Starting phenix.real_space_refine on Thu Sep 18 10:02:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k9r_62196/09_2025/9k9r_62196.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k9r_62196/09_2025/9k9r_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 { model { file = "/net/cci-nas-00/data/ceres_data/9k9r_62196/09_2025/9k9r_62196.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k9r_62196/09_2025/9k9r_62196.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k9r_62196/09_2025/9k9r_62196.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k9r_62196/09_2025/9k9r_62196.map" } 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-2.0-5805/lib/python3.9/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: 3.89, per 1000 atoms: 0.27 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: 1.32 Conformation dependent library (CDL) restraints added in 682.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 2.37 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: 3.16 Time building geometry restraints manager: 1.82 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=" N VAL C 50 " pdb=" CA VAL C 50 " ideal model delta sigma weight residual 1.458 1.493 -0.034 1.20e-02 6.94e+03 8.26e+00 bond pdb=" N LYS C 49 " pdb=" CA LYS C 49 " ideal model delta sigma weight residual 1.456 1.488 -0.033 1.22e-02 6.72e+03 7.21e+00 bond pdb=" C5 TTP A1102 " pdb=" C6 TTP A1102 " ideal model delta sigma weight residual 1.390 1.339 0.051 2.00e-02 2.50e+03 6.63e+00 bond pdb=" N ASP B 68 " pdb=" CA ASP B 68 " ideal model delta sigma weight residual 1.456 1.481 -0.025 1.04e-02 9.25e+03 5.96e+00 bond pdb=" N ARG B 185 " pdb=" CA ARG B 185 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.34e-02 5.57e+03 5.83e+00 ... (remaining 14613 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.21: 19841 3.21 - 6.42: 78 6.42 - 9.63: 7 9.63 - 12.84: 1 12.84 - 16.05: 2 Bond angle restraints: 19929 Sorted by residual: angle pdb=" PA TTP A1102 " pdb=" O3A TTP A1102 " pdb=" PB TTP A1102 " ideal model delta sigma weight residual 120.50 136.55 -16.05 3.00e+00 1.11e-01 2.86e+01 angle pdb=" PB TTP A1102 " pdb=" O3B TTP A1102 " pdb=" PG TTP A1102 " ideal model delta sigma weight residual 120.50 133.71 -13.21 3.00e+00 1.11e-01 1.94e+01 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=" CA ARG B 185 " pdb=" C ARG B 185 " pdb=" O ARG B 185 " ideal model delta sigma weight residual 122.01 117.71 4.30 1.05e+00 9.07e-01 1.67e+01 angle pdb=" N ASP B 186 " pdb=" CA ASP B 186 " pdb=" C ASP B 186 " ideal model delta sigma weight residual 113.23 108.37 4.86 1.22e+00 6.72e-01 1.59e+01 ... (remaining 19924 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.76: 8277 28.76 - 57.53: 428 57.53 - 86.29: 35 86.29 - 115.06: 2 115.06 - 143.82: 2 Dihedral angle restraints: 8744 sinusoidal: 3867 harmonic: 4877 Sorted by residual: dihedral pdb=" C2 TTP A1102 " pdb=" C1' TTP A1102 " pdb=" N1 TTP A1102 " pdb=" O4' TTP A1102 " ideal model delta sinusoidal sigma weight residual 301.68 157.86 143.82 1 2.00e+01 2.50e-03 4.34e+01 dihedral pdb=" O3B TTP A1102 " pdb=" O3A TTP A1102 " pdb=" PB TTP A1102 " pdb=" PA TTP A1102 " ideal model delta sinusoidal sigma weight residual 180.00 55.62 124.38 1 2.00e+01 2.50e-03 3.76e+01 dihedral pdb=" C5' TTP A1102 " pdb=" O5' TTP A1102 " pdb=" PA TTP A1102 " pdb=" O3A TTP A1102 " ideal model delta sinusoidal sigma weight residual 179.97 83.31 96.67 1 2.00e+01 2.50e-03 2.68e+01 ... (remaining 8741 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1710 0.049 - 0.098: 398 0.098 - 0.147: 95 0.147 - 0.195: 3 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=" C3' TTP A1102 " pdb=" C2' TTP A1102 " pdb=" C4' TTP A1102 " pdb=" O3' TTP A1102 " both_signs ideal model delta sigma weight residual False -2.51 -2.67 0.16 2.00e-01 2.50e+01 6.19e-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: 3.