Starting phenix.real_space_refine on Fri Jul 3 19:45:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k9r_62196/07_2026/9k9r_62196.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k9r_62196/07_2026/9k9r_62196.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k9r_62196/07_2026/9k9r_62196.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k9r_62196/07_2026/9k9r_62196.map" model { file = "/net/cci-nas-00/data/ceres_data/9k9r_62196/07_2026/9k9r_62196.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k9r_62196/07_2026/9k9r_62196.cif" } resolution = 2.61 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= 0.001 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2132 atoms to isotropic. 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 43 5.49 5 Mg 1 5.21 5 S 71 5.16 5 C 8989 2.51 5 N 2363 2.21 5 O 2763 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14230 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 8207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1005, 8207 Classifications: {'peptide': 1005} Link IDs: {'PTRANS': 37, 'TRANS': 967} Chain: "B" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1767 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 204} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3415 Classifications: {'peptide': 419} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 408} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "P" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 287 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Classifications: {'DNA': 2} Link IDs: {'rna3p': 1} Chain: "T" Number of atoms: 483 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 23, 463 Unusual residues: {'ORP': 1} Classifications: {'DNA': 22, 'undetermined': 1} Link IDs: {'rna3p': 21, None: 1} Not linked: pdbres="ORP T 5 " pdbres=" DC T 6 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Conformer: "B" Number of residues, atoms: 23, 463 Unusual residues: {'ORP': 1} Classifications: {'DNA': 22, 'undetermined': 1} Link IDs: {'rna3p': 21, None: 1} Not linked: pdbres="ORP T 5 " pdbres=" DC T 6 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 bond proxies already assigned to first conformer: 495 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" P A DT T 11 " occ=0.50 ... (38 atoms not shown) pdb=" C6 B DT T 11 " occ=0.50 Time building chain proxies: 2.79, per 1000 atoms: 0.20 Number of scatterers: 14230 At special positions: 0 Unit cell: (99.45, 124.95, 145.35, 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 71 16.00 P 43 15.00 Mg 1 11.99 O 2763 8.00 N 2363 7.00 C 8989 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 543.3 milliseconds 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3146 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 21 sheets defined 39.0% alpha, 20.6% beta 13 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 44 through 48 Processing helix chain 'A' and resid 108 through 118 Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 209 through 220 Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.504A pdb=" N GLU A 229 " --> pdb=" O SER A 226 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 226 through 230' Processing helix chain 'A' and resid 240 through 253 Processing helix chain 'A' and resid 267 through 280 Processing helix chain 'A' and resid 331 through 339 Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 380 through 389 Processing helix chain 'A' and resid 439 through 446 Processing helix chain 'A' and resid 448 through 473 removed outlier: 3.859A pdb=" N CYS A 466 " --> pdb=" O ASP A 462 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 487 Processing helix chain 'A' and resid 497 through 502 removed outlier: 3.567A pdb=" N ILE A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 514 removed outlier: 3.515A pdb=" N LEU A 506 " --> pdb=" O ILE A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 562 Processing helix chain 'A' and resid 564 through 566 No H-bonds generated for 'chain 'A' and resid 564 through 566' Processing helix chain 'A' and resid 576 through 591 removed outlier: 4.029A pdb=" N GLN A 589 " --> pdb=" O GLN A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 643 removed outlier: 3.959A pdb=" N ARG A 625 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN A 643 " --> pdb=" O LYS A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 672 removed outlier: 3.801A pdb=" N TYR A 668 " --> pdb=" O ALA A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 703 Processing helix chain 'A' and resid 763 through 782 removed outlier: 3.795A pdb=" N SER A 767 " --> pdb=" O ASP A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 857 Processing helix chain 'A' and resid 862 through 883 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.560A pdb=" N LEU A 889 " --> pdb=" O PRO A 886 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N MET A 891 " --> pdb=" O GLU A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 918 Processing helix chain 'A' and resid 947 through 949 No H-bonds generated for 'chain 'A' and resid 947 through 949' Processing helix chain 'A' and resid 967 through 981 removed outlier: 4.472A pdb=" N TYR A 971 " --> pdb=" O PHE A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 998 Processing helix chain 'B' and resid 16 through 20 Processing helix chain 'B' and resid 22 through 31 Processing helix chain 'B' and resid 33 through 38 Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 86 through 101 Processing helix chain 'B' and resid 133 through 150 removed outlier: 5.553A pdb=" N LYS B 139 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N ILE B 140 " --> pdb=" O TYR B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 205 Processing helix chain 'C' and resid 3 through 19 Processing helix chain 'C' and resid 24 through 43 Processing helix chain 'C' and resid 57 through 61 Processing helix chain 'C' and resid 107 through 121 removed outlier: 3.675A pdb=" N ASP C 121 " --> pdb=" O VAL C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 159 removed outlier: 3.585A pdb=" N GLY C 159 " --> pdb=" O ALA C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 189 removed outlier: 3.511A pdb=" N ASP C 189 " --> pdb=" O GLU C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 257 Processing helix chain 'C' and resid 286 through 298 removed outlier: 3.925A pdb=" N ILE C 294 " --> pdb=" O ILE C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 