Starting phenix.real_space_refine on Sun Jul 5 11:27:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lgj_23325/07_2026/7lgj_23325_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lgj_23325/07_2026/7lgj_23325.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lgj_23325/07_2026/7lgj_23325_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lgj_23325/07_2026/7lgj_23325_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lgj_23325/07_2026/7lgj_23325.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lgj_23325/07_2026/7lgj_23325.map" } resolution = 2.6 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= 0.005 sd= 0.134 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 12 5.21 5 S 96 5.16 5 C 16948 2.51 5 N 4756 2.21 5 O 5256 1.98 5 H 185 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 27277 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 6645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 869, 6645 Classifications: {'peptide': 869} Link IDs: {'PTRANS': 40, 'TRANS': 828} Chain breaks: 1 Chain: "B" Number of atoms: 6645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 869, 6645 Classifications: {'peptide': 869} Link IDs: {'PTRANS': 40, 'TRANS': 828} Chain breaks: 1 Chain: "C" Number of atoms: 6645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 869, 6645 Classifications: {'peptide': 869} Link IDs: {'PTRANS': 40, 'TRANS': 828} Chain breaks: 1 Chain: "D" Number of atoms: 6645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 869, 6645 Classifications: {'peptide': 869} Link IDs: {'PTRANS': 40, 'TRANS': 828} Chain breaks: 1 Chain: "E" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 109 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'7ID:plan-1': 1, '7ID:plan-2': 1, '7ID:plan-3': 1, '7ID:plan-4': 4} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 108 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'7ID:plan-1': 1, '7ID:plan-2': 1, '7ID:plan-3': 1, '7ID:plan-4': 4} Unresolved non-hydrogen planarities: 17 Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 108 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'7ID:plan-1': 1, '7ID:plan-2': 1, '7ID:plan-3': 1, '7ID:plan-4': 4} Unresolved non-hydrogen planarities: 17 Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 108 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'7ID:plan-1': 1, '7ID:plan-2': 1, '7ID:plan-3': 1, '7ID:plan-4': 4} Unresolved non-hydrogen planarities: 17 Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 65 Unusual residues: {' MG': 3, 'ACP': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 65 Unusual residues: {' MG': 3, 'ACP': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 65 Unusual residues: {' MG': 3, 'ACP': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 65 Unusual residues: {' MG': 3, 'ACP': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 5.93, per 1000 atoms: 0.22 Number of scatterers: 27277 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 12 11.99 O 5256 8.00 N 4756 7.00 C 16948 6.00 H 185 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.42 Conformation dependent library (CDL) restraints added in 1.2 seconds 6920 Ramachandran restraints generated. 3460 Oldfield, 0 Emsley, 3460 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6344 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 28 sheets defined 38.7% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 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: 4.405A pdb=" N ASP A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 177 removed outlier: 3.522A pdb=" N ILE A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) 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: 5.082A pdb=" N ASN A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 3.979A 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: 4.069A 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: 3.695A 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: 3.894A 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: 3.593A pdb=" N LYS A 600 " --> pdb=" O GLU A 596 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL A 604 " --> pdb=" O LYS A 600 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ILE A 605 " --> pdb=" O VAL A 601 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA A 606 " --> pdb=" O LYS A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 626 removed outlier: 3.872A 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: 3.994A pdb=" N GLN A 791 " --> pdb=" O GLN A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 824 removed outlier: 3.809A 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: 4.404A pdb=" N ASP B 150 " --> pdb=" O GLU B 146 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER B 161 " --> pdb=" O LEU B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 177 removed outlier: 3.522A pdb=" N ILE B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) 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: 5.083A pdb=" N ASN B 251 " --> pdb=" O GLU B 247 " (cutoff:3.500A) removed outlier: 3.979A 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: 4.069A 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: 3.695A 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: 3.894A 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: 3.593A pdb=" N LYS B 600 " --> pdb=" O GLU B 596 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL B 604 " --> pdb=" O LYS B 600 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ILE B 605 " --> pdb=" O VAL B 601 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA B 606 " --> pdb=" O LYS B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 626 removed outlier: 3.871A 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: 3.993A pdb=" N GLN B 791 " --> pdb=" O GLN B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 810 through 824 removed outlier: 3.809A 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: 4.406A pdb=" N ASP C 150 " --> pdb=" O GLU C 146 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER C 161 " --> pdb=" O LEU C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 177 removed outlier: 3.522A pdb=" N ILE C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) 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: 5.082A pdb=" N ASN C 251 " --> pdb=" O GLU C 247 " (cutoff:3.500A) removed outlier: 3.980A 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: 4.069A 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: 3.695A 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: 3.894A 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: 3.593A pdb=" N LYS C 600 " --> pdb=" O GLU C 596 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL C 604 " --> pdb=" O LYS C 600 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ILE C 605 " --> pdb=" O VAL C 601 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA C 606 " --> pdb=" O LYS C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 626 removed outlier: 3.871A 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: 3.809A 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: 4.405A pdb=" N ASP D 150 " --> pdb=" O GLU D 146 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER D 161 " --> pdb=" O LEU D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 177 removed outlier: 3.522A pdb=" N ILE D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) 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: 5.082A pdb=" N ASN D 251 " --> pdb=" O GLU D 247 " (cutoff:3.500A) removed outlier: 3.980A 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: 4.069A 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: 3.696A 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: 3.894A 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: 3.593A pdb=" N LYS D 600 " --> pdb=" O GLU D 596 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL D 604 " --> pdb=" O LYS D 600 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ILE D 605 " --> pdb=" O VAL D 601 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA D 606 " --> pdb=" O LYS D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 626 removed outlier: 3.871A 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: 6.721A pdb=" N ARG A 26 " --> pdb=" O LEU A 4 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N THR A 6 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL A 24 " --> pdb=" O THR A 6 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N THR A 8 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU A 22 " --> pdb=" O THR A 8 " (cutoff:3.500A) removed outlier: 4.286A 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: 5.507A pdb=" N ILE A 273 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 5.463A 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: 4.353A pdb=" N ASP A 307 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL A 433 " --> pdb=" O ILE A 448 " (cutoff:3.500A) removed outlier: 5.687A 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: 6.587A pdb=" N ILE A 525 " --> pdb=" O VAL A 532 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU A 491 " --> pdb=" O LEU A 557 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE A 490 " --> pdb=" O CYS A 574 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ASP A 575 " --> pdb=" O TYR A 614 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N VAL A 616 " --> pdb=" O ASP A 575 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLY A 577 " --> pdb=" O VAL A 616 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N ASN A 618 " --> pdb=" O GLY A 577 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N VAL A 579 " --> pdb=" O ASN A 618 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL A 635 " --> pdb=" O ILE A 656 " (cutoff:3.500A) removed outlier: 9.057A pdb=" N ALA A 658 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TYR