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.000 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:10.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 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 0.053 14620 Z= 0.215 Angle : 0.630 16.049 19929 Z= 0.335 Chirality : 0.044 0.244 2208 Planarity : 0.004 0.051 2391 Dihedral : 15.937 143.820 5598 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 aren 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 covalent geometry : bond 0.00478 (14618) covalent geometry : angle 0.63009 (19929) hydrogen bonds : bond 0.14255 ( 612) hydrogen bonds : angle 5.52221 ( 1715) Misc. bond : bond 0.03910 ( 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 : 0.644 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: 0.6698 time to fit residues: 247.0061 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 : 0.575 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 204 ASN A 211 GLN A 214 GLN A 413 ASN A 442 GLN B 111 ASN B 206 ASN C 9 ASN C 32 ASN C 304 ASN C 373 ASN C 391 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.165501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.124849 restraints weight = 29404.744| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.63 r_work: 0.3366 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3367 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3367 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 14620 Z= 0.246 Angle : 0.620 10.376 19929 Z= 0.330 Chirality : 0.045 0.190 2208 Planarity : 0.005 0.059 2391 Dihedral : 15.170 135.985 2277 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.22 % Favored : 95.53 % Rotamer: Outliers : 1.45 % Allowed : 9.37 % Favored : 89.17 % 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 aren not related in a simple way. whole: 0.18 (0.21), residues: 1634 helix: 1.47 (0.22), residues: 587 sheet: 0.67 (0.28), residues: 347 loop : -1.38 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 287 TYR 0.023 0.002 TYR A 528 PHE 0.017 0.002 PHE A 967 TRP 0.017 0.002 TRP A 470 HIS 0.007 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00593 (14618) covalent geometry : angle 0.62020 (19929) hydrogen bonds : bond 0.05949 ( 612) hydrogen bonds : angle 4.55267 ( 1715) Misc. bond : bond 0.00106 ( 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 352 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 330 time to evaluate : 0.615 Fit side-chains REVERT: A 209 THR cc_start: 0.8363 (m) cc_final: 0.8100 (m) REVERT: A 291 LYS cc_start: 0.8145 (mmtm) cc_final: 0.7910 (mmtm) REVERT: A 310 VAL cc_start: 0.8618 (p) cc_final: 0.8342 (t) REVERT: A 413 ASN cc_start: 0.7710 (t0) cc_final: 0.7403 (t160) REVERT: A 742 ARG cc_start: 0.7604 (ttm-80) cc_final: 0.7294 (ttm-80) REVERT: B 96 ILE cc_start: 0.8023 (tp) cc_final: 0.7738 (tp) REVERT: B 205 ASP cc_start: 0.7948 (t0) cc_final: 0.7493 (t0) REVERT: C 32 ASN cc_start: 0.7942 (m-40) cc_final: 0.7656 (m-40) REVERT: C 95 MET cc_start: 0.3540 (mmp) cc_final: 0.2565 (mmp) REVERT: C 184 MET cc_start: 0.8414 (mmp) cc_final: 0.8005 (mmp) REVERT: C 224 LYS cc_start: 0.7754 (ptpp) cc_final: 0.7446 (ptpp) REVERT: C 336 ASP cc_start: 0.7889 (m-30) cc_final: 0.7605 (m-30) REVERT: C 373 ASN cc_start: 0.7133 (m-40) cc_final: 0.6883 (m110) REVERT: C 419 ASP cc_start: 0.7426 (p0) cc_final: 0.7198 (p0) REVERT: C 422 LYS cc_start: 0.8096 (tptp) cc_final: 0.7735 (tptp) outliers start: 22 outliers final: 8 residues processed: 333 average time/residue: 0.6756 time to fit residues: 245.2802 Evaluate side-chains 322 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 314 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 688 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 18 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 107 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 