints excluded: chain D residue 621 ASP Chi-restraints excluded: chain D residue 677 GLU Chi-restraints excluded: chain D residue 732 MET Chi-restraints excluded: chain D residue 820 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 184 optimal weight: 5.9990 chunk 321 optimal weight: 0.9980 chunk 178 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 296 optimal weight: 2.9990 chunk 187 optimal weight: 0.0370 chunk 2 optimal weight: 3.9990 chunk 246 optimal weight: 8.9990 chunk 341 optimal weight: 20.0000 chunk 42 optimal weight: 4.9990 chunk 195 optimal weight: 0.6980 overall best weight: 1.7462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 707 ASN ** A 740 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 707 ASN I 9 ASN J 9 ASN K 9 ASN L 9 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.193556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.125558 restraints weight = 32543.903| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.53 r_work: 0.3305 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 27768 Z= 0.138 Angle : 0.532 9.957 37764 Z= 0.269 Chirality : 0.065 1.612 4348 Planarity : 0.003 0.033 4928 Dihedral : 16.583 150.221 4504 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.16 % Allowed : 10.55 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.07 (0.15), residues: 3456 helix: 0.87 (0.15), residues: 1396 sheet: 0.17 (0.20), residues: 648 loop : -1.03 (0.17), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 511 TYR 0.015 0.001 TYR A 829 PHE 0.025 0.001 PHE B 759 TRP 0.022 0.001 TRP A 278 HIS 0.004 0.001 HIS B 586 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (27768) covalent geometry : angle 0.53152 / 0.27 (37764) hydrogen bonds : bond 0.04594 / 3.09 ( 1124) hydrogen bonds : angle 4.35377 / 3.07 ( 3132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11570.79 seconds wall clock time: 197 minutes 8.32 seconds (11828.32 seconds total)