A 637 " --> pdb=" O ALA A 658 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N TYR A 660 " --> pdb=" O TYR A 637 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N SER A 639 " --> pdb=" O TYR A 660 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU A 677 " --> pdb=" O LEU A 665 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE A 667 " --> pdb=" O ARG A 675 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ARG A 675 " --> pdb=" O ILE A 667 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLU A 669 " --> pdb=" O THR A 673 " (cutoff:3.500A) removed outlier: 5.517A 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: 6.862A 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: 6.722A pdb=" N ARG B 26 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N THR B 6 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL B 24 " --> pdb=" O THR B 6 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N THR B 8 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU B 22 " --> pdb=" O THR B 8 " (cutoff:3.500A) removed outlier: 4.286A 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: 5.508A pdb=" N ILE B 273 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 5.463A 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: 4.353A pdb=" N ASP B 307 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL B 433 " --> pdb=" O ILE B 448 " (cutoff:3.500A) removed outlier: 5.688A 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: 6.587A pdb=" N ILE B 525 " --> pdb=" O VAL B 532 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU B 491 " --> pdb=" O LEU B 557 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE B 490 " --> pdb=" O CYS B 574 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ASP B 575 " --> pdb=" O TYR B 614 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N VAL B 616 " --> pdb=" O ASP B 575 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY B 577 " --> pdb=" O VAL B 616 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N ASN B 618 " --> pdb=" O GLY B 577 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N VAL B 579 " --> pdb=" O ASN B 618 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL B 635 " --> pdb=" O ILE B 656 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N ALA B 658 " --> pdb=" O VAL B 635 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR B 637 " --> pdb=" O ALA B 658 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N TYR B 660 " --> pdb=" O TYR B 637 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N SER B 639 " --> pdb=" O TYR B 660 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU B 677 " --> pdb=" O LEU B 665 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE B 667 " --> pdb=" O ARG B 675 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ARG B 675 " --> pdb=" O ILE B 667 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLU B 669 " --> pdb=" O THR B 673 " (cutoff:3.500A) removed outlier: 5.518A 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: 6.862A 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: 6.721A pdb=" N ARG C 26 " --> pdb=" O LEU C 4 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N THR C 6 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL C 24 " --> pdb=" O THR C 6 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N THR C 8 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU C 22 " --> pdb=" O THR C 8 " (cutoff:3.500A) removed outlier: 4.286A 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: 5.507A pdb=" N ILE C 273 " --> pdb=" O ILE C 260 " (cutoff:3.500A) removed outlier: 5.464A 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: 4.353A pdb=" N ASP C 307 " --> pdb=" O ARG C 323 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL C 433 " --> pdb=" O ILE C 448 " (cutoff:3.500A) removed outlier: 5.687A 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: 6.587A pdb=" N ILE C 525 " --> pdb=" O VAL C 532 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE C 490 " --> pdb=" O CYS C 574 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ASP C 575 " --> pdb=" O TYR C 614 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N VAL C 616 " --> pdb=" O ASP C 575 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLY C 577 " --> pdb=" O VAL C 616 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ASN C 618 " --> pdb=" O GLY C 577 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N VAL C 579 " --> pdb=" O ASN C 618 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL C 635 " --> pdb=" O ILE C 656 " (cutoff:3.500A) removed outlier: 9.057A pdb=" N ALA C 658 " --> pdb=" O VAL C 635 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR C 637 " --> pdb=" O ALA C 658 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N TYR C 660 " --> pdb=" O TYR C 637 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N SER C 639 " --> pdb=" O TYR C 660 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU C 677 " --> pdb=" O LEU C 665 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE C 667 " --> pdb=" O ARG C 675 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ARG C 675 " --> pdb=" O ILE C 667 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLU C 669 " --> pdb=" O THR C 673 " (cutoff:3.500A) removed outlier: 5.517A 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: 6.862A 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: 6.722A pdb=" N ARG D 26 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N THR D 6 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL D 24 " --> pdb=" O THR D 6 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N THR D 8 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU D 22 " --> pdb=" O THR D 8 " (cutoff:3.500A) removed outlier: 4.287A 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: 5.507A pdb=" N ILE D 273 " --> pdb=" O ILE D 260 " (cutoff:3.500A) removed outlier: 5.462A 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: 4.353A pdb=" N ASP D 307 " --> pdb=" O ARG D 323 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL D 433 " --> pdb=" O ILE D 448 " (cutoff:3.500A) removed outlier: 5.686A 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: 6.587A pdb=" N ILE D 525 " --> pdb=" O VAL D 532 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE D 490 " --> pdb=" O CYS D 574 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ASP D 575 " --> pdb=" O TYR D 614 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N VAL D 616 " --> pdb=" O ASP D 575 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLY D 577 " --> pdb=" O VAL D 616 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N ASN D 618 " --> pdb=" O GLY D 577 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N VAL D 579 " --> pdb=" O ASN D 618 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL D 635 " --> pdb=" O ILE D 656 " (cutoff:3.500A) removed outlier: 9.057A pdb=" N ALA D 658 " --> pdb=" O VAL D 635 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR D 637 " --> pdb=" O ALA D 658 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N TYR D 660 " --> pdb=" O TYR D 637 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N SER D 639 " --> pdb=" O TYR D 660 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU D 677 " --> pdb=" O LEU D 665 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE D 667 " --> pdb=" O ARG D 675 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ARG D 675 " --> pdb=" O ILE D 667 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLU D 669 " --> pdb=" O THR D 673 " (cutoff:3.500A) removed outlier: 5.517A 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: 6.862A pdb=" N GLY D 769 " --> pdb=" O VAL D 853 " (cutoff:3.500A) 1114 hydrogen bonds defined for protein. 3102 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: 5.69 Time building geometry restraints manager: 3.00 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: 185 1.05 - 1.25: 4639 1.25 - 1.45: 7619 1.45 - 1.64: 15098 1.64 - 1.84: 184 Bond restraints: 27725 Sorted by residual: 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 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 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 G 6 " pdb=" N 7ID G 7 " ideal model delta sigma weight residual 1.329 1.479 -0.150 1.40e-02 5.10e+03 1.15e+02 ... (remaining 27720 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.12: 36241 4.12 - 8.23: 1473 8.23 - 12.35: 124 12.35 - 16.46: 20 16.46 - 20.58: 16 Bond angle restraints: 37874 Sorted by residual: angle pdb=" N HIS B 353 " pdb=" CA HIS B 353 " pdb=" CB HIS B 353 " ideal model delta sigma weight residual 113.15 133.73 -20.58 1.63e+00 3.76e-01 1.59e+02 angle pdb=" N HIS D 353 " pdb=" CA HIS D 353 " pdb=" CB HIS D 353 " ideal model delta sigma weight residual 113.15 133.73 -20.58 1.63e+00 3.76e-01 1.59e+02 angle pdb=" N HIS A 353 " pdb=" CA HIS A 353 " pdb=" CB HIS A 353 " ideal model delta sigma weight residual 113.15 133.69 -20.54 1.63e+00 3.76e-01 1.59e+02 angle pdb=" N HIS C 353 " pdb=" CA HIS C 353 " pdb=" CB HIS C 353 " ideal model delta sigma weight residual 113.15 133.68 -20.53 1.63e+00 3.76e-01 1.59e+02 angle pdb=" N GLY D 424 " pdb=" CA GLY D 424 " pdb=" C GLY D 424 " ideal model delta sigma weight residual 113.48 128.98 -15.50 1.46e+00 4.69e-01 1.13e+02 ... (remaining 37869 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.32: 16621 35.32 - 70.64: 232 70.64 - 105.95: 80 105.95 - 141.27: 20 141.27 - 176.59: 24 Dihedral angle restraints: 16977 sinusoidal: 7037 harmonic: 9940 Sorted by residual: dihedral pdb=" N HIS B 353 " pdb=" C HIS B 353 " pdb=" CA HIS B 353 " pdb=" CB HIS B 353 " ideal model delta harmonic sigma weight residual 122.80 159.29 -36.49 0 2.50e+00 1.60e-01 2.13e+02 dihedral pdb=" N HIS C 353 " pdb=" C HIS C 353 " pdb=" CA HIS C 353 " pdb=" CB HIS C 353 " ideal model delta harmonic sigma