321 Processing helix chain 'C' and resid 331 through 334 Processing helix chain 'C' and resid 335 through 341 removed outlier: 3.909A pdb=" N ASN C 339 " --> pdb=" O VAL C 335 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS C 340 " --> pdb=" O ASP C 336 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 335 through 341' Processing helix chain 'C' and resid 341 through 351 Processing helix chain 'C' and resid 353 through 361 Processing helix chain 'C' and resid 365 through 373 Processing helix chain 'C' and resid 393 through 396 Processing helix chain 'C' and resid 397 through 406 removed outlier: 4.145A pdb=" N ASN C 406 " --> pdb=" O THR C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 424 removed outlier: 3.608A pdb=" N ARG C 423 " --> pdb=" O ASP C 419 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 124 through 126 removed outlier: 5.579A pdb=" N CYS A 5 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ARG A 23 " --> pdb=" O CYS A 5 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN A 7 " --> pdb=" O LYS A 21 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N PHE A 17 " --> pdb=" O SER A 11 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N TYR A 140 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N PHE A 31 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N CYS A 142 " --> pdb=" O PHE A 31 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ARG A 33 " --> pdb=" O CYS A 142 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N HIS A 141 " --> pdb=" O LYS A 134 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LYS A 134 " --> pdb=" O HIS A 141 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 43 removed outlier: 6.300A pdb=" N SER A 84 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ARG A 64 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ALA A 86 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LYS A 62 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N MET A 88 " --> pdb=" O MET A 60 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N ILE A 516 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ARG A 64 " --> pdb=" O ILE A 516 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N VAL A 518 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ILE A 66 " --> pdb=" O VAL A 518 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 73 removed outlier: 6.629A pdb=" N SER A 73 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU A 568 " --> pdb=" O ASP A 616 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASP A 616 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY A 570 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER A 574 " --> pdb=" O SER A 610 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER A 610 " --> pdb=" O SER A 574 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 223 removed outlier: 6.289A pdb=" N LEU A 222 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N VAL A 237 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N THR A 201 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N CYS A 239 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ILE A 203 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N SER A 184 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU A 163 " --> pdb=" O VAL A 260 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 285 through 287 Processing sheet with id=AA6, first strand: chain 'A' and resid 300 through 305 Processing sheet with id=AA7, first strand: chain 'A' and resid 355 through 362 removed outlier: 6.607A pdb=" N THR A 369 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LYS A 416 " --> pdb=" O LYS A 408 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LYS A 408 " --> pdb=" O LYS A 416 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL A 418 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LYS A 404 " --> pdb=" O SER A 420 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 732 through 734 removed outlier: 6.876A pdb=" N PHE A 756 " --> pdb=" O VAL A 748 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ALA A 793 " --> pdb=" O ILE A 547 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ASP A 549 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N PHE A 791 " --> pdb=" O ASP A 549 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N TYR A 795 " --> pdb=" O TYR A 811 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N TYR A 811 " --> pdb=" O TYR A 795 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ASN A 797 " --> pdb=" O MET A 809 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N MET A 809 " --> pdb=" O ASN A 797 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS A 805 " --> pdb=" O GLN A 801 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 892 through 895 Processing sheet with id=AB1, first strand: chain 'A' and resid 892 through 895 Processing sheet with id=AB2, first strand: chain 'B' and resid 2 through 5 Processing sheet with id=AB3, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AB4, first strand: chain 'B' and resid 116 through 120 removed outlier: 6.568A pdb=" N VAL B 62 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N TRP B 119 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL B 64 " --> pdb=" O TRP B 119 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N CYS B 63 " --> pdb=" O TYR B 156 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU B 158 " --> pdb=" O CYS B 63 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N CYS B 65 " --> pdb=" O LEU B 158 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 107 through 108 removed outlier: 3.843A pdb=" N GLY B 107 " --> pdb=" O ILE B 217 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 69 through 71 Processing sheet with id=AB7, first strand: chain 'C' and resid 166 through 168 removed outlier: 4.204A pdb=" N SER C 196 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN C 208 " --> pdb=" O TYR C 199 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 96 through 97 removed outlier: 3.555A pdb=" N VAL C 96 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N VAL C 130 " --> pdb=" O MET C 138 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N MET C 138 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 214 through 219 Processing sheet with id=AC1, first strand: chain 'C' and resid 222 through 229 removed outlier: 4.077A pdb=" N SER C 222 " --> pdb=" O ILE C 238 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE C 238 " --> pdb=" O SER C 222 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE C 228 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ILE C 232 " --> pdb=" O ILE C 228 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 302 through 304 Processing sheet with id=AC3, first strand: chain 'C' and resid 375 through 380 removed outlier: 6.344A pdb=" N GLU C 380 " --> pdb=" O VAL C 384 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N VAL C 384 " --> pdb=" O GLU C 380 " (cutoff:3.500A) 585 hydrogen bonds defined for protein. 