Starting phenix.real_space_refine on Mon May 4 10:14:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yp4_73283/05_2026/9yp4_73283.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yp4_73283/05_2026/9yp4_73283.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yp4_73283/05_2026/9yp4_73283.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yp4_73283/05_2026/9yp4_73283.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yp4_73283/05_2026/9yp4_73283.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yp4_73283/05_2026/9yp4_73283.map" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 S 112 5.16 5 C 12450 2.51 5 N 3336 2.21 5 O 3723 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19629 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 926, 7482 Classifications: {'peptide': 926} Link IDs: {'PTRANS': 32, 'TRANS': 893} Chain breaks: 2 Chain: "B" Number of atoms: 7395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 914, 7395 Classifications: {'peptide': 914} Link IDs: {'PTRANS': 31, 'TRANS': 882} Chain breaks: 2 Chain: "C" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1188 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 3, 'TRANS': 148} Chain: "D" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1188 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 3, 'TRANS': 148} Chain: "E" Number of atoms: 1127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1127 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 5, 'TRANS': 136} Chain: "F" Number of atoms: 1127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1127 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 5, 'TRANS': 136} Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {'2OW': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {'2OW': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.81, per 1000 atoms: 0.19 Number of scatterers: 19629 At special positions: 0 Unit cell: (95.45, 172.64, 169.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 112 16.00 P 6 15.00 F 2 9.00 O 3723 8.00 N 3336 7.00 C 12450 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 905 " - pdb=" SG CYS B 905 " distance=2.04 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.91 Conformation dependent library (CDL) restraints added in 793.2 milliseconds 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4560 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 19 sheets defined 60.8% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 6 through 16 removed outlier: 3.597A pdb=" N PHE A 9 " --> pdb=" O MET A 6 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ALA A 11 " --> pdb=" O VAL A 8 " (cutoff:3.500A) Proline residue: A 14 - end of helix Processing helix chain 'A' and resid 19 through 29 Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'A' and resid 97 through 110 Processing helix chain 'A' and resid 131 through 134 removed outlier: 3.576A pdb=" N TYR A 134 " --> pdb=" O LEU A 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 131 through 134' Processing helix chain 'A' and resid 135 through 141 removed outlier: 3.564A pdb=" N VAL A 139 " --> pdb=" O THR A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 169 Processing helix chain 'A' and resid 183 through 201 Processing helix chain 'A' and resid 214 through 232 removed outlier: 3.944A pdb=" N ASN A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Proline residue: A 225 - end of helix Processing helix chain 'A' and resid 270 through 274 Processing helix chain 'A' and resid 283 through 291 removed outlier: 4.130A pdb=" N TYR A 287 " --> pdb=" O TYR A 283 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE A 289 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 290 " --> pdb=" O PHE A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 306 through 309 Processing helix chain 'A' and resid 310 through 315 removed outlier: 3.644A pdb=" N GLN A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 339 Processing helix chain 'A' and resid 342 through 360 removed outlier: 3.829A pdb=" N GLY A 360 " --> pdb=" O ILE A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 388 Processing helix chain 'A' and resid 391 through 401 Processing helix chain 'A' and resid 416 through 448 Processing helix chain 'A' and resid 472 through 494 removed outlier: 3.713A pdb=" N ILE A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 504 Processing helix chain 'A' and resid 517 through 525 Processing helix chain 'A' and resid 529 through 538 Processing helix chain 'A' and resid 544 through 557 Processing helix chain 'A' and resid 592 through 599 Processing helix chain 'A' and resid 602 through 611 removed outlier: 3.859A pdb=" N LYS A 611 " --> pdb=" O GLY A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 621 removed outlier: 3.918A pdb=" N SER A 618 " --> pdb=" O LEU A 614 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE A 621 " --> pdb=" O LEU A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 664 Processing helix chain 'A' and resid 685 through 697 Processing helix chain 'A' and resid 697 through 707 Processing helix chain 'A' and resid 715 through 722 Processing helix chain 'A' and resid 737 through 748 Processing helix chain 'A' and resid 752 through 754 No H-bonds generated for 'chain 'A' and resid 752 through 754' Processing helix chain 'A' and resid 768 through 785 Processing helix chain 'A' and resid 785 through 824 removed outlier: 3.502A pdb=" N ARG A 819 " --> pdb=" O GLN A 815 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ALA A 820 " --> pdb=" O TRP A 816 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N PHE A 821 " --> pdb=" O ASN A 817 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N MET A 822 " --> pdb=" O ILE A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 837 removed outlier: 3.944A pdb=" N LYS A 835 " --> pdb=" O LYS A 831 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS A 837 " --> pdb=" O TYR A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 840 No H-bonds generated for 'chain 'A' and resid 838 through 840' Processing helix chain 'A' and resid 843 through 943 Processing helix chain 'B' and resid 4 through 8 removed outlier: 4.257A pdb=" N ALA B 7 " --> pdb=" O SER B 4 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL B 8 " --> pdb=" O GLU B 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4 through 8' Processing helix chain 'B' and resid 9 through 11 No H-bonds generated for 'chain 'B' and resid 9 through 11' Processing helix chain 'B' and resid 12 through 17 Processing helix chain 'B' and resid 19 through 28 Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'B' and resid 97 through 111 removed outlier: 3.803A pdb=" N VAL B 101 " --> pdb=" O HIS B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 142 Processing helix chain 'B' and resid 153 through 169 Processing helix chain 