weight residual 122.80 159.27 -36.47 0 2.50e+00 1.60e-01 2.13e+02 dihedral pdb=" N HIS A 353 " pdb=" C HIS A 353 " pdb=" CA HIS A 353 " pdb=" CB HIS A 353 " ideal model delta harmonic sigma weight residual 122.80 159.26 -36.46 0 2.50e+00 1.60e-01 2.13e+02 ... (remaining 16974 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.288: 4280 0.288 - 0.576: 32 0.576 - 0.864: 0 0.864 - 1.152: 0 1.152 - 1.440: 12 Chirality restraints: 4324 Sorted by residual: chirality pdb=" CA HIS B 353 " pdb=" N HIS B 353 " pdb=" C HIS B 353 " pdb=" CB HIS B 353 " both_signs ideal model delta sigma weight residual False 2.51 1.07 1.44 2.00e-01 2.50e+01 5.19e+01 chirality pdb=" CA HIS C 353 " pdb=" N HIS C 353 " pdb=" C HIS C 353 " pdb=" CB HIS C 353 " both_signs ideal model delta sigma weight residual False 2.51 1.07 1.44 2.00e-01 2.50e+01 5.19e+01 chirality pdb=" CA HIS A 353 " pdb=" N HIS A 353 " pdb=" C HIS A 353 " pdb=" CB HIS A 353 " both_signs ideal model delta sigma weight residual False 2.51 1.07 1.44 2.00e-01 2.50e+01 5.18e+01 ... (remaining 4321 not shown) Planarity restraints: 4876 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 353 " 0.048 2.00e-02 2.50e+03 3.88e-02 2.26e+01 pdb=" CG HIS A 353 " -0.077 2.00e-02 2.50e+03 pdb=" ND1 HIS A 353 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 HIS A 353 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS A 353 " 0.019 2.00e-02 2.50e+03 pdb=" NE2 HIS A 353 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 353 " -0.048 2.00e-02 2.50e+03 3.88e-02 2.26e+01 pdb=" CG HIS C 353 " 0.077 2.00e-02 2.50e+03 pdb=" ND1 HIS C 353 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 HIS C 353 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS C 353 " -0.019 2.00e-02 2.50e+03 pdb=" NE2 HIS C 353 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 353 " 0.048 2.00e-02 2.50e+03 3.88e-02 2.26e+01 pdb=" CG HIS B 353 " -0.077 2.00e-02 2.50e+03 pdb=" ND1 HIS B 353 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 HIS B 353 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS B 353 " 0.019 2.00e-02 2.50e+03 pdb=" NE2 HIS B 353 " 0.019 2.00e-02 2.50e+03 ... (remaining 4873 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.59: 459 2.59 - 3.09: 19097 3.09 - 3.59: 30326 3.59 - 4.10: 47936 4.10 - 4.60: 67806 Nonbonded interactions: 165624 Sorted by model distance: nonbonded pdb=" OG1 THR B 500 " pdb="MG MG B 902 " model vdw 2.082 2.050 nonbonded pdb=" OG1 THR C 500 " pdb="MG MG C 902 " model vdw 2.082 2.050 nonbonded pdb=" OG1 THR D 500 " pdb="MG MG D 902 " model vdw 2.082 2.050 nonbonded pdb=" OG1 THR A 500 " pdb="MG MG A 902 " model vdw 2.082 2.050 nonbonded pdb=" HG2 7ID G 6 " pdb=" HD3 7ID G 6 " model vdw 2.096 1.952 ... (remaining 165619 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' } 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: 4.300 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: 0.300 Extract box with map and model: 0.560 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 25.820 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.070 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:6.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 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 : 0.020 0.189 27544 Z= 1.068 Angle : 1.907 20.580 37460 Z= 1.248 Chirality : 0.119 1.440 4324 Planarity : 0.009 0.039 4872 Dihedral : 14.633 174.798 10500 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.28 % Allowed : 0.84 % Favored : 98.87 % Cbeta Deviations : 1.01 % 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: -0.68 (0.13), residues: 3460 helix: -1.01 (0.13), residues: 1240 sheet: 1.24 (0.22), residues: 564 loop : -0.49 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 177 TYR 0.043 0.008 TYR C 829 PHE 0.026 0.005 PHE B 58 TRP 0.012 0.004 TRP B 414 HIS 0.022 0.004 HIS C 353 Details of bonding type rmsd/Z covalent geometry : bond 0.01978 / 1.07 (27540) covalent geometry : angle 1.90655 / 1.25 (37460) hydrogen bonds : bond 0.20850 / 14.13 ( 1114) hydrogen bonds : angle 7.05252 / 4.93 ( 3102) Misc. bond : bond 0.01133 / 0.57 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6920 Ramachandran restraints generated. 3460 Oldfield, 0 Emsley, 3460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6920 Ramachandran restraints generated. 3460 Oldfield, 0 Emsley, 3460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 331 time to evaluate : 0.707 Fit side-chains revert: symmetry clash REVERT: A 5 LYS cc_start: 0.7151 (tttt) cc_final: 0.6692 (ttpp) REVERT: A 18 ARG cc_start: 0.6582 (mtm-85) cc_final: 0.6212 (mmp80) REVERT: A 168 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7047 (tm-30) REVERT: A 220 LYS cc_start: 0.7129 (mtpp) cc_final: 0.6571 (mmtt) REVERT: A 236 ARG cc_start: 0.7306 (ttt90) cc_final: 0.7005 (ttm-80) REVERT: A 301 ARG cc_start: 0.6778 (ttm170) cc_final: 0.6446 (ttp80) REVERT: A 316 LYS cc_start: 0.8669 (tttt) cc_final: 0.7786 (mtmt) REVERT: A 534 LYS cc_start: 0.7415 (mttt) cc_final: 0.7152 (mtpt) REVERT: A 630 LYS cc_start: 0.7163 (mmtt) cc_final: 0.6663 (mtmm) REVERT: A 641 ASN cc_start: 0.7074 (t0) cc_final: 0.6736 (t0) REVERT: A 689 MET cc_start: 0.7349 (mtm) cc_final: 0.6610 (mmp) REVERT: A 710 ASP cc_start: 0.6671 (t0) cc_final: 0.6443 (m-30) REVERT: B 5 LYS cc_start: 0.7195 (tttt) cc_final: 0.6751 (ttpp) REVERT: B 18 ARG cc_start: 0.6550 (mtm-85) cc_final: 0.6146 (mmp80) REVERT: B 168 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7050 (tm-30) REVERT: B 220 LYS cc_start: 0.7109 (mtpp) cc_final: 0.6557 (mmtt) REVERT: B 236 ARG cc_start: 0.7318 (ttt90) cc_final: 0.7013 (ttm-80) REVERT: B 301 ARG cc_start: 0.6760 (ttm170) cc_final: 0.6454 (ttp80) REVERT: B 316 LYS cc_start: 0.8669 (tttt) cc_final: 0.7792 (mtmt) REVERT: B 416 MET cc_start: 0.8538 (mmp) cc_final: 0.8327 (mmt) REVERT: B 534 LYS cc_start: 0.7380 (mttt) cc_final: 0.7116 (mtpt) REVERT: B 630 LYS cc_start: 0.7164 (mmtt) cc_final: 0.6663 (mtmm) REVERT: B 641 ASN cc_start: 0.7076 (t0) cc_final: 0.6745 (t0) REVERT: B 689 MET cc_start: 0.7367 (mtm) cc_final: 0.6612 (mmp) REVERT: B 710 ASP cc_start: 0.6687 (t0) cc_final: 0.6462 (m-30) REVERT: C 5 LYS cc_start: 0.7175 (tttt) cc_final: 0.6733 (ttpp) REVERT: C 18 ARG cc_start: 0.6487 (mtm-85) cc_final: 0.6082 (mmp80) REVERT: C 168 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7060 (tm-30) REVERT: C 220 LYS cc_start: 0.7106 (mtpp) cc_final: 0.6563 (mmtt) REVERT: C 236 ARG cc_start: 0.7324 (ttt90) cc_final: 0.7019 (ttm-80) REVERT: C 301 ARG cc_start: 0.6764 (ttm170) cc_final: 0.6459 (ttp80) REVERT: C 316 LYS cc_start: 0.8676 (tttt) cc_final: 0.7799 (mtmt) REVERT: C 416 MET cc_start: 0.8538 (mmp) cc_final: 0.8331 (mmt) REVERT: C 534 LYS cc_start: 0.7367 (mttt) cc_final: 0.7112 (mtpt) REVERT: C 630 LYS cc_start: 0.7146 (mmtt) cc_final: 0.6641 (mtmm) REVERT: C 641 ASN cc_start: 0.7093 (t0) cc_final: 0.6762 (t0) REVERT: C 689 MET cc_start: 0.7388 (mtm) cc_final: 0.6627 (mmp) REVERT: C 710 ASP cc_start: 0.6736 (t0) cc_final: 0.6510 (m-30) REVERT: D 5 LYS cc_start: 0.7214 (tttt) cc_final: 0.6743 (ttpp) REVERT: D 18 ARG cc_start: 0.6548 (mtm-85) cc_final: 0.6146 (mmp80) REVERT: D 168 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7072 (tm-30) REVERT: D 220 LYS cc_start: 0.7101 (mtpp) cc_final: 0.6556 (mmtt) REVERT: D 236 ARG cc_start: 0.7332 (ttt90) cc_final: 0.7027 (ttm-80) REVERT: D 301 ARG cc_start: 0.6763 (ttm170) cc_final: 0.6438 (ttp80) REVERT: D 316 LYS cc_start: 0.8666 (tttt) cc_final: 0.7789 (mtmt) REVERT: D 534 LYS cc_start: 0.7371 (mttt) cc_final: 0.7116 (mtpt) REVERT: D 630 LYS cc_start: 0.7167 (mmtt) cc_final: 0.6666 (mtmm) REVERT: D 641 ASN cc_start: 0.7066 (t0) cc_final: 0.6732 (t0) REVERT: D 689 MET cc_start: 0.7383 (mtm) cc_final: 0.6623 (mmp) REVERT: D 710 ASP cc_start: 0.6702 (t0) cc_final: 0.6477 (m-30) outliers start: 8 outliers final: 0 residues processed: 339 average time/residue: 0.7508 time to fit residues: 289.8704 Evaluate side-chains 219 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 1.019 ------------------------------------------------------------------------------- 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: 9.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 355 ASN A 394 ASN A 696 ASN A 748 HIS B 355 ASN B 394 ASN B 696 ASN B 748 HIS C 355 ASN C 394 ASN C 696 ASN C 748 HIS D 355 ASN D 394 ASN D 696 ASN D 748 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.223369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.137430 restraints weight = 29246.946| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.21 r_work: 0.3488 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 27544 Z= 0.134 Angle : 0.608 7.790 37460 Z= 0.331 Chirality : 0.044 0.195 4324 Planarity : 0.004 0.044 4872 Dihedral : 16.577 149.413 4272 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.48 % Allowed : 4.71 % Favored : 93.81 % 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: 3460 helix: 0.23 (0.14), residues: 1296 sheet: 0.85 (0.23), residues: 512 loop : -0.53 (0.15), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 10 TYR 0.017 0.002 TYR A 285 PHE 0.013 0.002 PHE A 759 TRP 0.008 0.001 TRP A 672 HIS 0.007 0.001 HIS A 586 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (27540) covalent geometry : angle 0.60778 / 0.33 (37460) hydrogen bonds : bond 0.05644 / 3.86 ( 1114) hydrogen bonds : angle 5.01704 / 3.59 ( 3102) Misc. bond : bond 0.00056 / 0.03 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6920 Ramachandran restraints generated. 3460 Oldfield, 0 Emsley, 3460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6920 Ramachandran restraints generated. 