1653 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 31 hydrogen bonds 62 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 2.08 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3699 1.33 - 1.45: 2841 1.45 - 1.57: 7886 1.57 - 1.69: 84 1.69 - 1.81: 108 Bond restraints: 14618 Sorted by residual: bond pdb=" O3B TTP A1102 " pdb=" PG TTP A1102 " ideal model delta sigma weight residual 1.748 1.594 0.154 2.00e-02 2.50e+03 5.94e+01 bond pdb=" O3A TTP A1102 " pdb=" PB TTP A1102 " ideal model delta sigma weight residual 1.675 1.596 0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" C3' DT T 25 " pdb=" C2' DT T 25 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.51e+00 bond pdb=" C3' DT P 15 " pdb=" C2' DT P 15 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.88e+00 bond pdb=" C3' DT T 10 " pdb=" C2' DT T 10 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.42e+00 ... (remaining 14613 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 19501 1.93 - 3.85: 384 3.85 - 5.78: 34 5.78 - 7.70: 6 7.70 - 9.63: 4 Bond angle restraints: 19929 Sorted by residual: angle pdb=" N ILE C 228 " pdb=" CA ILE C 228 " pdb=" C ILE C 228 " ideal model delta sigma weight residual 113.71 109.66 4.05 9.50e-01 1.11e+00 1.82e+01 angle pdb=" N3 DT T 22 " pdb=" C4 DT T 22 " pdb=" O4 DT T 22 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.76e+01 angle pdb=" N3 B DT T 11 " pdb=" C4 B DT T 11 " pdb=" O4 B DT T 11 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT T 10 " pdb=" C4 DT T 10 " pdb=" O4 DT T 10 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT T 18 " pdb=" C4 DT T 18 " pdb=" O4 DT T 18 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 ... (remaining 19924 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.41: 7833 19.41 - 38.83: 699 38.83 - 58.24: 203 58.24 - 77.65: 23 77.65 - 97.07: 10 Dihedral angle restraints: 8768 sinusoidal: 3891 harmonic: 4877 Sorted by residual: dihedral pdb=" CA CYS A 189 " pdb=" C CYS A 189 " pdb=" N TYR A 190 " pdb=" CA TYR A 190 " ideal model delta harmonic sigma weight residual -180.00 -159.29 -20.71 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA ASP A 904 " pdb=" C ASP A 904 " pdb=" N ASN A 905 " pdb=" CA ASN A 905 " ideal model delta harmonic sigma weight residual 180.00 162.10 17.90 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA ASP A 67 " pdb=" CB ASP A 67 " pdb=" CG ASP A 67 " pdb=" OD1 ASP A 67 " ideal model delta sinusoidal sigma weight residual -30.00 -86.75 56.75 1 2.00e+01 2.50e-03 1.08e+01 ... (remaining 8765 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1677 0.049 - 0.098: 417 0.098 - 0.147: 110 0.147 - 0.195: 2 0.195 - 0.244: 2 Chirality restraints: 2208 Sorted by residual: chirality pdb=" CB VAL A 310 " pdb=" CA VAL A 310 " pdb=" CG1 VAL A 310 " pdb=" CG2 VAL A 310 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CB VAL A 365 " pdb=" CA VAL A 365 " pdb=" CG1 VAL A 365 " pdb=" CG2 VAL A 365 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB ILE B 117 " pdb=" CA ILE B 117 " pdb=" CG1 ILE B 117 " pdb=" CG2 ILE B 117 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.13e-01 ... (remaining 2205 not shown) Planarity restraints: 2391 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 45 " -0.033 5.00e-02 4.00e+02 5.07e-02 4.11e+00 pdb=" N PRO B 46 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 46 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 46 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 592 " 0.029 5.00e-02 4.00e+02 4.39e-02 3.08e+00 pdb=" N PRO A 593 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 593 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 593 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 70 " -0.026 5.00e-02 4.00e+02 3.99e-02 2.54e+00 pdb=" N PRO B 71 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 71 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 71 " -0.022 5.00e-02 4.00e+02 ... (remaining 2388 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 252 2.67 - 3.23: 12928 3.23 - 3.79: 20947 3.79 - 4.34: 29004 4.34 - 4.90: 47886 Nonbonded interactions: 111017 Sorted by model distance: nonbonded pdb=" OD1 ASP A 373 " pdb=" N ASP A 374 " model vdw 2.117 3.120 nonbonded pdb=" OD1 ASP C 249 " pdb=" N VAL C 250 " model vdw 2.161 3.120 nonbonded pdb=" O ILE C 313 " pdb=" NE2 GLN C 409 " model vdw 2.218 3.120 nonbonded pdb=" OH TYR A 749 " pdb=" O LYS A 803 " model vdw 2.233 3.040 nonbonded pdb=" O VAL C 411 " pdb=" ND2 ASN C 415 " model vdw 2.236 3.120 ... (remaining 111012 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.810 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.154 14620 Z= 0.289 Angle : 0.624 9.629 19929 Z= 0.386 Chirality : 0.045 0.244 2208 Planarity : 0.004 0.051 2391 Dihedral : 15.935 97.068 5622 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.28 % Favored : 95.41 % Rotamer: Outliers : 0.07 % Allowed : 0.40 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.14 (0.21), residues: 1634 helix: 1.38 (0.22), residues: 580 sheet: 0.66 (0.29), residues: 346 loop : -1.33 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 97 TYR 0.019 0.001 TYR A 528 PHE 0.020 0.002 PHE A 838 TRP 0.015 0.001 TRP A 470 HIS 0.006 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.29 (14618) covalent geometry : angle 0.62439 / 0.39 (19929) hydrogen bonds : bond 0.14255 / 9.63 ( 612) hydrogen bonds : angle 5.52221 / 3.82 ( 1715) Misc. bond : bond 0.03910 / 1.96 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 338 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 209 THR cc_start: 0.8166 (m) cc_final: 0.7884 (m) REVERT: A 291 LYS cc_start: 0.7898 (mmtm) cc_final: 0.7655 (mmtm) REVERT: A 310 VAL cc_start: 0.8381 (p) cc_final: 0.8102 (t) REVERT: A 792 GLU cc_start: 0.7288 (mm-30) cc_final: 0.7047 (mm-30) REVERT: A 943 LYS cc_start: 0.8065 (mmtp) cc_final: 0.7811 (mmtp) REVERT: B 109 ASN cc_start: 