'B' and resid 183 through 200 Processing helix chain 'B' and resid 215 through 232 removed outlier: 3.556A pdb=" N ILE B 220 " --> pdb=" O LEU B 216 " (cutoff:3.500A) Proline residue: B 225 - end of helix removed outlier: 3.624A pdb=" N ASN B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 275 removed outlier: 4.411A pdb=" N ILE B 274 " --> pdb=" O LYS B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 291 removed outlier: 4.013A pdb=" N TYR B 287 " --> pdb=" O TYR B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 302 removed outlier: 3.516A pdb=" N LEU B 298 " --> pdb=" O LYS B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 324 through 340 Processing helix chain 'B' and resid 342 through 359 Processing helix chain 'B' and resid 360 through 362 No H-bonds generated for 'chain 'B' and resid 360 through 362' Processing helix chain 'B' and resid 378 through 389 Processing helix chain 'B' and resid 391 through 401 Processing helix chain 'B' and resid 416 through 448 Processing helix chain 'B' and resid 472 through 494 Processing helix chain 'B' and resid 494 through 504 Processing helix chain 'B' and resid 517 through 522 Processing helix chain 'B' and resid 529 through 540 Processing helix chain 'B' and resid 544 through 557 Processing helix chain 'B' and resid 592 through 599 Processing helix chain 'B' and resid 602 through 611 removed outlier: 3.566A pdb=" N LYS B 611 " --> pdb=" O GLY B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 625 removed outlier: 3.747A pdb=" N PHE B 621 " --> pdb=" O LEU B 617 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA B 622 " --> pdb=" O SER B 618 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ASN B 623 " --> pdb=" O THR B 619 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N TYR B 624 " --> pdb=" O LEU B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 664 Processing helix chain 'B' and resid 685 through 697 Processing helix chain 'B' and resid 697 through 708 Processing helix chain 'B' and resid 715 through 722 Processing helix chain 'B' and resid 723 through 726 Processing helix chain 'B' and resid 738 through 747 Processing helix chain 'B' and resid 766 through 826 Processing helix chain 'B' and resid 827 through 834 removed outlier: 3.912A pdb=" N LYS B 831 " --> pdb=" O TRP B 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 943 removed outlier: 4.197A pdb=" N GLU B 848 " --> pdb=" O GLU B 844 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN B 892 " --> pdb=" O GLN B 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 56 Processing helix chain 'C' and resid 66 through 75 removed outlier: 4.176A pdb=" N GLY C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASP C 71 " --> pdb=" O SER C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 90 removed outlier: 3.668A pdb=" N VAL C 85 " --> pdb=" O THR C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 100 Processing helix chain 'C' and resid 103 through 117 Proline residue: C 109 - end of helix Processing helix chain 'C' and resid 122 through 132 removed outlier: 3.764A pdb=" N VAL C 132 " --> pdb=" O GLU C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 153 Processing helix chain 'C' and resid 158 through 167 Processing helix chain 'C' and resid 177 through 187 Processing helix chain 'D' and resid 42 through 57 Processing helix chain 'D' and resid 65 through 67 No H-bonds generated for 'chain 'D' and resid 65 through 67' Processing helix chain 'D' and resid 68 through 74 Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 93 through 99 Processing helix chain 'D' and resid 106 through 118 removed outlier: 3.837A pdb=" N MET D 110 " --> pdb=" O GLN D 106 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS D 118 " --> pdb=" O ILE D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 131 removed outlier: 3.952A pdb=" N ARG D 131 " --> pdb=" O VAL D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 153 Processing helix chain 'D' and resid 158 through 167 Processing helix chain 'D' and resid 178 through 186 Processing helix chain 'E' and resid 23 through 38 removed outlier: 3.662A pdb=" N GLU E 32 " --> pdb=" O GLN E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 56 removed outlier: 4.501A pdb=" N ALA E 56 " --> pdb=" O ASP E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 72 removed outlier: 3.985A pdb=" N LYS E 72 " --> pdb=" O ASP E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 91 Processing helix chain 'E' and resid 96 through 108 Processing helix chain 'E' and resid 117 through 128 Processing helix chain 'E' and resid 132 through 140 Processing helix chain 'E' and resid 152 through 162 removed outlier: 3.859A pdb=" N ILE E 156 " --> pdb=" O ASP E 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 38 Processing helix chain 'F' and resid 48 through 54 removed outlier: 3.912A pdb=" N ASP F 52 " --> pdb=" O ASP F 49 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR F 53 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N PHE F 54 " --> pdb=" O ARG F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 72 removed outlier: 3.654A pdb=" N MET F 71 " --> pdb=" O LEU F 67 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS F 72 " --> pdb=" O ASP F 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 67 through 72' Processing helix chain 'F' and resid 80 through 90 removed outlier: 3.902A pdb=" N LEU F 84 " --> pdb=" O PHE F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 108 Processing helix chain 'F' and resid 116 through 126 removed outlier: 3.534A pdb=" N LEU F 120 " --> pdb=" O LYS F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 139 Processing helix chain 'F' and resid 140 through 142 No H-bonds generated for 'chain 'F' and resid 140 through 142' Processing helix chain 'F' and resid 152 through 162 removed outlier: 3.959A pdb=" N ILE F 156 " --> pdb=" O ASP F 152 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 40 removed outlier: 6.825A pdb=" N THR A 60 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ARG A 54 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LYS A 58 " --> pdb=" O ARG A 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 118 removed outlier: 6.867A pdb=" N CYS A 122 " --> pdb=" O ARG A 671 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ILE A 673 " --> pdb=" O CYS A 122 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N THR A 124 " --> pdb=" O ILE A 673 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ASN A 171 " --> pdb=" O HIS A 666 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N HIS A 668 " --> pdb=" O ASN A 171 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N SER A 173 " --> pdb=" O HIS A 668 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N VAL A 670 " --> pdb=" O SER A 173 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU A 175 " --> pdb=" O VAL A 670 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N CYS A 672 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 460 " --> pdb=" O ILE A 174 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE A 247 " --> pdb=" O GLU A 264 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU A 264 " --> pdb=" O PHE A 247 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 233 through 235 removed outlier: 5.773A pdb=" N ALA A 233 " --> pdb=" O ASN A 240 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ASN A 240 " --> pdb=" O ALA A 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 251 through 252 removed outlier: 6.925A pdb=" N HIS A 251 " --> pdb=" O ALA A 259 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 364 through 366 Processing sheet with id=AA6, first strand: chain 'A' and resid 403 through 406 Processing sheet with id=AA7, first strand: chain 'A' and resid 563 through 564 removed outlier: 3.672A pdb=" N PHE A 577 " --> pdb=" O TYR A 588 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 711 through 714 removed outlier: 3.809A pdb=" N PHE A 764 " --> pdb=" O LYS A 757 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS A 757 " --> pdb=" O PHE A 764 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 67 through 72 removed outlier: 3.588A pdb=" N LYS B 67 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N THR B 60 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL B 52 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET B 77 " --> pdb=" O PHE B 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 115 through 118 removed outlier: 6.790A pdb=" N CYS B 122 " --> pdb=" O ARG B 671 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N ILE B 673 " --> pdb=" O CYS B 122 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N THR B 124 " --> pdb=" O ILE B 673 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N THR B 177 " --> pdb=" O CYS B 672 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 171 through 173 removed outlier: 7.305A pdb=" N ASN B 171 " --> pdb=" O HIS B 666 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 258 through 266 removed outlier: 3.578A pdb=" N SER B 260 " --> pdb=" O HIS B 251 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 363 through 366 Processing sheet with id=AB5, first strand: chain 'B' and resid 563 through 564 removed outlier: 3.612A pdb=" N VAL B 586 " --> pdb=" O LEU B 579 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 711 through 714 removed outlier: 3.890A pdb=" N ILE B 713 " --> pdb=" O VAL B 763 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 763 " --> pdb=" O ILE B 713 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 64 through 65 removed outlier: 3.592A pdb=" N ILE C 64 " --> pdb=" O ILE C 102 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE C 102 " --> pdb=" O ILE C 64 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AB9, first strand: chain 'D' and resid 140 through 142 Processing sheet with id=AC1, first strand: chain 'E' and resid 115 through 116 1068 hydrogen bonds defined for protein. 3120 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.64 Time building geometry restraints manager: 2.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3667 1.33 - 1.46: 5199 1.46 - 1.58: 10921 1.58 - 1.71: 6 1.71 - 1.84: 198 Bond restraints: 19991 Sorted by residual: bond pdb=" C4 ADP B1402 " pdb=" C5 ADP B1402 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C14 2OW B1401 " pdb=" N15 2OW B1401 " ideal model delta sigma weight residual 1.398 1.494 -0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" C14 2OW A1401 " pdb=" N15 2OW A1401 " ideal model delta sigma weight residual 1.398 1.493 -0.095 2.00e-02 2.50e+03 2.27e+01 bond pdb=" C16 2OW A1401 " pdb=" N18 2OW A1401 " ideal model delta sigma weight residual 1.367 1.460 -0.093 2.00e-02 2.50e+03 2.16e+01 bond pdb=" C19 2OW A1401 " pdb=" N18 2OW A1401 " ideal model delta sigma weight residual 1.391 1.484 -0.093 2.00e-02 2.50e+03 2.16e+01 ... (remaining 19986 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 26643 2.84 - 5.67: 218 5.67 - 8.51: 21 8.51 - 11.35: 5 11.35 - 14.18: 2 Bond angle restraints: 26889 Sorted by residual: angle pdb=" N15 2OW A1401 " pdb=" C16 2OW A1401 " pdb=" N18 2OW A1401 " ideal model delta sigma weight residual 112.53 126.71 -14.18 3.00e+00 1.11e-01 2.24e+01 angle pdb=" N15 2OW B1401 " pdb=" C16 2OW B1401 " pdb=" N18 2OW B1401 " ideal model delta sigma weight residual 112.53 125.32 -12.79 3.00e+00 1.11e-01 1.82e+01 angle pdb=" C TYR A 310 " pdb=" CA TYR A 310 " pdb=" CB TYR A 310 " ideal model delta sigma weight residual 109.54 116.31 -6.77 1.84e+00 2.95e-01 1.36e+01 angle pdb=" N SER A 291 " pdb=" CA SER A 291 " pdb=" C SER A 291 " ideal model delta sigma weight residual 113.15 108.82 4.33 1.19e+00 7.06e-01 1.32e+01 angle pdb=" N MET A 528 " pdb=" CA MET A 528 " pdb=" CB MET A 528 " ideal model delta sigma weight residual 114.17 110.04 4.13 1.14e+00 7.69e-01 1.32e+01 ... (remaining 26884 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.15: 11313 22.15 - 44.29: 731 44.29 - 66.44: 109 66.44 - 88.59: 46 88.59 - 110.74: 5 Dihedral angle restraints: 12204 sinusoidal: 5152 harmonic: 7052 Sorted by residual: dihedral pdb=" CB CYS A 905 " pdb=" SG CYS A 905 " pdb=" SG CYS B 905 " pdb=" CB CYS B 905 " ideal model delta sinusoidal sigma weight residual -86.00 -26.73 -59.27 1 1.00e+01 1.00e-02 4.69e+01 dihedral pdb=" C5' ADP B1402 " pdb=" O5' ADP B1402 " pdb=" PA ADP B1402 " pdb=" O2A ADP B1402 " ideal model delta sinusoidal sigma weight residual -60.00 -170.73 110.74 1 2.00e+01 2.50e-03 3.25e+01 dihedral pdb=" CA TRP A 112 " pdb=" C TRP A 112 " pdb=" N MET A 113 " pdb=" CA MET A 113 " ideal model delta harmonic sigma weight residual 180.00 160.87 19.13 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 12201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2049 0.034 - 0.068: 563 0.068 - 0.102: 191 0.102 - 0.136: 80 0.136 - 0.170: 17 Chirality restraints: 2900 Sorted by residual: chirality pdb=" CA ILE A 303 " pdb=" N ILE A 303 " pdb=" C ILE A 303 " pdb=" CB ILE A 303 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.25e-01 chirality pdb=" CG LEU A 302 " pdb=" CB LEU A 302 " pdb=" CD1 LEU A 302 " pdb=" CD2 LEU A 302 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.23e-01 chirality pdb=" CA MET A 300 " pdb=" N MET A 300 " pdb=" C MET A 300 " pdb=" CB MET A 300 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.16e-01 ... (remaining 2897 not shown) Planarity restraints: 3492 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 144 " 0.046 5.00e-02 4.00e+02 6.94e-02 7.71e+00 pdb=" N PRO E 145 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO E 145 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO E 145 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 224 " 0.039 