3460 Oldfield, 0 Emsley, 3460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 248 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.7993 (tttt) cc_final: 0.7755 (ttpp) REVERT: A 18 ARG cc_start: 0.7202 (mtm-85) cc_final: 0.6974 (mmp80) REVERT: A 168 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7200 (tm-30) REVERT: A 220 LYS cc_start: 0.7250 (mtpp) cc_final: 0.6591 (mmtt) REVERT: A 316 LYS cc_start: 0.8731 (tttt) cc_final: 0.8111 (mtmt) REVERT: A 630 LYS cc_start: 0.7960 (mmtt) cc_final: 0.7407 (mtmm) REVERT: A 641 ASN cc_start: 0.7551 (t0) cc_final: 0.7317 (t0) REVERT: A 661 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7244 (pt0) REVERT: A 680 LYS cc_start: 0.7896 (pttt) cc_final: 0.7522 (mptp) REVERT: A 689 MET cc_start: 0.7720 (mtm) cc_final: 0.6920 (mmt) REVERT: B 5 LYS cc_start: 0.8033 (tttt) cc_final: 0.7795 (ttpp) REVERT: B 18 ARG cc_start: 0.7169 (mtm-85) cc_final: 0.6944 (mmp80) REVERT: B 168 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7183 (tm-30) REVERT: B 220 LYS cc_start: 0.7216 (mtpp) cc_final: 0.6568 (mmtt) REVERT: B 316 LYS cc_start: 0.8730 (tttt) cc_final: 0.8115 (mtmt) REVERT: B 416 MET cc_start: 0.8792 (mmp) cc_final: 0.8564 (mmt) REVERT: B 443 GLU cc_start: 0.7356 (mt-10) cc_final: 0.6888 (mm-30) REVERT: B 630 LYS cc_start: 0.7934 (mmtt) cc_final: 0.7377 (mtmm) REVERT: B 641 ASN cc_start: 0.7534 (t0) cc_final: 0.7296 (t0) REVERT: B 661 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7273 (pt0) REVERT: B 680 LYS cc_start: 0.7915 (pttt) cc_final: 0.7542 (mptp) REVERT: B 689 MET cc_start: 0.7755 (mtm) cc_final: 0.6932 (mmt) REVERT: C 18 ARG cc_start: 0.7162 (mtm-85) cc_final: 0.6954 (mmp80) REVERT: C 168 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7203 (tm-30) REVERT: C 220 LYS cc_start: 0.7218 (mtpp) cc_final: 0.6561 (mmtt) REVERT: C 316 LYS cc_start: 0.8717 (tttt) cc_final: 0.8097 (mtmt) REVERT: C 416 MET cc_start: 0.8774 (mmp) cc_final: 0.8555 (mmt) REVERT: C 443 GLU cc_start: 0.7367 (mt-10) cc_final: 0.6903 (mm-30) REVERT: C 630 LYS cc_start: 0.7961 (mmtt) cc_final: 0.7404 (mtmm) REVERT: C 641 ASN cc_start: 0.7455 (t0) cc_final: 0.7228 (t0) REVERT: C 661 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7273 (pt0) REVERT: C 680 LYS cc_start: 0.7892 (pttt) cc_final: 0.7547 (mptp) REVERT: D 5 LYS cc_start: 0.8015 (tttt) cc_final: 0.7775 (ttpp) REVERT: D 18 ARG cc_start: 0.7160 (mtm-85) cc_final: 0.6939 (mmp80) REVERT: D 168 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7170 (tm-30) REVERT: D 220 LYS cc_start: 0.7167 (mtpp) cc_final: 0.6512 (mmtt) REVERT: D 316 LYS cc_start: 0.8724 (tttt) cc_final: 0.8115 (mtmt) REVERT: D 443 GLU cc_start: 0.7344 (mt-10) cc_final: 0.6883 (mm-30) REVERT: D 630 LYS cc_start: 0.7955 (mmtt) cc_final: 0.7401 (mtmm) REVERT: D 641 ASN cc_start: 0.7528 (t0) cc_final: 0.7285 (t0) REVERT: D 661 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7297 (pt0) REVERT: D 680 LYS cc_start: 0.7923 (pttt) cc_final: 0.7561 (mptp) REVERT: D 689 MET cc_start: 0.7764 (mtm) cc_final: 0.6921 (mmt) outliers start: 42 outliers final: 21 residues processed: 279 average time/residue: 0.7979 time to fit residues: 253.3040 Evaluate side-chains 233 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 208 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 800 GLU Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 661 GLU Chi-restraints excluded: chain D residue 800 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 33 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 30 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 chunk 237 optimal weight: 2.9990 chunk 276 optimal weight: 3.9990 chunk 196 optimal weight: 8.9990 chunk 327 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 284 optimal weight: 5.9990 chunk 215 optimal weight: 0.4980 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 707 ASN D 707 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.217830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.131748 restraints weight = 28935.480| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.56 r_work: 0.3371 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 27544 Z= 0.207 Angle : 0.629 6.124 37460 Z= 0.339 Chirality : 0.047 0.178 4324 Planarity : 0.005 0.053 4872 Dihedral : 15.848 143.831 4272 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.00 % Allowed : 5.56 % Favored : 92.44 % 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: -0.27 (0.14), residues: 3460 helix: 0.33 (0.14), residues: 1312 sheet: 0.61 (0.22), residues: 520 loop : -0.81 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 511 TYR 0.021 0.002 TYR C 116 PHE 0.014 0.002 PHE A 457 TRP 0.009 0.001 TRP B 181 HIS 0.007 0.002 HIS C 650 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.21 (27540) covalent geometry : angle 0.62869 / 0.34 (37460) hydrogen bonds : bond 0.06546 / 4.45 ( 1114) hydrogen bonds : angle 4.83070 / 3.46 ( 3102) Misc. bond : bond 0.00027 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6920 Ramachandran restraints generated. 3460 Oldfield, 0 Emsley, 3460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6920 Ramachandran restraints generated. 3460 Oldfield, 0 Emsley, 3460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 228 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8024 (tttt) cc_final: 0.7788 (ttpp) REVERT: A 18 ARG cc_start: 0.7486 (mtm-85) cc_final: 0.7143 (mmp80) REVERT: A 168 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7395 (tm-30) REVERT: A 220 LYS cc_start: 0.7531 (mtpp) cc_final: 0.6871 (mmtt) REVERT: A 301 ARG cc_start: 0.7228 (ttm170) cc_final: 0.6760 (ttp80) REVERT: A 316 LYS cc_start: 0.8834 (tttt) cc_final: 0.8201 (mtmt) REVERT: A 558 GLU cc_start: 0.9325 (OUTLIER) cc_final: 0.8037 (pt0) REVERT: A 641 ASN cc_start: 0.7568 (t0) cc_final: 0.7258 (t0) REVERT: A 661 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7434 (pt0) REVERT: A 680 LYS cc_start: 0.8075 (pttt) cc_final: 0.7787 (mptp) REVERT: A 689 MET cc_start: 0.7820 (mtm) cc_final: 0.6477 (mmt) REVERT: B 5 LYS cc_start: 0.8073 (tttt) cc_final: 0.7800 (ttpp) REVERT: B 18 ARG cc_start: 0.7464 (mtm-85) cc_final: 0.7129 (mmp80) REVERT: B 168 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7390 (tm-30) REVERT: B 220 LYS cc_start: 0.7508 (mtpp) cc_final: 0.6840 (mmtt) REVERT: B 301 ARG cc_start: 0.7137 (ttm170) cc_final: 0.6695 (ttp80) REVERT: B 316 LYS cc_start: 0.8845 (tttt) cc_final: 0.8202 (mtmt) REVERT: B 443 GLU cc_start: 0.7339 (mt-10) cc_final: 0.6878 (mm-30) REVERT: B 558 GLU cc_start: 0.9332 (OUTLIER) cc_final: 0.7860 (pt0) REVERT: B 641 ASN cc_start: 0.7544 (t0) cc_final: 0.7238 (t0) REVERT: B 661 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7434 (pt0) REVERT: B 680 LYS cc_start: 0.8117 (pttt) cc_final: 0.7883 (mptp) REVERT: B 689 MET cc_start: 0.7817 (mtm) cc_final: 0.6467 (mmt) REVERT: C 18 ARG cc_start: 0.7468 (mtm-85) cc_final: 0.7122 (mmp80) REVERT: C 168 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7399 (tm-30) REVERT: C 220 LYS cc_start: 0.7537 (mtpp) cc_final: 0.6883 (mmtt) REVERT: C 301 ARG cc_start: 0.7209 (ttm170) cc_final: 0.6740 (ttp80) REVERT: C 316 LYS cc_start: 0.8831 (tttt) cc_final: 0.8190 (mtmt) REVERT: C 443 GLU cc_start: 0.7341 (mt-10) cc_final: 0.6887 (mm-30) REVERT: C 558 GLU cc_start: 0.9296 (OUTLIER) cc_final: 0.7931 (pt0) REVERT: C 641 ASN cc_start: 0.7535 (t0) cc_final: 0.7220 (t0) REVERT: C 661 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7492 (pt0) REVERT: C 680 LYS cc_start: 0.8117 (pttt) cc_final: 0.7875 (mptp) REVERT: C 689 MET cc_start: 0.7961 (mtm) cc_final: 0.7020 (mmt) REVERT: D 5 LYS cc_start: 0.8071 (tttt) cc_final: 0.7813 (ttpp) REVERT: D 18 ARG cc_start: 0.7454 (mtm-85) cc_final: 0.7111 (mmp80) REVERT: D 168 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7397 (tm-30) REVERT: D 220 LYS cc_start: 0.7477 (mtpp) cc_final: 0.6813 (mmtt) REVERT: D 301 ARG cc_start: 0.7198 (ttm170) cc_final: 0.6748 (ttp80) REVERT: D 316 LYS cc_start: 0.8826 (tttt) cc_final: 0.8193 (mtmt) REVERT: D 443 GLU cc_start: 0.7343 (mt-10) cc_final: 0.6882 (mm-30) REVERT: D 558 GLU cc_start: 0.9288 (OUTLIER) cc_final: 0.7925 (pt0) REVERT: D 641 ASN cc_start: 0.7545 (t0) cc_final: 0.7246 (t0) REVERT: D 661 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7511 (pt0) REVERT: D 680 LYS cc_start: 0.8137 (pttt) cc_final: 0.7894 (mptp) REVERT: D 689 MET cc_start: 0.7824 (mtm) cc_final: 0.6466 (mmt) outliers start: 57 outliers final: 28 residues processed: 260 average time/residue: 0.7464 time to fit residues: 221.9418 Evaluate side-chains 257 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 221 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 600 LYS Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 600 LYS Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 600 LYS Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 800 GLU Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 478 MET Chi-restraints excluded: chain D residue 558 GLU Chi-restraints excluded: chain D residue 600 LYS Chi-restraints excluded: chain D residue 661 GLU Chi-restraints excluded: chain D residue 800 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 30 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 chunk 238 optimal weight: 5.9990 chunk 213 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 229 optimal weight: 0.6980 chunk 58 optimal weight: 6.9990 chunk 274 optimal weight: 4.9990 chunk 326 optimal weight: 3.9990 chunk 275 optimal weight: 0.9980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 537 ASN B 537 ASN C 537 ASN D 537 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.215754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.121672 restraints weight = 27409.261| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.71 r_work: 0.3179 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 27544 Z= 0.156 Angle : 0.541 5.165 37460 Z= 0.292 Chirality : 0.045 0.165 4324 Planarity : 0.004 0.053 4872 Dihedral : 14.516 145.098 4272 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.83 % Allowed : 6.43 % Favored : 91.74 % 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: 3460 helix: 0.55 (0.15), residues: 1300 sheet: 0.82 (0.23), residues: 488 loop : -0.81 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 469 TYR 0.017 0.002 TYR D 519 PHE 0.015 0.002 PHE C 638 TRP 0.007 0.001 TRP D 181 HIS 0.005 0.001 HIS A 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (27540) covalent geometry : angle 0.54110 / 0.29 (37460) hydrogen bonds : bond 0.05136 / 3.48 ( 1114) hydrogen bonds : angle 4.57832 / 3.29 ( 3102) Misc. bond : bond 0.00044 / 0.02 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6920 Ramachandran restraints generated. 