0.7957 (t0) cc_final: 0.7757 (t0) REVERT: B 205 ASP cc_start: 0.7552 (t0) cc_final: 0.7136 (t0) REVERT: C 11 LYS cc_start: 0.8429 (mttm) cc_final: 0.8223 (mttp) REVERT: C 95 MET cc_start: 0.2994 (mmp) cc_final: 0.2169 (mmp) REVERT: C 184 MET cc_start: 0.8039 (mmp) cc_final: 0.7720 (mmp) REVERT: C 224 LYS cc_start: 0.7787 (ptpp) cc_final: 0.7502 (ptpp) REVERT: C 350 ASN cc_start: 0.7501 (m110) cc_final: 0.7193 (m110) REVERT: C 422 LYS cc_start: 0.8153 (tptp) cc_final: 0.7834 (tptp) outliers start: 1 outliers final: 0 residues processed: 338 average time/residue: 0.5453 time to fit residues: 202.3033 Evaluate side-chains 314 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 314 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 50.0000 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 30.0000 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 ASN A 214 GLN A 413 ASN A 442 GLN B 111 ASN B 206 ASN C 9 ASN C 304 ASN C 373 ASN C 391 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.165714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.124472 restraints weight = 29433.848| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.59 r_work: 0.3373 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.0846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 14620 Z= 0.238 Angle : 0.641 10.535 19929 Z= 0.341 Chirality : 0.046 0.318 2208 Planarity : 0.005 0.057 2391 Dihedral : 15.180 104.218 2301 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.59 % Favored : 95.17 % Rotamer: Outliers : 1.52 % Allowed : 9.17 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.18 (0.21), residues: 1634 helix: 1.50 (0.22), residues: 587 sheet: 0.65 (0.28), residues: 347 loop : -1.39 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 16 TYR 0.023 0.002 TYR A 528 PHE 0.018 0.002 PHE B 216 TRP 0.018 0.002 TRP A 470 HIS 0.007 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.24 (14618) covalent geometry : angle 0.64082 / 0.34 (19929) hydrogen bonds : bond 0.06197 / 4.22 ( 612) hydrogen bonds : angle 4.65131 / 3.20 ( 1715) Misc. bond : bond 0.00130 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 322 time to evaluate : 0.511 Fit side-chains REVERT: A 209 THR cc_start: 0.8540 (m) cc_final: 0.8321 (m) REVERT: A 291 LYS cc_start: 0.8294 (mmtm) cc_final: 0.8064 (mmtm) REVERT: A 310 VAL cc_start: 0.8682 (p) cc_final: 0.8436 (t) REVERT: A 413 ASN cc_start: 0.7770 (t0) cc_final: 0.7452 (t160) REVERT: A 742 ARG cc_start: 0.7979 (ttm-80) cc_final: 0.7711 (ttm-80) REVERT: A 792 GLU cc_start: 0.8263 (mm-30) cc_final: 0.8045 (mm-30) REVERT: B 96 ILE cc_start: 0.8133 (tp) cc_final: 0.7870 (tp) REVERT: B 109 ASN cc_start: 0.8445 (t0) cc_final: 0.8173 (t0) REVERT: B 205 ASP cc_start: 0.8204 (t0) cc_final: 0.7751 (t0) REVERT: C 32 ASN cc_start: 0.8092 (m110) cc_final: 0.7761 (m-40) REVERT: C 95 MET cc_start: 0.3761 (mmp) cc_final: 0.2679 (mmp) REVERT: C 184 MET cc_start: 0.8506 (mmp) cc_final: 0.8131 (mmp) REVERT: C 224 LYS cc_start: 0.7707 (ptpp) cc_final: 0.7410 (ptpp) REVERT: C 336 ASP cc_start: 0.7964 (m-30) cc_final: 0.7711 (m-30) REVERT: C 373 ASN cc_start: 0.7269 (m-40) cc_final: 0.6946 (m110) REVERT: C 419 ASP cc_start: 0.7464 (p0) cc_final: 0.7203 (p0) REVERT: C 422 LYS cc_start: 0.8192 (tptp) cc_final: 0.7864 (tptp) outliers start: 23 outliers final: 10 residues processed: 328 average time/residue: 0.4990 time to fit residues: 180.0331 Evaluate side-chains 325 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 315 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 646 SER Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 191 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 107 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 130 optimal weight: 40.0000 chunk 124 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 146 optimal weight: 20.0000 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 GLN A 204 ASN A 211 GLN A 214 GLN A 801 GLN A 816 ASN B 111 ASN C 32 ASN C 350 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.165879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.126489 restraints weight = 23314.137| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.19 r_work: 0.3413 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14620 Z= 0.207 Angle : 0.593 10.691 19929 Z= 0.318 Chirality : 0.045 0.327 2208 Planarity : 0.005 0.055 2391 Dihedral : 15.138 107.098 2301 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.10 % Favored : 95.65 % Rotamer: Outliers : 1.78 % Allowed : 11.22 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.22 (0.21), residues: 1634 helix: 1.55 (0.22), residues: 588 sheet: 0.64 (0.28), residues: 347 loop : -1.38 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 16 TYR 0.022 0.001 TYR A 528 PHE 0.015 0.002 PHE A 838 TRP 0.017 0.001 TRP A 470 HIS 0.006 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.21 (14618) covalent geometry : angle 0.59295 / 0.32 (19929) hydrogen bonds : bond 0.05719 / 3.90 ( 612) hydrogen bonds : angle 4.50799 / 3.10 ( 1715) Misc. bond : bond 0.00093 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 329 time to evaluate : 0.382 Fit side-chains REVERT: A 207 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8518 (ptp) REVERT: A 225 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8628 (mt0) REVERT: A 291 LYS cc_start: 0.8261 (mmtm) cc_final: 0.8025 (mmtm) REVERT: A 310 VAL cc_start: 0.8670 (p) cc_final: 0.8420 (t) REVERT: A 413 ASN cc_start: 0.7772 (t0) cc_final: 0.7521 (t0) REVERT: A 540 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.8182 (mtt) REVERT: A 742 ARG cc_start: 0.7874 (ttm-80) cc_final: 0.7603 (ttm-80) REVERT: A 816 ASN cc_start: 0.8512 (p0) cc_final: 0.8310 (p0) REVERT: A 943 LYS cc_start: 0.8608 (mmtp) cc_final: 0.8389 (mmtp) REVERT: B 96 ILE cc_start: 0.8101 (tp) cc_final: 0.7805 (tp) REVERT: B 109 ASN cc_start: 0.8441 (t0) cc_final: 0.8159 (t0) REVERT: B 205 ASP cc_start: 0.8104 (t0) cc_final: 0.7645 (t0) REVERT: C 32 ASN cc_start: 0.8063 (m-40) cc_final: 0.7775 (m-40) REVERT: C 95 MET cc_start: 0.3815 (mmp) cc_final: 0.2752 (mmp) REVERT: C 184 MET cc_start: 0.8494 (mmp) cc_final: 0.8108 (mmp) REVERT: C 224 LYS cc_start: 0.7694 (ptpp) cc_final: 0.7396 (ptpp) REVERT: C 336 ASP cc_start: 0.7983 (m-30) cc_final: 0.7717 (m-30) REVERT: C 397 ASN cc_start: 0.8078 (t0) cc_final: 0.7802 (t0) REVERT: C 419 ASP cc_start: 0.7420 (p0) cc_final: 0.7197 (p0) REVERT: C 422 LYS cc_start: 0.8126 (tptp) cc_final: 0.7744 (tptp) outliers start: 27 outliers final: 19 residues processed: 333 average time/residue: 0.5108 time to fit residues: 187.2049 Evaluate side-chains 343 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 321 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 445 LYS Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 646 SER Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain C residue 9 ASN Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 345 LYS Chi-restraints excluded: chain C residue 365 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 117 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 3 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 129 optimal weight: 9.9990 chunk 123 optimal weight: 10.0000 chunk 161 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 ASN A 801 GLN B 59 ASN B 111 ASN C 373 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.166541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.127480 restraints weight = 22847.553| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.21 r_work: 0.3410 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3253 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3253 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14620 Z= 0.171 Angle : 0.588 14.510 19929 Z= 0.312 Chirality : 0.044 0.319 2208 Planarity : 0.004 0.053 2391 Dihedral : 15.072 107.586 2301 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.79 % Favored : 95.96 % Rotamer: Outliers : 2.31 % Allowed : 13.14 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.21), residues: 1634 helix: 1.61 (0.22), residues: 588 sheet: 0.68 (0.28), residues: 345 loop : -1.37 (0.22), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 16 TYR 0.019 0.001 TYR A 528 PHE 0.015 0.001 PHE A 838 TRP 0.016 0.001 TRP A 470 HIS 0.006 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (14618) covalent geometry : angle 0.58817 / 0.31 (19929) hydrogen bonds : bond 0.05219 / 3.56 ( 612) hydrogen bonds : angle 4.43281 / 3.05 ( 1715) Misc. bond : bond 0.00063 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 327 time to evaluate : 0.354 Fit side-chains REVERT: A 225 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8618 (mt0) REVERT: A 291 LYS cc_start: 0.8259 (mmtm) cc_final: 0.8016 (mmtm) REVERT: A 292 LYS cc_start: 0.8459 (mtmm) cc_final: 0.8139 (mtmm) REVERT: A 341 LEU cc_start: 0.8995 (mt) cc_final: 0.8764 (mt) REVERT: A 413 ASN cc_start: 0.7803 (t0) cc_final: 0.7493 (t0) REVERT: A 540 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.8193 (mtt) REVERT: A 742 ARG cc_start: 0.7912 (ttm-80) cc_final: 0.7661 (ttm-80) REVERT: B 96 ILE cc_start: 0.8124 (tp) cc_final: 0.7820 (tp) REVERT: B 109 ASN cc_start: 0.8489 (t0) cc_final: 0.8193 (t0) REVERT: B 205 ASP cc_start: 0.8077 (t0) cc_final: 0.7643 (t0) REVERT: C 32 ASN cc_start: 0.8104 (m-40) cc_final: 0.7815 (m-40) REVERT: C 95 MET cc_start: 0.3784 (mmp) cc_final: 0.2711 (mmp) REVERT: C 184 MET cc_start: 0.8473 (mmp) cc_final: 0.8074 (mmp) REVERT: C 224 LYS cc_start: 0.7734 (ptpp) cc_final: 0.7424 (ptpp) REVERT: C 336 ASP cc_start: 0.8031 (m-30) cc_final: 0.7728 (m-30) REVERT: C 422 LYS cc_start: 0.8084 (tptp) cc_final: 0.7702 (tptp) outliers start: 35 outliers final: 23 residues processed: 332 average time/residue: 0.5086 time to fit residues: 185.3454 Evaluate side-chains 342 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 317 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 445 LYS Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 646 SER Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 945 VAL Chi-restraints excluded: chain A residue 959 LYS Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain C residue 9 ASN Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 345 LYS Chi-restraints excluded: chain C residue 365 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 133 optimal weight: 8.9990 chunk 101 optimal weight: 1.9990 chunk 44 optimal weight: 0.0570 chunk 51 optimal weight: 0.5980 chunk 121 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 162 optimal weight: 9.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 ASN A 214 GLN A 556 ASN A 801 GLN A 899 ASN C 373 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.167340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.128598 restraints weight = 23287.949| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.29 r_work: 0.3424 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14620 Z= 0.136 Angle : 0.557 10.455 19929 Z= 0.298 Chirality : 0.043 0.313 2208 Planarity : 0.004 0.051 2391 Dihedral : 14.952 106.170 2301 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.04 % Favored : 95.72 % Rotamer: Outliers : 2.18 % Allowed : 14.06 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.31 (0.21), residues: 1634 helix: 1.69 (0.22), residues: 588 sheet: 0.58 (0.28), residues: 347 loop : -1.32 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 292 TYR 0.017 0.001 TYR A 190 PHE 0.013 0.001 PHE B 216 TRP 0.015 0.001 TRP A 470 HIS 0.005 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (14618) covalent geometry : angle 0.55684 / 0.30 (19929) hydrogen bonds : bond 0.04694 / 3.20 ( 612) hydrogen bonds : angle 4.34341 / 2.99 ( 1715) Misc. bond : bond 0.00043 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 324 time to evaluate : 0.518 Fit side-chains REVERT: A 225 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8628 (mt0) REVERT: A 291 LYS cc_start: 0.8260 (mmtm) cc_final: 0.8014 (mmtm) REVERT: A 341 LEU cc_start: 0.8975 (mt) cc_final: 0.8765 (mt) REVERT: A 373 ASP cc_start: 0.7990 (t0) cc_final: 0.7705 (t0) REVERT: A 413 ASN cc_start: 0.7804 (t0) cc_final: 0.7459 (t0) REVERT: A 540 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8194 (mtt) REVERT: A 742 ARG cc_start: 0.7920 (ttm-80) cc_final: 0.7658 (ttm-80) REVERT: A 943 LYS cc_start: 0.8594 (mmtp) cc_final: 0.8362 (mmtp) REVERT: B 96 ILE cc_start: 0.8092 (tp) cc_final: 0.7778 (tp) REVERT: B 109 ASN cc_start: 0.8510 (t0) cc_final: 0.8233 (t0) REVERT: B 205 ASP cc_start: 0.8051 (t0) cc_final: 0.7625 (t0) REVERT: C 32 ASN cc_start: 0.8064 (m-40) cc_final: 0.7776 (m-40) REVERT: C 95 MET cc_start: 0.3936 (mmp) cc_final: 0.2853 (mmp) REVERT: C 184 MET cc_start: 0.8503 (mmp) cc_final: 0.8103 (mmp) REVERT: C 224 LYS cc_start: 0.7674 (ptpp) cc_final: 0.7380 (ptpp) REVERT: C 336 ASP cc_start: 0.8049 (m-30) cc_final: 0.7735 (m-30) REVERT: C 397 ASN cc_start: 