5.00e-02 4.00e+02 5.88e-02 5.53e+00 pdb=" N PRO B 225 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO B 225 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 225 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET B 528 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.18e+00 pdb=" C MET B 528 " 0.039 2.00e-02 2.50e+03 pdb=" O MET B 528 " -0.015 2.00e-02 2.50e+03 pdb=" N GLY B 529 " -0.013 2.00e-02 2.50e+03 ... (remaining 3489 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 308 2.50 - 3.10: 17299 3.10 - 3.70: 34614 3.70 - 4.30: 48648 4.30 - 4.90: 75505 Nonbonded interactions: 176374 Sorted by model distance: nonbonded pdb=" OG1 THR B 188 " pdb=" OD2 ASP B 461 " model vdw 1.898 3.040 nonbonded pdb=" O GLU B 269 " pdb=" OH TYR B 283 " model vdw 1.956 3.040 nonbonded pdb=" OH TYR B 715 " pdb=" O GLY B 759 " model vdw 1.963 3.040 nonbonded pdb=" OG SER A 842 " pdb=" OE1 GLU A 844 " model vdw 1.980 3.040 nonbonded pdb=" O LYS B 184 " pdb=" OG1 THR B 188 " model vdw 2.006 3.040 ... (remaining 176369 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 203 or resid 214 through 628 or resid 645 throug \ h 1403)) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } 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 group one per residue 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: 6.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 18.130 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 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 : 0.009 0.745 19994 Z= 0.762 Angle : 0.700 14.184 26891 Z= 0.380 Chirality : 0.040 0.170 2900 Planarity : 0.005 0.087 3492 Dihedral : 15.410 110.737 7641 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.10 % Allowed : 0.19 % Favored : 99.71 % 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: -1.28 (0.17), residues: 2408 helix: -0.22 (0.14), residues: 1316 sheet: -1.66 (0.48), residues: 125 loop : -1.52 (0.20), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 777 TYR 0.014 0.002 TYR B 287 PHE 0.017 0.001 PHE E 30 TRP 0.018 0.002 TRP A 827 HIS 0.006 0.001 HIS B 666 Details of bonding type rmsd covalent geometry : bond 0.00468 (19991) covalent geometry : angle 0.69942 (26889) SS BOND : bond 0.00994 ( 1) SS BOND : angle 3.37446 ( 2) hydrogen bonds : bond 0.16778 ( 1068) hydrogen bonds : angle 7.26586 ( 3120) Misc. bond : bond 0.71966 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 255 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 GLU cc_start: 0.8982 (pm20) cc_final: 0.8728 (pm20) REVERT: A 213 LYS cc_start: 0.5410 (mmtm) cc_final: 0.5185 (mmtm) REVERT: A 435 MET cc_start: 0.8645 (ttt) cc_final: 0.7868 (tpt) REVERT: A 539 MET cc_start: 0.9032 (mpp) cc_final: 0.8690 (mpp) REVERT: A 801 TYR cc_start: 0.7263 (t80) cc_final: 0.6334 (t80) REVERT: A 898 LEU cc_start: 0.8434 (mm) cc_final: 0.8225 (mm) REVERT: B 262 ASP cc_start: 0.8497 (m-30) cc_final: 0.8165 (p0) REVERT: B 684 MET cc_start: 0.7715 (mtp) cc_final: 0.7349 (mtp) REVERT: B 887 LEU cc_start: 0.7828 (mt) cc_final: 0.7521 (mt) REVERT: B 890 GLN cc_start: 0.8945 (pp30) cc_final: 0.8513 (pp30) REVERT: B 891 VAL cc_start: 0.8489 (p) cc_final: 0.8202 (p) REVERT: E 64 ASN cc_start: 0.8415 (m110) cc_final: 0.7983 (t0) REVERT: E 127 GLN cc_start: 0.4046 (pt0) cc_final: 0.3512 (mp10) REVERT: E 139 MET cc_start: 0.1434 (tpt) cc_final: 0.0859 (tpt) REVERT: F 41 ARG cc_start: 0.6791 (mmm-85) cc_final: 0.6204 (mmm-85) outliers start: 2 outliers final: 0 residues processed: 257 average time/residue: 0.1339 time to fit residues: 54.7001 Evaluate side-chains 199 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 216 optimal weight: 20.0000 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 235 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 ASN A 292 ASN ** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 ASN ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 882 GLN ** B 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.073615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.057800 restraints weight = 168476.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.058727 restraints weight = 119427.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.058641 restraints weight = 99726.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.059175 restraints weight = 88034.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.059309 restraints weight = 74379.049| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 19994 Z= 0.232 Angle : 0.726 10.074 26891 Z= 0.377 Chirality : 0.046 0.206 2900 Planarity : 0.005 0.056 3492 Dihedral : 7.456 119.937 2651 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 22.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 0.14 % Allowed : 5.14 % Favored : 94.72 % 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: -1.25 (0.17), residues: 2408 helix: -0.19 (0.13), residues: 1370 sheet: -2.09 (0.42), residues: 147 loop : -1.48 (0.22), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 712 TYR 0.020 0.002 TYR A 266 PHE 0.019 0.002 PHE E 87 TRP 0.025 0.002 TRP B 827 HIS 0.011 0.002 HIS B 666 Details of bonding type rmsd covalent geometry : bond 0.00490 (19991) covalent geometry : angle 0.72498 (26889) SS BOND : bond 0.00865 ( 1) SS BOND : angle 3.66308 ( 2) hydrogen bonds : bond 0.05586 ( 1068) hydrogen bonds : angle 5.84931 ( 3120) Misc. bond : bond 0.00165 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 242 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 GLU cc_start: 0.9165 (pm20) cc_final: 0.8928 (pm20) REVERT: A 246 LYS cc_start: 0.8819 (ptpt) cc_final: 0.8256 (pttm) REVERT: A 801 TYR cc_start: 0.7865 (t80) cc_final: 0.6949 (t80) REVERT: A 852 MET cc_start: 0.8707 (ptp) cc_final: 0.8366 (ptm) REVERT: A 898 LEU cc_start: 0.8687 (mm) cc_final: 0.8410 (mm) REVERT: B 262 ASP cc_start: 0.8608 (m-30) cc_final: 0.8139 (p0) REVERT: B 473 PHE cc_start: 0.9192 (t80) cc_final: 0.8979 (t80) REVERT: B 684 MET cc_start: 0.7723 (mtp) cc_final: 0.7503 (mtp) REVERT: B 890 GLN cc_start: 0.8968 (pp30) cc_final: 0.8476 (pp30) REVERT: C 56 PHE cc_start: 0.8054 (m-10) cc_final: 0.7343 (m-10) REVERT: D 157 MET cc_start: 0.8922 (mpp) cc_final: 0.8362 (mpp) REVERT: E 64 ASN cc_start: 0.8656 (m110) cc_final: 0.8368 (t0) REVERT: E 127 GLN cc_start: 0.4432 (pt0) cc_final: 0.3993 (mp10) outliers start: 3 outliers final: 2 residues processed: 245 average time/residue: 0.1308 time to fit residues: 51.2376 Evaluate side-chains 202 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 200 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 141 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 71 optimal weight: 30.0000 chunk 157 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 100 optimal weight: 0.2980 chunk 15 optimal weight: 0.7980 chunk 183 optimal weight: 8.9990 chunk 4 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 ASN ** A 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 ASN ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 597 ASN ** B 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 HIS ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.075767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.060534 restraints weight = 165380.