3460 Oldfield, 0 Emsley, 3460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6920 Ramachandran restraints generated. 3460 Oldfield, 0 Emsley, 3460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 228 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8071 (tttt) cc_final: 0.7811 (ttpp) REVERT: A 18 ARG cc_start: 0.7671 (mtm-85) cc_final: 0.7336 (mmp80) REVERT: A 156 ASP cc_start: 0.6216 (OUTLIER) cc_final: 0.5507 (m-30) REVERT: A 168 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7457 (tm-30) REVERT: A 182 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8304 (mtp) REVERT: A 220 LYS cc_start: 0.7570 (mtpp) cc_final: 0.6895 (mmtt) REVERT: A 301 ARG cc_start: 0.7398 (ttm170) cc_final: 0.6848 (ttp80) REVERT: A 316 LYS cc_start: 0.8980 (tttt) cc_final: 0.8385 (mtmt) REVERT: A 372 ARG cc_start: 0.6976 (OUTLIER) cc_final: 0.6614 (ttt180) REVERT: A 534 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8067 (mmtt) REVERT: A 641 ASN cc_start: 0.7768 (t0) cc_final: 0.7373 (t0) REVERT: A 661 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7232 (pp20) REVERT: A 680 LYS cc_start: 0.8156 (pttt) cc_final: 0.7950 (mptp) REVERT: A 689 MET cc_start: 0.7915 (mtm) cc_final: 0.6827 (mmt) REVERT: A 722 THR cc_start: 0.7864 (p) cc_final: 0.7541 (t) REVERT: B 18 ARG cc_start: 0.7668 (mtm-85) cc_final: 0.7330 (mmp80) REVERT: B 156 ASP cc_start: 0.6205 (OUTLIER) cc_final: 0.5518 (m-30) REVERT: B 168 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7431 (tm-30) REVERT: B 182 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8302 (mtp) REVERT: B 220 LYS cc_start: 0.7558 (mtpp) cc_final: 0.6901 (mmtt) REVERT: B 301 ARG cc_start: 0.7351 (ttm170) cc_final: 0.6825 (ttp80) REVERT: B 316 LYS cc_start: 0.8975 (tttt) cc_final: 0.8368 (mtmt) REVERT: B 372 ARG cc_start: 0.6985 (OUTLIER) cc_final: 0.6627 (ttt180) REVERT: B 443 GLU cc_start: 0.7452 (mt-10) cc_final: 0.6951 (mm-30) REVERT: B 641 ASN cc_start: 0.7736 (t0) cc_final: 0.7348 (t0) REVERT: B 661 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7229 (pp20) REVERT: B 680 LYS cc_start: 0.8171 (pttt) cc_final: 0.7960 (mptp) REVERT: B 689 MET cc_start: 0.7925 (mtm) cc_final: 0.6835 (mmt) REVERT: B 722 THR cc_start: 0.7922 (p) cc_final: 0.7624 (t) REVERT: C 18 ARG cc_start: 0.7663 (mtm-85) cc_final: 0.7324 (mmp80) REVERT: C 156 ASP cc_start: 0.6199 (OUTLIER) cc_final: 0.5511 (m-30) REVERT: C 168 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7439 (tm-30) REVERT: C 182 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.8295 (mtp) REVERT: C 220 LYS cc_start: 0.7556 (mtpp) cc_final: 0.6880 (mmtt) REVERT: C 301 ARG cc_start: 0.7356 (ttm170) cc_final: 0.6817 (ttp80) REVERT: C 316 LYS cc_start: 0.8981 (tttt) cc_final: 0.8381 (mtmt) REVERT: C 372 ARG cc_start: 0.6979 (OUTLIER) cc_final: 0.6623 (ttt180) REVERT: C 443 GLU cc_start: 0.7449 (mt-10) cc_final: 0.6958 (mm-30) REVERT: C 534 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8064 (mmtt) REVERT: C 641 ASN cc_start: 0.7751 (t0) cc_final: 0.7369 (t0) REVERT: C 661 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7264 (pp20) REVERT: C 680 LYS cc_start: 0.8173 (pttt) cc_final: 0.7952 (mptp) REVERT: C 722 THR cc_start: 0.7921 (p) cc_final: 0.7624 (t) REVERT: D 18 ARG cc_start: 0.7660 (mtm-85) cc_final: 0.7322 (mmp80) REVERT: D 156 ASP cc_start: 0.6197 (OUTLIER) cc_final: 0.5511 (m-30) REVERT: D 168 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7436 (tm-30) REVERT: D 182 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8301 (mtp) REVERT: D 220 LYS cc_start: 0.7549 (mtpp) cc_final: 0.6892 (mmtt) REVERT: D 301 ARG cc_start: 0.7350 (ttm170) cc_final: 0.6821 (ttp80) REVERT: D 316 LYS cc_start: 0.8980 (tttt) cc_final: 0.8380 (mtmt) REVERT: D 372 ARG cc_start: 0.6979 (OUTLIER) cc_final: 0.6622 (ttt180) REVERT: D 443 GLU cc_start: 0.7445 (mt-10) cc_final: 0.6961 (mm-30) REVERT: D 534 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8067 (mmtt) REVERT: D 641 ASN cc_start: 0.7748 (t0) cc_final: 0.7363 (t0) REVERT: D 661 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7239 (pp20) REVERT: D 680 LYS cc_start: 0.8164 (pttt) cc_final: 0.7946 (mptp) REVERT: D 722 THR cc_start: 0.7916 (p) cc_final: 0.7618 (t) outliers start: 52 outliers final: 21 residues processed: 251 average time/residue: 0.7157 time to fit residues: 206.1408 Evaluate side-chains 250 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 210 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 534 LYS Chi-restraints excluded: chain A residue 600 LYS Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 372 ARG Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 600 LYS Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 372 ARG Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain C residue 534 LYS Chi-restraints excluded: chain C residue 600 LYS Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 478 MET Chi-restraints excluded: chain D residue 534 LYS Chi-restraints excluded: chain D residue 600 LYS Chi-restraints excluded: chain D residue 661 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 264 optimal weight: 0.0000 chunk 305 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 165 optimal weight: 30.0000 chunk 123 optimal weight: 7.9990 chunk 53 optimal weight: 0.5980 chunk 263 optimal weight: 6.9990 chunk 282 optimal weight: 0.5980 chunk 87 optimal weight: 5.9990 chunk 218 optimal weight: 0.3980 chunk 117 optimal weight: 0.8980 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 707 ASN B 707 ASN C 497 ASN D 497 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.219438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.136564 restraints weight = 27587.357| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.73 r_work: 0.3248 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.022 27544 Z= 0.071 Angle : 0.424 5.135 37460 Z= 0.227 Chirality : 0.041 0.134 4324 Planarity : 0.003 0.049 4872 Dihedral : 13.487 145.152 4272 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.90 % Allowed : 7.14 % Favored : 90.96 % 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: 0.25 (0.15), residues: 3460 helix: 0.96 (0.15), residues: 1364 sheet: 1.00 (0.24), residues: 472 loop : -0.75 (0.16), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 504 TYR 0.008 0.001 TYR B 519 PHE 0.007 0.001 PHE C 638 TRP 0.006 0.001 TRP D 278 HIS 0.002 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00142 / 0.07 (27540) covalent geometry : angle 0.42449 / 0.23 (37460) hydrogen bonds : bond 0.03174 / 2.17 ( 1114) hydrogen bonds : angle 4.20187 / 3.04 ( 3102) Misc. bond : bond 0.00018 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6920 Ramachandran restraints generated. 3460 Oldfield, 0 Emsley, 3460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6920 Ramachandran restraints generated. 3460 Oldfield, 0 Emsley, 3460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 240 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.7657 (mtm-85) cc_final: 0.7336 (mmp80) REVERT: A 156 ASP cc_start: 0.6200 (OUTLIER) cc_final: 0.5489 (m-30) REVERT: A 168 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7501 (tm-30) REVERT: A 220 LYS cc_start: 0.7383 (mtpp) cc_final: 0.6714 (mmtt) REVERT: A 301 ARG cc_start: 0.7260 (ttm170) cc_final: 0.6756 (ttp80) REVERT: A 316 LYS cc_start: 0.8944 (tttt) cc_final: 0.8428 (mtmt) REVERT: A 372 ARG cc_start: 0.6997 (OUTLIER) cc_final: 0.6640 (ttt180) REVERT: A 534 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8506 (mtpt) REVERT: A 558 GLU cc_start: 0.9211 (OUTLIER) cc_final: 0.7815 (pt0) REVERT: A 641 ASN cc_start: 0.7696 (t0) cc_final: 0.7285 (t0) REVERT: A 661 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7349 (pp20) REVERT: A 680 LYS cc_start: 0.8087 (pttt) cc_final: 0.7853 (mptp) REVERT: A 722 THR cc_start: 0.7807 (p) cc_final: 0.7605 (t) REVERT: B 18 ARG cc_start: 0.7642 (mtm-85) cc_final: 0.7325 (mmp80) REVERT: B 156 ASP cc_start: 0.6227 (OUTLIER) cc_final: 0.5539 (m-30) REVERT: B 168 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7490 (tm-30) REVERT: B 220 LYS cc_start: 0.7406 (mtpp) cc_final: 0.6740 (mmtt) REVERT: B 301 ARG cc_start: 0.7230 (ttm170) cc_final: 0.6748 (ttp80) REVERT: B 316 LYS cc_start: 0.8973 (tttt) cc_final: 0.8472 (mtmt) REVERT: B 372 ARG cc_start: 0.6976 (OUTLIER) cc_final: 0.6626 (ttt180) REVERT: B 443 GLU cc_start: 0.7429 (mt-10) cc_final: 0.6967 (mm-30) REVERT: B 534 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8503 (mmpt) REVERT: B 558 GLU cc_start: 0.9211 (OUTLIER) cc_final: 0.7818 (pt0) REVERT: B 641 ASN cc_start: 0.7703 (t0) cc_final: 0.7292 (t0) REVERT: B 661 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7333 (pp20) REVERT: B 680 LYS cc_start: 0.8102 (pttt) cc_final: 0.7877 (mptp) REVERT: B 722 THR cc_start: 0.7840 (p) cc_final: 0.7632 (t) REVERT: C 18 ARG cc_start: 0.7631 (mtm-85) cc_final: 0.7314 (mmp80) REVERT: C 156 ASP cc_start: 0.6224 (OUTLIER) cc_final: 0.5534 (m-30) REVERT: C 168 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7494 (tm-30) REVERT: C 220 LYS cc_start: 0.7396 (mtpp) cc_final: 0.6727 (mmtt) REVERT: C 301 ARG cc_start: 0.7263 (ttm170) cc_final: 0.6770 (ttp80) REVERT: C 316 LYS cc_start: 0.8941 (tttt) cc_final: 0.8439 (mtmt) REVERT: C 372 ARG cc_start: 0.6971 (OUTLIER) cc_final: 0.6631 (ttt180) REVERT: C 443 GLU cc_start: 0.7419 (mt-10) cc_final: 0.6959 (mm-30) REVERT: C 558 GLU cc_start: 0.9202 (OUTLIER) cc_final: 0.7839 (pt0) REVERT: C 641 ASN cc_start: 0.7704 (t0) cc_final: 0.7298 (t0) REVERT: C 661 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7347 (pp20) REVERT: C 680 LYS cc_start: 0.8103 (pttt) cc_final: 0.7903 (mptp) REVERT: C 722 THR cc_start: 0.7835 (p) cc_final: 0.7624 (t) REVERT: D 18 ARG cc_start: 0.7642 (mtm-85) cc_final: 0.7319 (mmp80) REVERT: D 156 ASP cc_start: 0.6235 (OUTLIER) cc_final: 0.5542 (m-30) REVERT: D 168 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7482 (tm-30) REVERT: D 220 LYS cc_start: 0.7383 (mtpp) cc_final: 0.6734 (mmtt) REVERT: D 301 ARG cc_start: 0.7257 (ttm170) cc_final: 0.6759 (ttp80) REVERT: D 316 LYS cc_start: 0.8935 (tttt) cc_final: 0.8427 (mtmt) REVERT: D 372 ARG cc_start: 0.6979 (OUTLIER) cc_final: 0.6643 (ttt180) REVERT: D 443 GLU cc_start: 0.7425 (mt-10) cc_final: 0.6969 (mm-30) REVERT: D 558 GLU cc_start: 0.9199 (OUTLIER) cc_final: 0.7841 (pt0) REVERT: D 641 ASN cc_start: 0.7709 (t0) cc_final: 0.7301 (t0) REVERT: D 661 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7339 (pp20) REVERT: D 680 LYS cc_start: 0.8101 (pttt) cc_final: 0.7859 (mptp) REVERT: D 722 THR cc_start: 0.7819 (p) cc_final: 0.7612 (t) outliers start: 54 outliers final: 10 residues processed: 268 average time/residue: 0.6543 time to fit residues: 202.6596 Evaluate side-chains 245 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 217 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 534 LYS Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 372 ARG Chi-restraints excluded: chain B residue 534 LYS Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 372 ARG Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 800 GLU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain D residue 558 GLU Chi-restraints excluded: chain D residue 600 LYS Chi-restraints excluded: chain D residue 661 GLU Chi-restraints excluded: chain D residue 800 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 126 optimal weight: 3.9990 chunk 280 optimal weight: 0.9990 chunk 271 optimal weight: 10.0000 chunk 174 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 309 optimal weight: 0.0670 chunk 166 optimal weight: 2.9990 chunk 253 optimal weight: 6.9990 chunk 195 optimal weight: 5.9990 chunk 7 optimal weight: 0.5980 chunk 308 optimal weight: 3.9990 overall best weight: 1.7324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 497 ASN B 497 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.215498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.121731 restraints weight = 27413.532| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.36 r_work: 0.3206 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 27544 Z= 0.140 Angle : 0.511 4.954 37460 Z= 0.272 Chirality : 0.044 0.172 4324 Planarity : 0.004 0.053 4872 Dihedral : 13.336 145.094 4272 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.76 % Allowed : 8.23 % Favored : 90.01 % 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: 3460 helix: 0.89 (0.15), residues: 1340 sheet: 0.71 (0.24), residues: 496 loop : -0.77 (0.16), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 715 TYR 0.016 0.001 TYR D 519 PHE 0.011 0.002 PHE C 638 TRP 0.007 0.001 TRP B 181 HIS 0.005 0.001 HIS A 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (27540) covalent geometry : angle 0.51094 / 0.27 (37460) hydrogen bonds : bond 0.05088 / 3.45 ( 1114) hydrogen bonds : angle 4.40224 / 3.18 ( 3102) Misc. bond : bond 0.00031 / 0.02 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6920 Ramachandran restraints generated. 3460 Oldfield, 0 Emsley, 3460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6920 Ramachandran restraints generated. 3460 Oldfield, 0 Emsley, 3460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 231 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.7651 (mtm-85) cc_final: 0.7325 (mmp80) REVERT: A 31 ASP cc_start: 0.6463 (t0) cc_final: 0.6101 (m-30) REVERT: A 156 ASP cc_start: 0.6120 (OUTLIER) cc_final: 0.5461 (m-30) REVERT: A 168 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7506 (tm-30) REVERT: A 220 LYS cc_start: 0.7507 (mtpp) cc_final: 0.6792 (mmtt) REVERT: A 301 ARG cc_start: 0.7250 (ttm170) cc_final: 0.6746 (ttp80) REVERT: A 316 LYS cc_start: 0.8922 (tttt) cc_final: 0.8374 (mtmt) REVERT: A 372 ARG cc_start: 0.7026 (OUTLIER) cc_final: 0.6703 (ttt180) REVERT: A 558 GLU cc_start: 0.9304 (OUTLIER) cc_final: 0.7805 (pt0) REVERT: A 641 ASN cc_start: 0.7733 (t0) cc_final: 0.7332 (t0) REVERT: A 661 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7204 (pp20) REVERT: A 722 THR cc_start: 0.7989 (p) cc_final: 0.7719 (t) REVERT: B 18 ARG cc_start: 0.7646 (mtm-85) cc_final: 0.7312 (mmp80) REVERT: B 31 ASP cc_start: 0.6527 (t0) cc_final: 0.6136 (m-30) REVERT: B 156 ASP cc_start: 0.6217 (OUTLIER) cc_final: 0.5477 (m-30) REVERT: B 168 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7508 (tm-30) REVERT: B 220 LYS cc_start: 0.7479 (mtpp) cc_final: 0.6779 (mmtt) REVERT: B 301 ARG cc_start: 0.7237 (ttm170) cc_final: 0.6736 (ttp80) REVERT: B 316 LYS cc_start: 0.8918 (tttt) cc_final: 0.8358 (mtmt) REVERT: B 372 ARG cc_start: 0.7016 (OUTLIER) cc_final: 0.6689 (ttt180) REVERT: B 443 GLU cc_start: 0.7392 (mt-10) cc_final: 0.6909 (mm-30) REVERT: B 558 GLU cc_start: 0.9299 (OUTLIER) cc_final: 0.7808 (pt0) REVERT: B 641 ASN cc_start: 0.7742 (t0) cc_final: 0.7338 (t0) REVERT: B 661 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7203 (pp20) REVERT: B 722 THR cc_start: 0.7977 (p) cc_final: 0.7725 (t) REVERT: C 18 ARG cc_start: 0.7634 (mtm-85) cc_final: 0.7311 (mmp80) REVERT: C 31 ASP cc_start: 0.6551 (t0) cc_final: 0.6141 (m-30) REVERT: C 156 ASP cc_start: 0.6252 (OUTLIER) cc_final: 0.5507 (m-30) REVERT: C 168 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7509 (tm-30) REVERT: C 220 LYS cc_start: 0.7495 (mtpp) cc_final: 0.6780 (mmtt) REVERT: C 301 ARG cc_start: 0.7255 (ttm170) cc_final: 0.6755 (ttp80) REVERT: C 316 LYS cc_start: 0.8923 (tttt) cc_final: 0.8370 (mtmt) REVERT: C 372 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.6694 (ttt180) REVERT: C 443 GLU cc_start: 0.7369 (mt-10) cc_final: 0.6893 (mm-30) REVERT: C 534 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8482 (mmtt) REVERT: C 558 GLU cc_start: 0.9270 (OUTLIER) cc_final: 0.7827 (pt0) REVERT: C 641 ASN cc_start: 0.7782 (t0) cc_final: 0.7378 (t0) REVERT: C 661 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7211 (pp20) REVERT: C 722 THR cc_start: 0.7975 (p) cc_final: 0.7722 (t) REVERT: D 18 ARG cc_start: 0.7635 (mtm-85) cc_final: 0.7310 (mmp80) REVERT: D 31 ASP cc_start: 0.6555 (t0) cc_final: 0.6168 (m-30) REVERT: D 156 ASP cc_start: 0.6244 (OUTLIER) cc_final: 0.5501 (m-30) REVERT: D 168 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7512 (tm-30) REVERT: D 220 LYS cc_start: 0.7472 (mtpp) cc_final: 0.6770 (mmtt) REVERT: D 301 ARG cc_start: 0.7213 (ttm170) cc_final: 0.6730 (ttp80) REVERT: D 316 LYS cc_start: 0.8920 (tttt) cc_final: 0.8367 (mtmt) REVERT: D 372 ARG cc_start: 0.7026 (OUTLIER) cc_final: 0.6705 (ttt180) REVERT: D 443 GLU cc_start: 0.7376 (mt-10) cc_final: 0.6905 (mm-30) REVERT: D 534 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8482 (mmtt) REVERT: D 558 GLU cc_start: 0.9259 (OUTLIER) cc_final: 0.7804 (pt0) REVERT: D 641 ASN cc_start: 0.7773 (t0) cc_final: 0.7364 (t0) REVERT: D 661 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7217 (pp20) REVERT: D 680 LYS cc_start: 0.8095 (pttt) cc_final: 0.7890 (mptp) REVERT: D 722 THR cc_start: 0.7972 (p) cc_final: 0.7717 (t) outliers start: 50 outliers final: 10 residues processed: 249 average time/residue: 0.7228 time to fit residues: 207.2127 Evaluate side-chains 255 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 227 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 372 ARG Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 600 LYS Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 372 ARG Chi-restraints excluded: chain C residue 534 LYS Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain D residue 534 LYS Chi-restraints excluded: chain D residue 558 GLU Chi-restraints excluded: chain D residue 600 LYS Chi-restraints excluded: chain D residue 661 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 83 optimal weight: 4.9990 chunk 58 optimal weight: 8.9990 chunk 267 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 252 optimal weight: 20.0000 chunk 188 optimal weight: 4.9990 chunk 337 optimal weight: 20.0000 chunk 149 optimal weight: 0.8980 chunk 326 optimal weight: 8.9990 chunk 106 optimal weight: 0.5980 chunk 161 optimal weight: 6.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.213235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.119321 restraints weight = 27155.407| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.25 r_work: 0.3184 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 27544 Z= 0.206 Angle : 0.598 6.186 37460 Z= 0.317 Chirality : 0.046 0.178 4324 Planarity : 0.005 0.056 4872 Dihedral : 13.517 146.515 4272 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.90 % Allowed : 8.47 % 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: -0.26 (0.14), residues: 3460 helix: 0.53 (0.15), residues: 1332 sheet: 0.48 (0.23), residues: 532 loop : -0.97 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 715 TYR 0.020 0.002 TYR C 116 PHE 0.012 0.002 PHE D 58 TRP 0.007 0.001 TRP C 181 HIS 0.008 0.002 HIS C 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.21 (27540) covalent geometry : angle 0.59751 / 0.32 (37460) hydrogen bonds : bond 0.06254 / 4.24 ( 1114) hydrogen bonds : angle 4.70689 / 3.39 ( 3102) Misc. bond : bond 0.00058 / 0.03 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6920 Ramachandran restraints generated. 