130 optimal weight: 50.0000 chunk 124 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 146 optimal weight: 20.0000 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN A 214 GLN A 801 GLN A 816 ASN B 109 ASN B 111 ASN C 350 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.165665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.126037 restraints weight = 23380.582| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.10 r_work: 0.3415 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3259 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 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 = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3259 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14620 Z= 0.205 Angle : 0.577 9.187 19929 Z= 0.309 Chirality : 0.044 0.186 2208 Planarity : 0.004 0.056 2391 Dihedral : 15.056 137.110 2277 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.10 % Favored : 95.65 % Rotamer: Outliers : 1.85 % Allowed : 12.28 % Favored : 85.87 % 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 aren not related in a simple way. whole: 0.21 (0.21), residues: 1634 helix: 1.53 (0.22), residues: 588 sheet: 0.62 (0.28), residues: 362 loop : -1.41 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 16 TYR 0.021 0.001 TYR A 528 PHE 0.015 0.001 PHE A 838 TRP 0.017 0.001 TRP A 470 HIS 0.006 0.001 HIS A 839 Details of bonding type rmsd covalent geometry : bond 0.00491 (14618) covalent geometry : angle 0.57737 (19929) hydrogen bonds : bond 0.05409 ( 612) hydrogen bonds : angle 4.40324 ( 1715) Misc. bond : bond 0.00076 ( 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 358 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 330 time to evaluate : 0.582 Fit side-chains REVERT: A 209 THR cc_start: 0.8450 (m) cc_final: 0.8231 (m) REVERT: A 225 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8604 (mt0) REVERT: A 230 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.7056 (tpp) REVERT: A 291 LYS cc_start: 0.8248 (mmtm) cc_final: 0.8009 (mmtm) REVERT: A 341 LEU cc_start: 0.8967 (mt) cc_final: 0.8730 (mt) REVERT: A 413 ASN cc_start: 0.7766 (t0) cc_final: 0.7391 (t0) REVERT: A 540 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.8190 (mtt) REVERT: A 742 ARG cc_start: 0.7908 (ttm-80) cc_final: 0.7602 (ttm-80) REVERT: B 96 ILE cc_start: 0.8110 (tp) cc_final: 0.7792 (tp) REVERT: B 205 ASP cc_start: 0.8071 (t0) cc_final: 0.7640 (t0) REVERT: C 32 ASN cc_start: 0.8058 (m-40) cc_final: 0.7806 (m-40) REVERT: C 95 MET cc_start: 0.3887 (mmp) cc_final: 0.2813 (mmp) REVERT: C 184 MET cc_start: 0.8507 (mmp) cc_final: 0.8088 (mmp) REVERT: C 224 LYS cc_start: 0.7718 (ptpp) cc_final: 0.7413 (ptpp) REVERT: C 336 ASP cc_start: 0.8034 (m-30) cc_final: 0.7702 (m-30) REVERT: C 383 LYS cc_start: 0.7692 (mtmm) cc_final: 0.7367 (mmmt) REVERT: C 397 ASN cc_start: 0.8096 (t0) cc_final: 0.7809 (t0) REVERT: C 419 ASP cc_start: 0.7524 (p0) cc_final: 0.7240 (p0) REVERT: C 422 LYS cc_start: 0.8128 (tptp) cc_final: 0.7782 (tptp) outliers start: 28 outliers final: 15 residues processed: 335 average time/residue: 0.6568 time to fit residues: 240.8529 Evaluate side-chains 339 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 321 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 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 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 688 THR 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 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: 2.9990 chunk 70 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 3 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 129 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 161 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN A 556 ASN A 801 GLN A 899 ASN B 59 ASN B 109 ASN B 111 ASN C 373 ASN C 391 