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.060722 restraints weight = 119296.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.060940 restraints weight = 97495.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.061110 restraints weight = 94084.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.061232 restraints weight = 82654.939| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19994 Z= 0.151 Angle : 0.662 9.905 26891 Z= 0.338 Chirality : 0.044 0.221 2900 Planarity : 0.004 0.052 3492 Dihedral : 7.067 117.198 2651 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % 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: -1.02 (0.17), residues: 2408 helix: 0.00 (0.13), residues: 1373 sheet: -2.00 (0.45), residues: 135 loop : -1.39 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 712 TYR 0.021 0.002 TYR A 266 PHE 0.033 0.002 PHE E 30 TRP 0.013 0.001 TRP A 438 HIS 0.009 0.001 HIS B 666 Details of bonding type rmsd covalent geometry : bond 0.00319 (19991) covalent geometry : angle 0.66142 (26889) SS BOND : bond 0.00918 ( 1) SS BOND : angle 3.97188 ( 2) hydrogen bonds : bond 0.04858 ( 1068) hydrogen bonds : angle 5.53507 ( 3120) Misc. bond : bond 0.00045 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 HIS cc_start: 0.8619 (t70) cc_final: 0.8201 (t70) REVERT: A 246 LYS cc_start: 0.8993 (ptpt) cc_final: 0.8444 (pttm) REVERT: A 801 TYR cc_start: 0.7761 (t80) cc_final: 0.6967 (t80) REVERT: A 852 MET cc_start: 0.8715 (ptp) cc_final: 0.8232 (ptm) REVERT: A 898 LEU cc_start: 0.8592 (mm) cc_final: 0.8344 (mm) REVERT: B 262 ASP cc_start: 0.8689 (m-30) cc_final: 0.8163 (p0) REVERT: B 473 PHE cc_start: 0.9178 (t80) cc_final: 0.8946 (t80) REVERT: B 684 MET cc_start: 0.7635 (mtp) cc_final: 0.6900 (mtt) REVERT: B 888 GLN cc_start: 0.8579 (mt0) cc_final: 0.8235 (mt0) REVERT: E 64 ASN cc_start: 0.8666 (m110) cc_final: 0.8354 (t0) REVERT: F 40 ASN cc_start: 0.8925 (t0) cc_final: 0.8694 (t0) REVERT: F 41 ARG cc_start: 0.6706 (mmm-85) cc_final: 0.6501 (mmm-85) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.1303 time to fit residues: 53.1992 Evaluate side-chains 200 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 98 optimal weight: 3.9990 chunk 232 optimal weight: 20.0000 chunk 145 optimal weight: 4.9990 chunk 227 optimal weight: 9.9990 chunk 209 optimal weight: 6.9990 chunk 205 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 230 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 117 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 ASN ** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 ASN ** A 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN B 80 ASN B 171 ASN ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN F 138 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.072490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.057542 restraints weight = 171124.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.057252 restraints weight = 127969.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.057731 restraints weight = 104672.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.057867 restraints weight = 95939.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.057926 restraints weight = 86550.573| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 19994 Z= 0.271 Angle : 0.755 9.523 26891 Z= 0.391 Chirality : 0.047 0.231 2900 Planarity : 0.005 0.064 3492 Dihedral : 7.611 149.029 2651 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 27.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % 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: -1.37 (0.17), residues: 2408 helix: -0.25 (0.13), residues: 1373 sheet: -2.37 (0.42), residues: 141 loop : -1.57 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 712 TYR 0.028 0.002 TYR A 266 PHE 0.018 0.002 PHE E 87 TRP 0.024 0.002 TRP B 827 HIS 0.013 0.002 HIS B 666 Details of bonding type rmsd covalent geometry : bond 0.00571 (19991) covalent geometry : angle 0.75422 (26889) SS BOND : bond 0.00928 ( 1) SS BOND : angle 4.02379 ( 2) hydrogen bonds : bond 0.05434 ( 1068) hydrogen bonds : angle 5.80129 ( 3120) Misc. bond : bond 0.00108 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 LYS cc_start: 0.8908 (ptpt) cc_final: 0.8350 (pttm) REVERT: A 429 LYS cc_start: 0.8504 (ttmt) cc_final: 0.8238 (tttt) REVERT: A 460 LEU cc_start: 0.8997 (tp) cc_final: 0.8795 (tt) REVERT: A 653 GLU cc_start: 0.9417 (tm-30) cc_final: 0.9193 (tm-30) REVERT: A 801 TYR cc_start: 0.7858 (t80) cc_final: 0.7051 (t80) REVERT: A 852 MET cc_start: 0.8753 (ptp) cc_final: 0.8260 (ptm) REVERT: A 898 LEU cc_start: 0.8632 (mm) cc_final: 0.8332 (mm) REVERT: B 609 TYR cc_start: 0.8756 (m-80) cc_final: 0.8537 (m-10) REVERT: B 684 MET cc_start: 0.7839 (mtp) cc_final: 0.6955 (mtt) REVERT: B 719 ARG cc_start: 0.8132 (tpt90) cc_final: 0.7479 (tpt90) REVERT: C 56 PHE cc_start: 0.7775 (m-10) cc_final: 0.7470 (m-10) REVERT: D 157 MET cc_start: 0.9027 (mpp) cc_final: 0.8557 (mpp) REVERT: E 64 ASN cc_start: 0.8619 (m110) cc_final: 0.8244 (t0) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.1396 time to fit residues: 53.4032 Evaluate side-chains 193 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 12 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 112 optimal weight: 4.9990 chunk 123 optimal weight: 0.7980 chunk 201 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 198 optimal weight: 1.9990 chunk 227 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN A 160 ASN ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 ASN A 576 HIS ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 597 ASN ** B 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 791 GLN ** B 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 HIS D 79 ASN D 112 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.074324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.059272 restraints weight = 166962.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.059088 restraints weight = 125398.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.059413 restraints weight = 105058.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.059587 restraints weight = 98384.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.059654 restraints weight = 88402.888| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19994 Z= 0.179 Angle : 0.694 10.508 26891 Z= 0.355 Chirality : 0.044 0.262 2900 Planarity : 0.005 0.051 3492 Dihedral : 7.485 158.143 2651 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 21.