3460 Oldfield, 0 Emsley, 3460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6920 Ramachandran restraints generated. 3460 Oldfield, 0 Emsley, 3460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 241 time to evaluate : 1.155 Fit side-chains REVERT: A 18 ARG cc_start: 0.7749 (mtm-85) cc_final: 0.7426 (mmp80) REVERT: A 31 ASP cc_start: 0.6891 (t0) cc_final: 0.6374 (m-30) REVERT: A 156 ASP cc_start: 0.6321 (OUTLIER) cc_final: 0.5565 (m-30) REVERT: A 220 LYS cc_start: 0.7641 (mtpp) cc_final: 0.6950 (mmtt) REVERT: A 301 ARG cc_start: 0.7358 (ttm170) cc_final: 0.6758 (ttp80) REVERT: A 316 LYS cc_start: 0.8971 (tttt) cc_final: 0.8368 (mtmt) REVERT: A 558 GLU cc_start: 0.9316 (OUTLIER) cc_final: 0.7944 (pt0) REVERT: A 641 ASN cc_start: 0.7835 (t0) cc_final: 0.7396 (t0) REVERT: A 722 THR cc_start: 0.7987 (p) cc_final: 0.7729 (t) REVERT: B 18 ARG cc_start: 0.7756 (mtm-85) cc_final: 0.7433 (mmp80) REVERT: B 70 ARG cc_start: 0.6166 (OUTLIER) cc_final: 0.5885 (mpt-90) REVERT: B 156 ASP cc_start: 0.6289 (OUTLIER) cc_final: 0.5552 (m-30) REVERT: B 220 LYS cc_start: 0.7649 (mtpp) cc_final: 0.6960 (mmtt) REVERT: B 301 ARG cc_start: 0.7356 (ttm170) cc_final: 0.6766 (ttp80) REVERT: B 316 LYS cc_start: 0.8957 (tttt) cc_final: 0.8370 (mtmt) REVERT: B 443 GLU cc_start: 0.7424 (mt-10) cc_final: 0.6955 (mm-30) REVERT: B 558 GLU cc_start: 0.9318 (OUTLIER) cc_final: 0.7956 (pt0) REVERT: B 641 ASN cc_start: 0.7827 (t0) cc_final: 0.7388 (t0) REVERT: B 722 THR cc_start: 0.7978 (p) cc_final: 0.7715 (t) REVERT: C 18 ARG cc_start: 0.7761 (mtm-85) cc_final: 0.7429 (mmp80) REVERT: C 31 ASP cc_start: 0.6854 (t0) cc_final: 0.6347 (m-30) REVERT: C 70 ARG cc_start: 0.6142 (OUTLIER) cc_final: 0.5864 (mpt-90) REVERT: C 156 ASP cc_start: 0.6308 (OUTLIER) cc_final: 0.5564 (m-30) REVERT: C 220 LYS cc_start: 0.7639 (mtpp) cc_final: 0.6949 (mmtt) REVERT: C 301 ARG cc_start: 0.7347 (ttm170) cc_final: 0.6774 (ttp80) REVERT: C 316 LYS cc_start: 0.8967 (tttt) cc_final: 0.8366 (mtmt) REVERT: C 443 GLU cc_start: 0.7413 (mt-10) cc_final: 0.6985 (mm-30) REVERT: C 558 GLU cc_start: 0.9288 (OUTLIER) cc_final: 0.7909 (pt0) REVERT: C 641 ASN cc_start: 0.7814 (t0) cc_final: 0.7393 (t0) REVERT: C 722 THR cc_start: 0.7976 (p) cc_final: 0.7711 (t) REVERT: D 18 ARG cc_start: 0.7739 (mtm-85) cc_final: 0.7428 (mmp80) REVERT: D 31 ASP cc_start: 0.6827 (t0) cc_final: 0.6329 (m-30) REVERT: D 70 ARG cc_start: 0.6132 (OUTLIER) cc_final: 0.5852 (mpt-90) REVERT: D 156 ASP cc_start: 0.6300 (OUTLIER) cc_final: 0.5562 (m-30) REVERT: D 220 LYS cc_start: 0.7642 (mtpp) cc_final: 0.6961 (mmtt) REVERT: D 301 ARG cc_start: 0.7336 (ttm170) cc_final: 0.6756 (ttp80) REVERT: D 316 LYS cc_start: 0.8967 (tttt) cc_final: 0.8367 (mtmt) REVERT: D 443 GLU cc_start: 0.7407 (mt-10) cc_final: 0.6983 (mm-30) REVERT: D 558 GLU cc_start: 0.9288 (OUTLIER) cc_final: 0.7910 (pt0) REVERT: D 641 ASN cc_start: 0.7801 (t0) cc_final: 0.7378 (t0) REVERT: D 722 THR cc_start: 0.7970 (p) cc_final: 0.7704 (t) outliers start: 54 outliers final: 13 residues processed: 260 average time/residue: 0.7079 time to fit residues: 212.2605 Evaluate side-chains 253 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 229 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 651 VAL Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 558 GLU Chi-restraints excluded: chain D residue 651 VAL Chi-restraints excluded: chain D residue 661 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 319 optimal weight: 2.9990 chunk 254 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 125 optimal weight: 5.9990 chunk 333 optimal weight: 20.0000 chunk 296 optimal weight: 3.9990 chunk 287 optimal weight: 10.0000 chunk 105 optimal weight: 1.9990 chunk 324 optimal weight: 3.9990 chunk 272 optimal weight: 8.9990 chunk 246 optimal weight: 20.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.211710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.118088 restraints weight = 27190.793| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.25 r_work: 0.3165 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 27544 Z= 0.253 Angle : 0.653 6.635 37460 Z= 0.347 Chirality : 0.049 0.178 4324 Planarity : 0.005 0.060 4872 Dihedral : 13.672 149.109 4272 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.86 % Allowed : 9.07 % Favored : 89.06 % 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: -0.53 (0.14), residues: 3460 helix: 0.21 (0.15), residues: 1336 sheet: 0.35 (0.22), residues: 608 loop : -1.10 (0.16), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 715 TYR 0.022 0.002 TYR C 116 PHE 0.016 0.002 PHE D 58 TRP 0.008 0.001 TRP C 181 HIS 0.011 0.002 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00627 / 0.25 (27540) covalent geometry : angle 0.65347 / 0.35 (37460) hydrogen bonds : bond 0.06900 / 4.67 ( 1114) hydrogen bonds : angle 4.85223 / 3.48 ( 3102) Misc. bond : bond 0.00075 / 0.04 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6920 Ramachandran restraints generated. 3460 Oldfield, 0 Emsley, 3460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6920 Ramachandran restraints generated. 3460 Oldfield, 0 Emsley, 3460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 226 time to evaluate : 1.010 Fit side-chains revert: symmetry clash REVERT: A 18 ARG cc_start: 0.7714 (mtm-85) cc_final: 0.7452 (mmp80) REVERT: A 156 ASP cc_start: 0.6400 (OUTLIER) cc_final: 0.5651 (m-30) REVERT: A 220 LYS cc_start: 0.7681 (mtpp) cc_final: 0.6977 (mmtt) REVERT: A 301 ARG cc_start: 0.7425 (ttm170) cc_final: 0.6785 (ttp80) REVERT: A 316 LYS cc_start: 0.8993 (tttt) cc_final: 0.8367 (mtmt) REVERT: A 558 GLU cc_start: 0.9316 (OUTLIER) cc_final: 0.7967 (pt0) REVERT: A 641 ASN cc_start: 0.7804 (t0) cc_final: 0.7506 (m-40) REVERT: A 722 THR cc_start: 0.7998 (p) cc_final: 0.7716 (t) REVERT: B 18 ARG cc_start: 0.7742 (mtm-85) cc_final: 0.7435 (mmp80) REVERT: B 70 ARG cc_start: 0.6176 (OUTLIER) cc_final: 0.5911 (mpt-90) REVERT: B 156 ASP cc_start: 0.6402 (OUTLIER) cc_final: 0.5663 (m-30) REVERT: B 220 LYS cc_start: 0.7643 (mtpp) cc_final: 0.6940 (mmtt) REVERT: B 301 ARG cc_start: 0.7455 (ttm170) cc_final: 0.6804 (ttp80) REVERT: B 316 LYS cc_start: 0.8990 (tttt) cc_final: 0.8371 (mtmt) REVERT: B 443 GLU cc_start: 0.7405 (mt-10) cc_final: 0.6941 (mm-30) REVERT: B 558 GLU cc_start: 0.9319 (OUTLIER) cc_final: 0.7977 (pt0) REVERT: B 641 ASN cc_start: 0.7820 (t0) cc_final: 0.7519 (m-40) REVERT: B 722 THR cc_start: 0.8007 (p) cc_final: 0.7722 (t) REVERT: C 18 ARG cc_start: 0.7734 (mtm-85) cc_final: 0.7436 (mmp80) REVERT: C 70 ARG cc_start: 0.6163 (OUTLIER) cc_final: 0.5900 (mpt-90) REVERT: C 156 ASP cc_start: 0.6423 (OUTLIER) cc_final: 0.5682 (m-30) REVERT: C 220 LYS cc_start: 0.7682 (mtpp) cc_final: 0.6984 (mmtt) REVERT: C 301 ARG cc_start: 0.7466 (ttm170) cc_final: 0.6850 (ttp80) REVERT: C 316 LYS cc_start: 0.8984 (tttt) cc_final: 0.8362 (mtmt) REVERT: C 443 GLU cc_start: 0.7450 (mt-10) cc_final: 0.6987 (mm-30) REVERT: C 558 GLU cc_start: 0.9299 (OUTLIER) cc_final: 0.7909 (pt0) REVERT: C 641 ASN cc_start: 0.7815 (t0) cc_final: 0.7523 (m-40) REVERT: C 722 THR cc_start: 0.7996 (p) cc_final: 0.7712 (t) REVERT: D 18 ARG cc_start: 0.7728 (mtm-85) cc_final: 0.7433 (mmp80) REVERT: D 70 ARG cc_start: 0.6170 (OUTLIER) cc_final: 0.5903 (mpt-90) REVERT: D 156 ASP cc_start: 0.6402 (OUTLIER) cc_final: 0.5666 (m-30) REVERT: D 220 LYS cc_start: 0.7636 (mtpp) cc_final: 0.6912 (mmtt) REVERT: D 301 ARG cc_start: 0.7450 (ttm170) cc_final: 0.6828 (ttp80) REVERT: D 316 LYS cc_start: 0.8985 (tttt) cc_final: 0.8366 (mtmt) REVERT: D 443 GLU cc_start: 0.7430 (mt-10) cc_final: 0.6970 (mm-30) REVERT: D 558 GLU cc_start: 0.9296 (OUTLIER) cc_final: 0.7912 (pt0) REVERT: D 641 ASN cc_start: 0.7801 (t0) cc_final: 0.7506 (m-40) REVERT: D 722 THR cc_start: 0.8017 (p) cc_final: 0.7724 (t) outliers start: 53 outliers final: 20 residues processed: 250 average time/residue: 0.7376 time to fit residues: 213.1285 Evaluate side-chains 252 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 221 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 449 VAL 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 651 VAL Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 651 VAL Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 478 MET Chi-restraints excluded: chain D residue 558 GLU Chi-restraints excluded: chain D residue 651 VAL Chi-restraints excluded: chain D residue 661 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 194 optimal weight: 1.9990 chunk 36 optimal weight: 0.0870 chunk 71 optimal weight: 3.9990 chunk 289 optimal weight: 2.9990 chunk 311 optimal weight: 0.9980 chunk 48 optimal weight: 0.0970 chunk 296 optimal weight: 0.9990 chunk 342 optimal weight: 8.9990 chunk 100 optimal weight: 4.9990 chunk 257 optimal weight: 20.0000 chunk 209 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 791 GLN D 791 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.216425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.124205 restraints weight = 27379.306| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.26 r_work: 0.3226 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 27544 Z= 0.082 Angle : 0.448 5.447 37460 Z= 0.239 Chirality : 0.041 0.134 4324 Planarity : 0.004 0.060 4872 Dihedral : 13.187 149.786 4272 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.81 % Allowed : 10.09 % Favored : 89.10 % 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: -0.05 (0.15), residues: 3460 helix: 0.74 (0.15), residues: 1368 sheet: 1.00 (0.25), residues: 472 loop : -1.02 (0.16), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 10 TYR 0.009 0.001 TYR B 519 PHE 0.010 0.001 PHE D 638 TRP 0.009 0.001 TRP B 278 HIS 0.003 0.001 HIS C 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00170 / 0.08 (27540) covalent geometry : angle 0.44777 / 0.24 (37460) hydrogen bonds : bond 0.03511 / 2.39 ( 1114) hydrogen bonds : angle 4.37979 / 3.17 ( 3102) Misc. bond : bond 0.00017 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6920 Ramachandran restraints generated. 