0.8038 (t0) cc_final: 0.7748 (t0) REVERT: C 422 LYS cc_start: 0.8114 (tptp) cc_final: 0.7709 (tptp) outliers start: 33 outliers final: 19 residues processed: 329 average time/residue: 0.5095 time to fit residues: 184.1609 Evaluate side-chains 337 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 316 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 445 LYS Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 646 SER Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 945 VAL Chi-restraints excluded: chain A residue 959 LYS Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 142 LYS Chi-restraints excluded: chain C residue 345 LYS Chi-restraints excluded: chain C residue 365 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 82 optimal weight: 2.9990 chunk 134 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 78 optimal weight: 0.0170 chunk 20 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 overall best weight: 0.9622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 ASN A 801 GLN A 816 ASN B 120 ASN C 373 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.166638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.127213 restraints weight = 22867.856| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.20 r_work: 0.3432 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3278 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3278 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14620 Z= 0.169 Angle : 0.574 9.872 19929 Z= 0.305 Chirality : 0.044 0.359 2208 Planarity : 0.004 0.053 2391 Dihedral : 14.920 106.001 2301 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.10 % Favored : 95.65 % Rotamer: Outliers : 2.57 % Allowed : 14.65 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.31 (0.21), residues: 1634 helix: 1.71 (0.22), residues: 588 sheet: 0.49 (0.28), residues: 350 loop : -1.30 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 58 TYR 0.019 0.001 TYR A 528 PHE 0.015 0.001 PHE A 838 TRP 0.015 0.001 TRP A 470 HIS 0.006 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (14618) covalent geometry : angle 0.57389 / 0.31 (19929) hydrogen bonds : bond 0.05004 / 3.41 ( 612) hydrogen bonds : angle 4.34775 / 2.99 ( 1715) Misc. bond : bond 0.00062 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 326 time to evaluate : 0.364 Fit side-chains REVERT: A 225 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8582 (mt0) REVERT: A 291 LYS cc_start: 0.8256 (mmtm) cc_final: 0.8001 (mmtm) REVERT: A 373 ASP cc_start: 0.7984 (t0) cc_final: 0.7634 (t0) REVERT: A 413 ASN cc_start: 0.7779 (t0) cc_final: 0.7388 (t0) REVERT: A 540 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.8184 (mtt) REVERT: A 742 ARG cc_start: 0.7901 (ttm-80) cc_final: 0.7640 (ttm-80) REVERT: B 96 ILE cc_start: 0.8083 (tp) cc_final: 0.7769 (tp) REVERT: B 205 ASP cc_start: 0.8045 (t0) cc_final: 0.7623 (t0) REVERT: C 32 ASN cc_start: 0.8096 (m-40) cc_final: 0.7791 (m-40) REVERT: C 95 MET cc_start: 0.3800 (mmp) cc_final: 0.2750 (mmp) REVERT: C 184 MET cc_start: 0.8461 (mmp) cc_final: 0.8049 (mmp) REVERT: C 224 LYS cc_start: 0.7712 (ptpp) cc_final: 0.7417 (ptpp) REVERT: C 336 ASP cc_start: 0.8098 (m-30) cc_final: 0.7769 (m-30) REVERT: C 397 ASN cc_start: 0.8049 (t0) cc_final: 0.7769 (t0) REVERT: C 422 LYS cc_start: 0.8074 (tptp) cc_final: 0.7680 (tptp) outliers start: 39 outliers final: 23 residues processed: 335 average time/residue: 0.5076 time to fit residues: 186.9938 Evaluate side-chains 342 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 317 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 445 LYS Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 646 SER Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 945 VAL Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 142 LYS Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 345 LYS Chi-restraints excluded: chain C residue 365 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 15 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 131 optimal weight: 7.9990 chunk 60 optimal weight: 0.0770 chunk 3 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 94 optimal weight: 0.0270 chunk 32 optimal weight: 0.4980 chunk 159 optimal weight: 5.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 ASN A 214 GLN A 801 GLN B 109 ASN C 373 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.168080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.129193 restraints weight = 22856.422| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.15 r_work: 0.3449 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3294 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3294 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14620 Z= 0.118 Angle : 0.549 9.047 19929 Z= 0.294 Chirality : 0.043 0.367 2208 Planarity : 0.004 0.053 2391 Dihedral : 14.783 103.728 2301 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.79 % Favored : 95.96 % Rotamer: Outliers : 2.05 % Allowed : 15.84 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.40 (0.21), residues: 1634 helix: 1.80 (0.22), residues: 587 sheet: 0.47 (0.28), residues: 355 loop : -1.22 (0.22), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 577 TYR 0.017 0.001 TYR B 11 PHE 0.012 0.001 PHE B 216 TRP 0.014 0.001 TRP A 470 HIS 0.005 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (14618) covalent geometry : angle 0.54911 / 0.29 (19929) hydrogen bonds : bond 0.04321 / 2.95 ( 612) hydrogen bonds : angle 4.27665 / 2.94 ( 1715) Misc. bond : bond 0.00029 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 332 time to evaluate : 0.524 Fit side-chains REVERT: A 225 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.8559 (mt0) REVERT: A 291 LYS cc_start: 0.8246 (mmtm) cc_final: 0.7991 (mmtm) REVERT: A 292 LYS cc_start: 0.8448 (mtmm) cc_final: 0.8144 (mtmm) REVERT: A 373 ASP cc_start: 0.7967 (t0) cc_final: 0.7648 (t0) REVERT: A 413 ASN cc_start: 0.7777 (t0) cc_final: 0.7347 (t160) REVERT: A 540 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.8149 (mtt) REVERT: A 742 ARG cc_start: 0.7916 (ttm-80) cc_final: 0.7659 (ttm-80) REVERT: B 96 ILE cc_start: 0.8075 (tp) cc_final: 0.7756 (tp) REVERT: B 205 ASP cc_start: 0.8015 (t0) cc_final: 0.7586 (t0) REVERT: C 32 ASN cc_start: 0.8076 (m-40) cc_final: 0.7775 (m-40) REVERT: C 95 MET cc_start: 0.3752 (mmp) cc_final: 0.2725 (mmp) REVERT: C 184 MET cc_start: 0.8455 (mmp) cc_final: 0.8041 (mmp) REVERT: C 224 LYS cc_start: 0.7718 (ptpp) cc_final: 0.7424 (ptpp) REVERT: C 336 ASP cc_start: 0.8066 (m-30) cc_final: 0.7730 (m-30) REVERT: C 397 ASN cc_start: 0.8014 (t0) cc_final: 0.7735 (t0) REVERT: C 422 LYS cc_start: 0.8011 (tptp) cc_final: 0.7601 (tptp) outliers start: 31 outliers final: 20 residues processed: 338 average time/residue: 0.5107 time to fit residues: 189.7289 Evaluate side-chains 349 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 327 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 445 LYS Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 646 SER Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 945 VAL Chi-restraints excluded: chain A residue 959 LYS Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 142 LYS Chi-restraints excluded: chain C residue 345 LYS Chi-restraints excluded: chain C residue 365 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 90 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 ASN A 204 ASN A 214 GLN A 801 GLN A 816 ASN B 109 ASN C 373 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.166742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.127284 restraints weight = 23368.649| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.42 r_work: 0.3390 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3223 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3223 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14620 Z= 0.189 Angle : 0.585 10.268 19929 Z= 0.311 Chirality : 0.045 0.402 2208 Planarity : 0.004 0.052 2391 Dihedral : 14.786 104.662 2301 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.92 % Favored : 95.84 % Rotamer: Outliers : 2.05 % Allowed : 16.83 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.34 (0.21), residues: 1634 helix: 1.74 (0.22), residues: 587 sheet: 0.49 (0.28), residues: 350 loop : -1.27 (0.22), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 58 TYR 0.020 0.001 TYR A 528 PHE 0.027 0.002 PHE C 407 TRP 0.014 0.001 TRP A 470 HIS 0.006 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 (14618) covalent geometry : angle 0.58458 / 0.31 (19929) hydrogen bonds : bond 0.05007 / 3.41 ( 612) hydrogen bonds : angle 4.31927 / 2.97 ( 1715) Misc. bond : bond 0.00075 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 330 time to evaluate : 0.319 Fit side-chains REVERT: A 225 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.8638 (mt0) REVERT: A 291 LYS cc_start: 0.8293 (mmtm) cc_final: 0.8041 (mmtm) REVERT: A 373 ASP cc_start: 0.8061 (t0) cc_final: 0.7746 (t0) REVERT: A 413 ASN cc_start: 0.7852 (t0) cc_final: 0.7403 (t160) REVERT: A 540 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8301 (mtt) REVERT: A 742 ARG cc_start: 0.8022 (ttm-80) cc_final: 0.7774 (ttm-80) REVERT: B 96 ILE cc_start: 0.8116 (tp) cc_final: 0.7797 (tp) REVERT: B 205 ASP cc_start: 0.8177 (t0) cc_final: 0.7757 (t0) REVERT: C 32 ASN cc_start: 0.8127 (m-40) cc_final: 0.7823 (m-40) REVERT: C 95 MET cc_start: 0.3732 (mmp) cc_final: 0.2698 (mmp) REVERT: C 160 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.7057 (tm) REVERT: C 184 MET cc_start: 0.8506 (mmp) cc_final: 0.8091 (mmp) REVERT: C 224 LYS cc_start: 0.7692 (ptpp) cc_final: 0.7404 (ptpp) REVERT: C 336 ASP cc_start: 0.8136 (m-30) cc_final: 0.7795 (m-30) REVERT: C 374 ASN cc_start: 0.7129 (p0) cc_final: 0.6815 (p0) REVERT: C 391 ASN cc_start: 0.8321 (m-40) cc_final: 0.8086 (m-40) REVERT: C 397 ASN cc_start: 0.8052 (t0) cc_final: 0.7842 (t0) REVERT: C 422 LYS cc_start: 0.8082 (tptp) cc_final: 0.7681 (tptp) outliers start: 31 outliers final: 20 residues processed: 335 average time/residue: 0.4849 time to fit residues: 178.1650 Evaluate side-chains 349 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 326 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 445 LYS Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 646 SER Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 945 VAL Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 142 LYS Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 345 LYS Chi-restraints excluded: chain C residue 365 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 46 optimal weight: 0.9990 chunk 146 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 44 optimal weight: 0.0870 chunk 137 optimal weight: 5.9990 chunk 142 optimal weight: 40.0000 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 162 optimal weight: 9.9990 chunk 52 optimal weight: 0.6980 chunk 25 optimal weight: 0.0170 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 ASN A 801 GLN C 373 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.167946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.126884 restraints weight = 29651.007| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.58 r_work: 0.3410 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3410 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3410 r_free = 0.3410 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3410 r_free = 0.3410 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3410 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14620 Z= 0.126 Angle : 0.565 9.346 19929 Z= 0.302 Chirality : 0.043 0.395 2208 Planarity : 0.004 0.053 2391 Dihedral : 14.698 103.750 2301 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.92 % Favored : 95.84 % Rotamer: Outliers : 1.85 % Allowed : 16.96 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.38 (0.21), residues: 1634 helix: 1.80 (0.22), residues: 587 sheet: 0.43 (0.27), residues: 355 loop : -1.23 (0.22), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 16 TYR 0.019 0.001 TYR B 11 PHE 0.013 0.001 PHE B 216 TRP 0.015 0.001 TRP A 470 HIS 0.006 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (14618) covalent geometry : angle 0.56509 / 0.30 (19929) hydrogen bonds : bond 0.04412 / 3.01 ( 612) hydrogen bonds : angle 4.27455 / 2.93 ( 1715) Misc. bond : bond 0.00030 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 330 time to evaluate : 0.466 Fit side-chains REVERT: A 225 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8398 (mt0) REVERT: A 291 LYS cc_start: 0.8128 (mmtm) cc_final: 0.7873 (mmtm) REVERT: A 373 ASP cc_start: 0.7777 (t0) cc_final: 0.7460 (t0) REVERT: A 413 ASN cc_start: 0.7712 (t0) cc_final: 0.7286 (t160) REVERT: A 540 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7959 (mtt) REVERT: A 742 ARG cc_start: 0.7632 (ttm-80) cc_final: 0.7372 (ttm-80) REVERT: A 834 ASP cc_start: 0.8298 (p0) cc_final: 0.8083 (p0) REVERT: B 96 ILE cc_start: 0.8005 (tp) cc_final: 