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % 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: -1.19 (0.17), residues: 2408 helix: -0.11 (0.13), residues: 1377 sheet: -2.14 (0.44), residues: 135 loop : -1.50 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 147 TYR 0.033 0.002 TYR B 455 PHE 0.034 0.002 PHE E 30 TRP 0.028 0.002 TRP B 827 HIS 0.011 0.001 HIS B 666 Details of bonding type rmsd covalent geometry : bond 0.00384 (19991) covalent geometry : angle 0.69296 (26889) SS BOND : bond 0.00961 ( 1) SS BOND : angle 4.13721 ( 2) hydrogen bonds : bond 0.04834 ( 1068) hydrogen bonds : angle 5.58136 ( 3120) Misc. bond : bond 0.00043 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 GLU cc_start: 0.9202 (pm20) cc_final: 0.8735 (pm20) REVERT: A 246 LYS cc_start: 0.8911 (ptpt) cc_final: 0.8280 (pttm) REVERT: A 429 LYS cc_start: 0.8392 (ttmt) cc_final: 0.8105 (tttt) REVERT: A 436 PHE cc_start: 0.8611 (t80) cc_final: 0.8330 (t80) REVERT: A 801 TYR cc_start: 0.7874 (t80) cc_final: 0.7055 (t80) REVERT: A 852 MET cc_start: 0.8777 (ptp) cc_final: 0.8505 (ptm) REVERT: A 898 LEU cc_start: 0.8581 (mm) cc_final: 0.8309 (mm) REVERT: A 932 MET cc_start: 0.6329 (tmm) cc_final: 0.5233 (mtt) REVERT: B 300 MET cc_start: 0.8158 (pmm) cc_final: 0.7947 (pmm) REVERT: B 473 PHE cc_start: 0.9262 (t80) cc_final: 0.9054 (t80) REVERT: B 684 MET cc_start: 0.7815 (mtp) cc_final: 0.7084 (mtt) REVERT: B 717 ASP cc_start: 0.8377 (t70) cc_final: 0.8161 (t70) REVERT: B 719 ARG cc_start: 0.8147 (tpt90) cc_final: 0.7472 (tpt90) REVERT: B 922 MET cc_start: -0.0682 (tpt) cc_final: -0.0960 (tpp) REVERT: B 932 MET cc_start: 0.4371 (ppp) cc_final: 0.4078 (ppp) REVERT: C 56 PHE cc_start: 0.7829 (m-10) cc_final: 0.7471 (m-10) REVERT: E 64 ASN cc_start: 0.8649 (m110) cc_final: 0.8315 (t0) REVERT: E 126 THR cc_start: 0.7962 (p) cc_final: 0.7730 (p) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.1339 time to fit residues: 52.6758 Evaluate side-chains 196 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 30 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 221 optimal weight: 10.0000 chunk 215 optimal weight: 8.9990 chunk 152 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 166 optimal weight: 0.9990 chunk 115 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 201 optimal weight: 10.0000 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 ASN ** A 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 372 GLN ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.075526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.059289 restraints weight = 165619.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.060327 restraints weight = 121012.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.060540 restraints weight = 100106.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.060965 restraints weight = 82975.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.061032 restraints weight = 77086.995| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19994 Z= 0.145 Angle : 0.657 10.565 26891 Z= 0.335 Chirality : 0.044 0.262 2900 Planarity : 0.004 0.050 3492 Dihedral : 7.342 161.507 2651 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 19.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % 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: -0.95 (0.17), residues: 2408 helix: 0.09 (0.13), residues: 1367 sheet: -2.02 (0.45), residues: 134 loop : -1.39 (0.22), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 712 TYR 0.023 0.002 TYR A 266 PHE 0.022 0.001 PHE C 181 TRP 0.026 0.002 TRP B 827 HIS 0.011 0.001 HIS B 666 Details of bonding type rmsd covalent geometry : bond 0.00310 (19991) covalent geometry : angle 0.65648 (26889) SS BOND : bond 0.00896 ( 1) SS BOND : angle 4.10065 ( 2) hydrogen bonds : bond 0.04474 ( 1068) hydrogen bonds : angle 5.38057 ( 3120) Misc. bond : bond 0.00006 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 GLU cc_start: 0.9204 (pm20) cc_final: 0.8715 (pm20) REVERT: A 153 HIS cc_start: 0.8523 (t70) cc_final: 0.8169 (t70) REVERT: A 349 MET cc_start: 0.8079 (mtt) cc_final: 0.7850 (mtt) REVERT: A 429 LYS cc_start: 0.8360 (ttmt) cc_final: 0.8141 (tttt) REVERT: A 539 MET cc_start: 0.8987 (mpp) cc_final: 0.8785 (mpp) REVERT: A 801 TYR cc_start: 0.7757 (t80) cc_final: 0.6895 (t80) REVERT: A 852 MET cc_start: 0.8806 (ptp) cc_final: 0.8436 (ptm) REVERT: A 898 LEU cc_start: 0.8687 (mm) cc_final: 0.8418 (mm) REVERT: B 262 ASP cc_start: 0.8721 (m-30) cc_final: 0.8097 (t0) REVERT: B 272 ARG cc_start: 0.7864 (ttp80) cc_final: 0.7352 (mtp180) REVERT: B 473 PHE cc_start: 0.9282 (t80) cc_final: 0.9049 (t80) REVERT: B 489 PHE cc_start: 0.8746 (t80) cc_final: 0.8450 (t80) REVERT: B 609 TYR cc_start: 0.8750 (m-80) cc_final: 0.8385 (m-80) REVERT: B 684 MET cc_start: 0.7585 (mtp) cc_final: 0.6547 (mtt) REVERT: B 922 MET cc_start: -0.0401 (tpt) cc_final: -0.0867 (tpp) REVERT: C 56 PHE cc_start: 0.7840 (m-10) cc_final: 0.7436 (m-10) REVERT: D 157 MET cc_start: 0.8958 (mpp) cc_final: 0.8560 (mpp) REVERT: E 64 ASN cc_start: 0.8620 (m110) cc_final: 0.8312 (t0) outliers start: 0 outliers final: 0 residues processed: 255 average time/residue: 0.1323 time to fit residues: 53.8750 Evaluate side-chains 201 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 60 optimal weight: 6.9990 chunk 180 optimal weight: 4.9990 chunk 186 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 224 optimal weight: 5.9990 chunk 161 optimal weight: 0.0870 chunk 98 optimal weight: 8.9990 chunk 175 optimal weight: 10.0000 chunk 130 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 190 optimal weight: 8.9990 overall best weight: 4.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 817 ASN A 895 GLN ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 GLN ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 791 GLN ** B 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 ASN D 79 ASN ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.072606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.056847 restraints weight = 170367.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.057812 restraints weight = 123314.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.058436 restraints weight = 94946.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.058556 restraints weight = 84944.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.058524 restraints weight = 75586.720| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 19994 Z= 0.257 Angle : 0.753 11.166 26891 Z= 0.390 Chirality : 0.046 0.204 2900 Planarity : 0.005 0.057 3492 Dihedral : 7.766 172.074 2651 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 27.