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.164620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.125112 restraints weight = 20885.137| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.06 r_work: 0.3388 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3235 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3235 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 14620 Z= 0.272 Angle : 0.625 10.982 19929 Z= 0.333 Chirality : 0.046 0.322 2208 Planarity : 0.005 0.059 2391 Dihedral : 15.153 136.401 2277 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.22 % Favored : 95.53 % Rotamer: Outliers : 2.38 % Allowed : 14.19 % Favored : 83.43 % 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 aren not related in a simple way. whole: 0.12 (0.21), residues: 1634 helix: 1.43 (0.22), residues: 593 sheet: 0.52 (0.27), residues: 374 loop : -1.46 (0.22), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 16 TYR 0.025 0.002 TYR A 528 PHE 0.017 0.002 PHE A 560 TRP 0.018 0.002 TRP A 470 HIS 0.007 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00662 (14618) covalent geometry : angle 0.62484 (19929) hydrogen bonds : bond 0.06126 ( 612) hydrogen bonds : angle 4.47872 ( 1715) Misc. bond : bond 0.00110 ( 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 363 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 327 time to evaluate : 0.583 Fit side-chains REVERT: A 225 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8567 (mt0) REVERT: A 230 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.7168 (tpp) REVERT: A 291 LYS cc_start: 0.8260 (mmtm) cc_final: 0.8026 (mmtm) REVERT: A 310 VAL cc_start: 0.8627 (p) cc_final: 0.8366 (t) REVERT: A 341 LEU cc_start: 0.8970 (mt) cc_final: 0.8767 (mt) REVERT: A 351 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8652 (tttm) REVERT: A 373 ASP cc_start: 0.8013 (t0) cc_final: 0.7644 (t0) REVERT: A 413 ASN cc_start: 0.7825 (t0) cc_final: 0.7512 (t0) REVERT: A 540 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.8289 (mtt) REVERT: A 742 ARG cc_start: 0.7904 (ttm-80) cc_final: 0.7613 (ttm-80) REVERT: B 96 ILE cc_start: 0.8179 (tp) cc_final: 0.7859 (tp) REVERT: B 205 ASP cc_start: 0.8089 (t0) cc_final: 0.7662 (t0) REVERT: C 32 ASN cc_start: 0.8138 (m-40) cc_final: 0.7884 (m-40) REVERT: C 95 MET cc_start: 0.3516 (mmp) cc_final: 0.2480 (mmp) REVERT: C 184 MET cc_start: 0.8489 (mmp) cc_final: 0.8069 (mmp) REVERT: C 224 LYS cc_start: 0.7749 (ptpp) cc_final: 0.7452 (ptpp) REVERT: C 336 ASP cc_start: 0.8106 (m-30) cc_final: 0.7758 (m-30) REVERT: C 397 ASN cc_start: 0.8143 (t0) cc_final: 0.7942 (t0) REVERT: C 419 ASP cc_start: 0.7466 (p0) cc_final: 0.7251 (p0) REVERT: C 422 LYS cc_start: 0.8147 (tptp) cc_final: 0.7794 (tptp) outliers start: 36 outliers final: 21 residues processed: 336 average time/residue: 0.6583 time to fit residues: 241.6970 Evaluate side-chains 343 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 318 time to evaluate : 0.556 ------------------------------------------------------------------------------- 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 230 MET Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 351 LYS 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 522 THR Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 587 LEU 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 130 THR Chi-restraints excluded: chain B residue 175 THR 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: 0.6980 chunk 117 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 133 optimal weight: 0.0870 chunk 101 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 121 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4108 r_free = 0.4108 target = 0.167505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.127795 restraints weight = 21761.358| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.30 r_work: 0.3411 