0.7672 (tp) REVERT: B 205 ASP cc_start: 0.7832 (t0) cc_final: 0.7411 (t0) REVERT: C 9 ASN cc_start: 0.7933 (OUTLIER) cc_final: 0.7617 (m-40) REVERT: C 21 ARG cc_start: 0.6886 (ptm160) cc_final: 0.6140 (ptm160) REVERT: C 32 ASN cc_start: 0.7911 (m-40) cc_final: 0.7608 (m-40) REVERT: C 95 MET cc_start: 0.3450 (mmp) cc_final: 0.2436 (mmp) REVERT: C 160 LEU cc_start: 0.7261 (OUTLIER) cc_final: 0.7008 (tm) REVERT: C 184 MET cc_start: 0.8430 (mmp) cc_final: 0.8017 (mmp) REVERT: C 224 LYS cc_start: 0.7689 (ptpp) cc_final: 0.7399 (ptpp) REVERT: C 336 ASP cc_start: 0.8004 (m-30) cc_final: 0.7667 (m-30) REVERT: C 422 LYS cc_start: 0.8016 (tptp) cc_final: 0.7602 (tptp) outliers start: 28 outliers final: 20 residues processed: 337 average time/residue: 0.5243 time to fit residues: 194.0470 Evaluate side-chains 350 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 326 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 646 SER Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 860 ASN Chi-restraints excluded: chain A residue 945 VAL Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 142 LYS Chi-restraints excluded: chain C residue 9 ASN Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 345 LYS Chi-restraints excluded: chain C residue 365 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 106 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 98 optimal weight: 0.0470 chunk 158 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 155 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 ASN A 214 GLN A 362 ASN A 801 GLN A 816 ASN C 397 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.167788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.129149 restraints weight = 23392.702| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.24 r_work: 0.3440 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3286 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3286 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14620 Z= 0.142 Angle : 0.585 14.050 19929 Z= 0.309 Chirality : 0.043 0.409 2208 Planarity : 0.004 0.053 2391 Dihedral : 14.640 104.396 2301 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.86 % Favored : 95.90 % Rotamer: Outliers : 1.85 % Allowed : 17.62 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.36 (0.21), residues: 1634 helix: 1.77 (0.22), residues: 587 sheet: 0.48 (0.28), residues: 349 loop : -1.26 (0.22), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 16 TYR 0.019 0.001 TYR B 11 PHE 0.013 0.001 PHE A 838 TRP 0.014 0.001 TRP A 470 HIS 0.006 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (14618) covalent geometry : angle 0.58546 / 0.31 (19929) hydrogen bonds : bond 0.04562 / 3.12 ( 612) hydrogen bonds : angle 4.28120 / 2.94 ( 1715) Misc. bond : bond 0.00041 / 0.02 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 331 time to evaluate : 0.519 Fit side-chains REVERT: A 225 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8561 (mt0) REVERT: A 230 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.6967 (tpp) REVERT: A 291 LYS cc_start: 0.8246 (mmtm) cc_final: 0.7991 (mmtm) REVERT: A 373 ASP cc_start: 0.7969 (t0) cc_final: 0.7641 (t0) REVERT: A 413 ASN cc_start: 0.7805 (t0) cc_final: 0.7357 (t160) REVERT: A 540 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8192 (mtt) REVERT: A 742 ARG cc_start: 0.7930 (ttm-80) cc_final: 0.7667 (ttm-80) REVERT: B 96 ILE cc_start: 0.8064 (tp) cc_final: 0.7731 (tp) REVERT: B 205 ASP cc_start: 0.8059 (t0) cc_final: 0.7635 (t0) REVERT: C 9 ASN cc_start: 0.7980 (OUTLIER) cc_final: 0.7610 (m-40) REVERT: C 21 ARG cc_start: 0.7095 (ptm160) cc_final: 0.6354 (ptm160) REVERT: C 95 MET cc_start: 0.3451 (mmp) cc_final: 0.2431 (mmp) REVERT: C 160 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.7013 (tm) REVERT: C 184 MET cc_start: 0.8443 (mmp) cc_final: 0.8034 (mmp) REVERT: C 224 LYS cc_start: 0.7713 (ptpp) cc_final: 0.7424 (ptpp) REVERT: C 336 ASP cc_start: 0.8097 (m-30) cc_final: 0.7741 (m-30) REVERT: C 373 ASN cc_start: 0.7274 (m-40) cc_final: 0.6979 (m110) REVERT: C 395 LEU cc_start: 0.7386 (mp) cc_final: 0.6952 (mt) REVERT: C 397 ASN cc_start: 0.7857 (t0) cc_final: 0.7579 (t0) REVERT: C 422 LYS cc_start: 0.8039 (tptp) cc_final: 0.7624 (tptp) outliers start: 28 outliers final: 20 residues processed: 339 average time/residue: 0.5020 time to fit residues: 186.8839 Evaluate side-chains 352 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 327 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 646 SER Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 860 ASN Chi-restraints excluded: chain A residue 945 VAL Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 142 LYS Chi-restraints excluded: chain C residue 9 ASN Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 345 LYS Chi-restraints excluded: chain C residue 365 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 39 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 104 optimal weight: 0.0980 chunk 49 optimal weight: 0.0770 chunk 97 optimal weight: 1.9990 chunk 14 optimal weight: 0.0970 chunk 103 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 ASN A 801 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.168023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.129198 restraints weight = 22238.166| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.19 r_work: 0.3444 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3291 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3291 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14620 Z= 0.136 Angle : 0.587 17.032 19929 Z= 0.308 Chirality : 0.043 0.410 2208 Planarity : 0.004 0.053 2391 Dihedral : 14.606 105.788 2301 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.04 % Favored : 95.72 % Rotamer: Outliers : 2.05 % Allowed : 17.16 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.38 (0.21), residues: 1634 helix: 1.80 (0.22), residues: 587 sheet: 0.52 (0.28), residues: 347 loop : -1.27 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 577 TYR 0.020 0.001 TYR B 11 PHE 0.013 0.001 PHE A 838 TRP 0.014 0.001 TRP A 470 HIS 0.005 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (14618) covalent geometry : angle 0.58699 / 0.31 (19929) hydrogen bonds : bond 0.04460 / 3.04 ( 612) hydrogen bonds : angle 4.27569 / 2.94 ( 1715) Misc. bond : bond 0.00036 / 0.02 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6909.02 seconds wall clock time: 117 minutes 38.73 seconds (7058.73 seconds total)