3460 Oldfield, 0 Emsley, 3460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6920 Ramachandran restraints generated. 3460 Oldfield, 0 Emsley, 3460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 222 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.7730 (mtm-85) cc_final: 0.7427 (mmp80) REVERT: A 156 ASP cc_start: 0.6215 (OUTLIER) cc_final: 0.5510 (m-30) REVERT: A 220 LYS cc_start: 0.7428 (mtpp) cc_final: 0.6726 (mmtt) REVERT: A 301 ARG cc_start: 0.7334 (ttm170) cc_final: 0.6721 (ttp80) REVERT: A 316 LYS cc_start: 0.8930 (tttt) cc_final: 0.8337 (mtmt) REVERT: A 558 GLU cc_start: 0.9194 (OUTLIER) cc_final: 0.7831 (pt0) REVERT: A 641 ASN cc_start: 0.7730 (t0) cc_final: 0.7420 (m110) REVERT: A 661 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7160 (pp20) REVERT: B 18 ARG cc_start: 0.7725 (mtm-85) cc_final: 0.7418 (mmp80) REVERT: B 156 ASP cc_start: 0.6211 (OUTLIER) cc_final: 0.5513 (m-30) REVERT: B 220 LYS cc_start: 0.7418 (mtpp) cc_final: 0.6716 (mmtt) REVERT: B 301 ARG cc_start: 0.7335 (ttm170) cc_final: 0.6721 (ttp80) REVERT: B 316 LYS cc_start: 0.8948 (tttt) cc_final: 0.8391 (mtmt) REVERT: B 443 GLU cc_start: 0.7396 (mt-10) cc_final: 0.6959 (mm-30) REVERT: B 558 GLU cc_start: 0.9198 (OUTLIER) cc_final: 0.7809 (pt0) REVERT: B 641 ASN cc_start: 0.7746 (t0) cc_final: 0.7461 (m-40) REVERT: B 661 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7164 (pp20) REVERT: C 18 ARG cc_start: 0.7713 (mtm-85) cc_final: 0.7412 (mmp80) REVERT: C 156 ASP cc_start: 0.6238 (OUTLIER) cc_final: 0.5533 (m-30) REVERT: C 220 LYS cc_start: 0.7423 (mtpp) cc_final: 0.6719 (mmtt) REVERT: C 301 ARG cc_start: 0.7318 (ttm170) cc_final: 0.6718 (ttp80) REVERT: C 316 LYS cc_start: 0.8914 (tttt) cc_final: 0.8325 (mtmt) REVERT: C 443 GLU cc_start: 0.7388 (mt-10) cc_final: 0.6952 (mm-30) REVERT: C 534 LYS cc_start: 0.8584 (mtpt) cc_final: 0.8381 (mmtt) REVERT: C 558 GLU cc_start: 0.9175 (OUTLIER) cc_final: 0.7838 (pt0) REVERT: C 641 ASN cc_start: 0.7756 (t0) cc_final: 0.7462 (m110) REVERT: C 661 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7175 (pp20) REVERT: D 18 ARG cc_start: 0.7698 (mtm-85) cc_final: 0.7410 (mmp80) REVERT: D 156 ASP cc_start: 0.6218 (OUTLIER) cc_final: 0.5518 (m-30) REVERT: D 220 LYS cc_start: 0.7403 (mtpp) cc_final: 0.6710 (mmtt) REVERT: D 301 ARG cc_start: 0.7322 (ttm170) cc_final: 0.6724 (ttp80) REVERT: D 316 LYS cc_start: 0.8937 (tttt) cc_final: 0.8334 (mtmt) REVERT: D 443 GLU cc_start: 0.7393 (mt-10) cc_final: 0.6961 (mm-30) REVERT: D 534 LYS cc_start: 0.8586 (mtpt) cc_final: 0.8384 (mmtt) REVERT: D 558 GLU cc_start: 0.9171 (OUTLIER) cc_final: 0.7839 (pt0) REVERT: D 641 ASN cc_start: 0.7752 (t0) cc_final: 0.7450 (m110) REVERT: D 661 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7176 (pp20) outliers start: 23 outliers final: 6 residues processed: 237 average time/residue: 0.7486 time to fit residues: 204.0244 Evaluate side-chains 231 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 213 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 651 VAL Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 558 GLU Chi-restraints excluded: chain D residue 651 VAL Chi-restraints excluded: chain D residue 661 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 214 optimal weight: 0.0270 chunk 85 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 chunk 116 optimal weight: 0.6980 chunk 194 optimal weight: 0.8980 chunk 318 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 246 optimal weight: 0.0060 chunk 73 optimal weight: 10.0000 chunk 317 optimal weight: 0.9990 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 791 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.217305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.125444 restraints weight = 27463.580| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.26 r_work: 0.3243 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 27544 Z= 0.074 Angle : 0.423 4.884 37460 Z= 0.224 Chirality : 0.041 0.146 4324 Planarity : 0.003 0.059 4872 Dihedral : 12.788 150.158 4272 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.74 % Allowed : 10.23 % Favored : 89.03 % 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 (0.15), residues: 3460 helix: 1.20 (0.15), residues: 1368 sheet: 0.65 (0.24), residues: 508 loop : -0.89 (0.16), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 70 TYR 0.012 0.001 TYR D 519 PHE 0.010 0.001 PHE C 692 TRP 0.005 0.001 TRP D 181 HIS 0.003 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00156 / 0.07 (27540) covalent geometry : angle 0.42256 / 0.22 (37460) hydrogen bonds : bond 0.03244 / 2.20 ( 1114) hydrogen bonds : angle 4.06424 / 2.95 ( 3102) Misc. bond : bond 0.00012 / 0.01 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6920 Ramachandran restraints generated. 3460 Oldfield, 0 Emsley, 3460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6920 Ramachandran restraints generated. 3460 Oldfield, 0 Emsley, 3460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 213 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.7687 (mtm-85) cc_final: 0.7388 (mmp80) REVERT: A 156 ASP cc_start: 0.6073 (OUTLIER) cc_final: 0.5477 (m-30) REVERT: A 220 LYS cc_start: 0.7417 (mtpp) cc_final: 0.6725 (mmtt) REVERT: A 301 ARG cc_start: 0.7272 (ttm170) cc_final: 0.6739 (ttp80) REVERT: A 316 LYS cc_start: 0.8891 (tttt) cc_final: 0.8362 (mtmt) REVERT: A 558 GLU cc_start: 0.9220 (OUTLIER) cc_final: 0.7882 (pt0) REVERT: A 641 ASN cc_start: 0.7809 (t0) cc_final: 0.7481 (m-40) REVERT: A 661 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.7101 (pp20) REVERT: B 18 ARG cc_start: 0.7699 (mtm-85) cc_final: 0.7359 (mmp80) REVERT: B 156 ASP cc_start: 0.6042 (OUTLIER) cc_final: 0.5452 (m-30) REVERT: B 220 LYS cc_start: 0.7419 (mtpp) cc_final: 0.6723 (mmtt) REVERT: B 301 ARG cc_start: 0.7255 (ttm170) cc_final: 0.6715 (ttp80) REVERT: B 316 LYS cc_start: 0.8869 (tttt) cc_final: 0.8313 (mtmt) REVERT: B 443 GLU cc_start: 0.7399 (mt-10) cc_final: 0.6933 (mm-30) REVERT: B 558 GLU cc_start: 0.9221 (OUTLIER) cc_final: 0.7759 (pt0) REVERT: B 641 ASN cc_start: 0.7813 (t0) cc_final: 0.7477 (m-40) REVERT: B 661 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7124 (pp20) REVERT: C 18 ARG cc_start: 0.7690 (mtm-85) cc_final: 0.7344 (mmp80) REVERT: C 156 ASP cc_start: 0.6045 (OUTLIER) cc_final: 0.5454 (m-30) REVERT: C 220 LYS cc_start: 0.7426 (mtpp) cc_final: 0.6726 (mmtt) REVERT: C 301 ARG cc_start: 0.7242 (ttm170) cc_final: 0.6688 (ttp80) REVERT: C 316 LYS cc_start: 0.8863 (tttt) cc_final: 0.8329 (mtmt) REVERT: C 443 GLU cc_start: 0.7354 (mt-10) cc_final: 0.6898 (mm-30) REVERT: C 558 GLU cc_start: 0.9217 (OUTLIER) cc_final: 0.7701 (pt0) REVERT: C 641 ASN cc_start: 0.7828 (t0) cc_final: 0.7503 (m-40) REVERT: C 661 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7123 (pp20) REVERT: D 18 ARG cc_start: 0.7687 (mtm-85) cc_final: 0.7348 (mmp80) REVERT: D 156 ASP cc_start: 0.6046 (OUTLIER) cc_final: 0.5456 (m-30) REVERT: D 220 LYS cc_start: 0.7408 (mtpp) cc_final: 0.6699 (mmtt) REVERT: D 301 ARG cc_start: 0.7258 (ttm170) cc_final: 0.6695 (ttp80) REVERT: D 316 LYS cc_start: 0.8877 (tttt) cc_final: 0.8317 (mtmt) REVERT: D 443 GLU cc_start: 0.7342 (mt-10) cc_final: 0.6890 (mm-30) REVERT: D 558 GLU cc_start: 0.9207 (OUTLIER) cc_final: 0.7706 (pt0) REVERT: D 641 ASN cc_start: 0.7818 (t0) cc_final: 0.7490 (m-40) REVERT: D 661 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.7135 (pp20) outliers start: 21 outliers final: 7 residues processed: 228 average time/residue: 0.7756 time to fit residues: 201.9906 Evaluate side-chains 228 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 209 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 600 LYS Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain C residue 651 VAL Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 558 GLU Chi-restraints excluded: chain D residue 651 VAL Chi-restraints excluded: chain D residue 661 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 43 optimal weight: 3.9990 chunk 205 optimal weight: 0.9980 chunk 259 optimal weight: 4.9990 chunk 340 optimal weight: 30.0000 chunk 272 optimal weight: 0.0670 chunk 224 optimal weight: 3.9990 chunk 280 optimal weight: 0.9980 chunk 339 optimal weight: 6.9990 chunk 187 optimal weight: 7.9990 chunk 159 optimal weight: 20.0000 chunk 57 optimal weight: 5.9990 overall best weight: 2.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.215295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.119243 restraints weight = 27101.494| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.40 r_work: 0.3157 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 27544 Z= 0.150 Angle : 0.511 4.771 37460 Z= 0.272 Chirality : 0.044 0.168 4324 Planarity : 0.004 0.059 4872 Dihedral : 13.060 150.018 4272 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.80 % Favored : 95.09 % Rotamer: Outliers : 0.81 % Allowed : 10.58 % Favored : 88.61 % 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: 0.06 (0.15), residues: 3460 helix: 0.93 (0.15), residues: 1364 sheet: 0.45 (0.23), residues: 556 loop : -0.88 (0.16), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 511 TYR 0.016 0.001 TYR C 519 PHE 0.010 0.002 PHE D 638 TRP 0.008 0.001 TRP C 181 HIS 0.006 0.001 HIS C 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (27540) covalent geometry : angle 0.51113 / 0.27 (37460) hydrogen bonds : bond 0.05078 / 3.44 ( 1114) hydrogen bonds : angle 4.38226 / 3.17 ( 3102) Misc. bond : bond 0.00040 / 0.02 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12513.26 seconds wall clock time: 212 minutes 51.64 seconds (12771.64 seconds total)