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % 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: -1.25 (0.17), residues: 2408 helix: -0.12 (0.13), residues: 1359 sheet: -2.21 (0.45), residues: 135 loop : -1.59 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 712 TYR 0.025 0.002 TYR A 266 PHE 0.018 0.002 PHE B 489 TRP 0.027 0.002 TRP B 827 HIS 0.015 0.002 HIS B 666 Details of bonding type rmsd covalent geometry : bond 0.00544 (19991) covalent geometry : angle 0.75242 (26889) SS BOND : bond 0.00945 ( 1) SS BOND : angle 4.18828 ( 2) hydrogen bonds : bond 0.05123 ( 1068) hydrogen bonds : angle 5.64109 ( 3120) Misc. bond : bond 0.00109 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 LYS cc_start: 0.8500 (ttmt) cc_final: 0.8292 (tttt) REVERT: A 653 GLU cc_start: 0.9423 (tm-30) cc_final: 0.9160 (tm-30) REVERT: A 801 TYR cc_start: 0.7705 (t80) cc_final: 0.6826 (t80) REVERT: A 852 MET cc_start: 0.8784 (ptp) cc_final: 0.8312 (ptm) REVERT: A 898 LEU cc_start: 0.8675 (mm) cc_final: 0.8435 (mm) REVERT: A 932 MET cc_start: 0.6268 (tmm) cc_final: 0.5216 (mtt) REVERT: B 300 MET cc_start: 0.8097 (pmm) cc_final: 0.7870 (pmm) REVERT: B 609 TYR cc_start: 0.8769 (m-80) cc_final: 0.8400 (m-80) REVERT: B 684 MET cc_start: 0.7709 (mtp) cc_final: 0.6894 (mtt) REVERT: B 922 MET cc_start: 0.0016 (tpt) cc_final: -0.0693 (tpp) REVERT: B 932 MET cc_start: 0.4460 (ppp) cc_final: 0.4219 (ppp) REVERT: C 56 PHE cc_start: 0.7754 (m-10) cc_final: 0.7367 (m-10) REVERT: E 64 ASN cc_start: 0.8613 (m110) cc_final: 0.8233 (t0) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.1351 time to fit residues: 50.4074 Evaluate side-chains 190 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 107 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 205 optimal weight: 0.0870 chunk 100 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 135 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 209 optimal weight: 9.9990 chunk 197 optimal weight: 7.9990 chunk 224 optimal weight: 1.9990 chunk 202 optimal weight: 0.8980 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN A 160 ASN ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 ASN ** A 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 597 ASN ** B 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 HIS ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.075690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.060839 restraints weight = 164020.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.060940 restraints weight = 112906.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.061222 restraints weight = 94361.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.061438 restraints weight = 86043.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.061474 restraints weight = 78322.129| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19994 Z= 0.140 Angle : 0.677 10.886 26891 Z= 0.343 Chirality : 0.044 0.191 2900 Planarity : 0.004 0.050 3492 Dihedral : 7.536 174.052 2651 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 19.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % 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: -0.95 (0.17), residues: 2408 helix: 0.08 (0.13), residues: 1372 sheet: -2.09 (0.45), residues: 134 loop : -1.37 (0.22), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 712 TYR 0.026 0.002 TYR A 266 PHE 0.028 0.001 PHE B 473 TRP 0.031 0.002 TRP B 827 HIS 0.010 0.001 HIS B 666 Details of bonding type rmsd covalent geometry : bond 0.00301 (19991) covalent geometry : angle 0.67631 (26889) SS BOND : bond 0.00907 ( 1) SS BOND : angle 4.10422 ( 2) hydrogen bonds : bond 0.04404 ( 1068) hydrogen bonds : angle 5.35071 ( 3120) Misc. bond : bond 0.00018 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 VAL cc_start: 0.8140 (t) cc_final: 0.7939 (t) REVERT: A 153 HIS cc_start: 0.8555 (t70) cc_final: 0.8212 (t70) REVERT: A 349 MET cc_start: 0.8081 (mtt) cc_final: 0.7819 (mtt) REVERT: A 429 LYS cc_start: 0.8292 (ttmt) cc_final: 0.8072 (tttt) REVERT: A 539 MET cc_start: 0.8941 (mpp) cc_final: 0.8725 (mpp) REVERT: A 609 TYR cc_start: 0.9022 (m-10) cc_final: 0.8696 (m-10) REVERT: A 801 TYR cc_start: 0.7629 (t80) cc_final: 0.6681 (t80) REVERT: A 852 MET cc_start: 0.8707 (ptp) cc_final: 0.8228 (ptm) REVERT: A 898 LEU cc_start: 0.8552 (mm) cc_final: 0.8300 (mm) REVERT: A 932 MET cc_start: 0.6290 (tmm) cc_final: 0.5120 (mtt) REVERT: B 38 PHE cc_start: 0.7117 (m-10) cc_final: 0.6728 (m-80) REVERT: B 300 MET cc_start: 0.8019 (pmm) cc_final: 0.7767 (pmm) REVERT: B 379 GLU cc_start: 0.8916 (mp0) cc_final: 0.8509 (tm-30) REVERT: B 473 PHE cc_start: 0.9123 (t80) cc_final: 0.8821 (t80) REVERT: B 656 ASN cc_start: 0.9194 (m-40) cc_final: 0.8825 (m-40) REVERT: B 684 MET cc_start: 0.7489 (mtp) cc_final: 0.6536 (mtt) REVERT: B 922 MET cc_start: -0.0465 (tpt) cc_final: -0.0950 (tpp) REVERT: C 56 PHE cc_start: 0.7596 (m-10) cc_final: 0.7319 (m-10) REVERT: D 157 MET cc_start: 0.8930 (mpp) cc_final: 0.8529 (mpp) REVERT: E 64 ASN cc_start: 0.8586 (m110) cc_final: 0.8219 (t0) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.1336 time to fit residues: 53.3979 Evaluate side-chains 197 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 190 optimal weight: 0.2980 chunk 208 optimal weight: 10.0000 chunk 165 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 69 optimal weight: 0.4980 chunk 144 optimal weight: 0.9980 chunk 136 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 207 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 ASN ** A 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 HIS ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN B 454 GLN ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 791 GLN B 933 ASN C 173 ASN D 79 ASN ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.076309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.061211 restraints weight = 163418.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.061065 restraints weight = 123782.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.061610 restraints weight = 106139.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.061772 restraints weight = 96359.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.061847 restraints weight = 84926.622| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19994 Z= 0.135 Angle : 0.669 11.220 26891 Z= 0.337 Chirality : 0.044 0.249 2900 Planarity : 0.004 0.052 3492 Dihedral : 7.385 171.899 2651 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % 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: -0.76 (0.17), residues: 2408 helix: 0.24 (0.14), residues: 1362 sheet: -1.92 (0.46), residues: 130 loop : -1.32 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 712 TYR 0.020 0.001 TYR B 609 PHE 0.025 0.001 PHE B 473 TRP 0.026 0.002 TRP B 827 HIS 0.010 0.001 HIS B 666 Details of bonding type rmsd covalent geometry : bond 0.00289 (19991) covalent geometry : angle 0.66831 (26889) SS BOND : bond 0.00864 ( 1) SS BOND : angle 4.13070 ( 2) hydrogen bonds : bond 0.04277 ( 1068) hydrogen bonds : angle 5.22841 ( 3120) Misc. bond : bond 0.00007 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 VAL cc_start: 0.8054 (t) cc_final: 0.7849 (t) REVERT: A 153 HIS cc_start: 0.8558 (t70) cc_final: 0.8198 (t70) REVERT: A 349 MET cc_start: 0.7888 (mtt) cc_final: 0.7666 (mtt) REVERT: A 429 LYS cc_start: 0.8220 (ttmt) cc_final: 0.7995 (tttt) REVERT: A 460 LEU cc_start: 0.9027 (tp) cc_final: 0.8758 (tt) REVERT: A 653 GLU cc_start: 0.9496 (tm-30) cc_final: 0.9254 (tm-30) REVERT: A 801 TYR cc_start: 0.7656 (t80) cc_final: 0.6715 (t80) REVERT: A 852 MET cc_start: 0.8650 (ptp) cc_final: 0.8160 (ptm) REVERT: A 898 LEU cc_start: 0.8604 (mm) cc_final: 0.8329 (mm) REVERT: A 932 MET cc_start: 0.6332 (tmm) cc_final: 0.5223 (mtt) REVERT: B 38 PHE cc_start: 0.6986 (m-10) cc_final: 0.6682 (m-80) REVERT: B 379 GLU cc_start: 0.8890 (mp0) cc_final: 0.8509 (tm-30) REVERT: B 473 PHE cc_start: 0.9143 (t80) cc_final: 0.8825 (t80) REVERT: B 609 TYR cc_start: 0.8790 (m-80) cc_final: 0.8467 (m-80) REVERT: B 656 ASN cc_start: 0.9191 (m-40) cc_final: 0.8805 (m-40) REVERT: B 684 MET cc_start: 0.7398 (mtp) cc_final: 0.6371 (mtt) REVERT: B 922 MET cc_start: -0.0372 (tpt) cc_final: -0.0935 (tpp) REVERT: B 932 MET cc_start: 0.4155 (ppp) cc_final: 0.3924 (ppp) REVERT: C 56 PHE cc_start: 0.7645 (m-10) cc_final: 0.7352 (m-10) REVERT: E 64 ASN cc_start: 0.8622 (m110) cc_final: 0.8304 (t0) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.1274 time to fit residues: 49.9705 Evaluate side-chains 201 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 221 optimal weight: 7.9990 chunk 136 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 142 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 188 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 193 optimal weight: 30.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN B 454 GLN ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 654 ASN ** B 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.075406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.059032 restraints weight = 166370.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.060610 restraints weight = 123660.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.060624 restraints weight = 90042.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.061087 restraints weight = 83926.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.061180 restraints weight = 74412.571| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19994 Z= 0.160 Angle : 0.695 11.624 26891 Z= 0.352 Chirality : 0.044 0.248 2900 Planarity : 0.004 0.050 3492 Dihedral : 7.324 162.493 2651 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 20.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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: -0.76 (0.17), residues: 2408 helix: 0.22 (0.14), residues: 1363 sheet: -1.57 (0.50), residues: 111 loop : -1.37 (0.21), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 108 TYR 0.036 0.002 TYR A 266 PHE 0.027 0.002 PHE B 489 TRP 0.050 0.002 TRP A 827 HIS 0.010 0.001 HIS B 666 Details of bonding type rmsd covalent geometry : bond 0.00345 (19991) covalent geometry : angle 0.69455 (26889) SS BOND : bond 0.00888 ( 1) SS BOND : angle 4.15437 ( 2) hydrogen bonds : bond 0.04371 ( 1068) hydrogen bonds : angle 5.30155 ( 3120) Misc. bond : bond 0.00015 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 MET cc_start: 0.8025 (mtt) cc_final: 0.7808 (mtt) REVERT: A 460 LEU cc_start: 0.8992 (tp) cc_final: 0.8668 (tt) REVERT: A 539 MET cc_start: 0.8916 (mpp) cc_final: 0.8712 (mpp) REVERT: A 653 GLU cc_start: 0.9482 (tm-30) cc_final: 0.9273 (tm-30) REVERT: A 801 TYR cc_start: 0.7748 (t80) cc_final: 0.6838 (t80) REVERT: A 852 MET cc_start: 0.8716 (ptp) cc_final: 0.8241 (ptm) REVERT: A 898 LEU cc_start: 0.8686 (mm) cc_final: 0.8410 (mm) REVERT: A 932 MET cc_start: 0.6341 (tmm) cc_final: 0.5330 (mtt) REVERT: B 38 PHE cc_start: 0.7069 (m-10) cc_final: 0.6731 (m-80) REVERT: B 357 MET cc_start: 0.9018 (tmm) cc_final: 0.8758 (ttt) REVERT: B 379 GLU cc_start: 0.8894 (mp0) cc_final: 0.8496 (tm-30) REVERT: B 473 PHE cc_start: 0.9183 (t80) cc_final: 0.8887 (t80) REVERT: B 609 TYR cc_start: 0.8698 (m-80) cc_final: 0.8421 (m-80) REVERT: B 656 ASN cc_start: 0.9239 (m-40) cc_final: 0.8838 (m-40) REVERT: B 684 MET cc_start: 0.7515 (mtp) cc_final: 0.6418 (mtt) REVERT: B 922 MET cc_start: -0.0225 (tpt) cc_final: -0.0665 (tpp) REVERT: B 932 MET cc_start: 0.4397 (ppp) cc_final: 0.4168 (ppp) REVERT: C 56 PHE cc_start: 0.7738 (m-10) cc_final: 0.7328 (m-10) REVERT: D 157 MET cc_start: 0.8915 (mpp) cc_final: 0.8345 (mpp) REVERT: E 64 ASN cc_start: 0.8699 (m110) cc_final: 0.8383 (t0) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.1344 time to fit residues: 50.6403 Evaluate side-chains 198 residues out of total 2103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 193 optimal weight: 40.0000 chunk 94 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 52 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 199 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 98 optimal weight: 20.0000 chunk 147 optimal weight: 10.0000 chunk 188 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN B 454 GLN ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 791 GLN C 184 HIS D 79 ASN E 138 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.074377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.056364 restraints weight = 168523.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.057611 restraints weight = 116380.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.058433 restraints weight = 89288.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.059018 restraints weight = 75572.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.059276 restraints weight = 67833.742| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19994 Z= 0.182 Angle : 0.709 11.428 26891 Z= 0.362 Chirality : 0.045 0.250 2900 Planarity : 0.005 0.049 3492 Dihedral : 7.254 144.887 2651 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 21.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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: -0.89 (0.17), residues: 2408 helix: 0.15 (0.14), residues: 1353 sheet: -1.54 (0.50), residues: 112 loop : -1.49 (0.21), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 108 TYR 0.030 0.002 TYR D 123 PHE 0.026 0.002 PHE B 489 TRP 0.037 0.002 TRP A 827 HIS 0.009 0.001 HIS B 666 Details of bonding type rmsd covalent geometry : bond 0.00392 (19991) covalent geometry : angle 0.70844 (26889) SS BOND : bond 0.00902 ( 1) SS BOND : angle 4.14855 ( 2) hydrogen bonds : bond 0.04554 ( 1068) hydrogen bonds : angle 5.37677 ( 3120) Misc. bond : bond 0.00042 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3249.74 seconds wall clock time: 57 minutes 43.88 seconds (3463.88 seconds total)