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3246 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3246 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14620 Z= 0.132 Angle : 0.540 10.028 19929 Z= 0.289 Chirality : 0.041 0.224 2208 Planarity : 0.004 0.051 2391 Dihedral : 14.974 137.427 2277 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.67 % Favored : 96.08 % Rotamer: Outliers : 1.98 % Allowed : 15.71 % Favored : 82.31 % 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 aren not related in a simple way. whole: 0.28 (0.21), residues: 1634 helix: 1.69 (0.22), residues: 587 sheet: 0.46 (0.28), residues: 347 loop : -1.30 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 16 TYR 0.021 0.001 TYR B 11 PHE 0.012 0.001 PHE A 838 TRP 0.015 0.001 TRP A 470 HIS 0.005 0.001 HIS A 839 Details of bonding type rmsd covalent geometry : bond 0.00301 (14618) covalent geometry : angle 0.54003 (19929) hydrogen bonds : bond 0.04390 ( 612) hydrogen bonds : angle 4.26168 ( 1715) Misc. bond : bond 0.00029 ( 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: 30 poor density : 327 time to evaluate : 0.584 Fit side-chains REVERT: A 207 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8460 (mtp) REVERT: A 291 LYS cc_start: 0.8271 (mmtm) cc_final: 0.8041 (mmtm) REVERT: A 292 LYS cc_start: 0.8498 (mtmm) cc_final: 0.8181 (mtmm) REVERT: A 373 ASP cc_start: 0.8036 (t0) cc_final: 0.7672 (t0) REVERT: A 413 ASN cc_start: 0.7813 (t0) cc_final: 0.7460 (t0) REVERT: A 540 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.8253 (mtt) REVERT: A 742 ARG cc_start: 0.8015 (ttm-80) cc_final: 0.7760 (ttm-80) REVERT: B 96 ILE cc_start: 0.8123 (tp) cc_final: 0.7802 (tp) REVERT: B 205 ASP cc_start: 0.8069 (t0) cc_final: 0.7651 (t0) REVERT: C 21 ARG cc_start: 0.7133 (ptm160) cc_final: 0.6390 (ptm160) REVERT: C 32 ASN cc_start: 0.8083 (m-40) cc_final: 0.7838 (m-40) REVERT: C 95 MET cc_start: 0.3524 (mmp) cc_final: 0.2474 (mmp) REVERT: C 184 MET cc_start: 0.8483 (mmp) cc_final: 0.8054 (mmp) REVERT: C 224 LYS cc_start: 0.7717 (ptpp) cc_final: 0.7430 (ptpp) REVERT: C 336 ASP cc_start: 0.8103 (m-30) cc_final: 0.7740 (m-30) REVERT: C 397 ASN cc_start: 0.8090 (t0) cc_final: 0.7833 (t0) REVERT: C 422 LYS cc_start: 0.8101 (tptp) cc_final: 0.7674 (tptp) outliers start: 30 outliers final: 18 residues processed: 333 average time/residue: 0.6541 time to fit residues: 238.0055 Evaluate side-chains 342 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 322 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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 209 THR Chi-restraints excluded: chain A residue 215 GLU 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 688 THR 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 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: 20.0000 chunk 121 optimal weight: 4.9990 chunk 95 optimal weight: 0.5980 chunk 78 optimal weight: 0.0970 chunk 20 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN A 801 GLN A 816 ASN B 120 ASN C 373 ASN C 391 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.167647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.128372 restraints weight = 22832.650| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.19 r_work: 0.3441 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3287 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3287 r_free = 0.3287 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 = 0.3287 r_free = 0.3287 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3287 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14620 Z= 0.134 Angle : 0.543 9.691 19929 Z= 0.289 Chirality : 0.042 0.344 2208 Planarity : 0.004 0.053 2391 Dihedral : 15.034 137.382 2277 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.92 % Favored : 95.84 % Rotamer: Outliers : 2.11 % Allowed : 16.50 % Favored : 81.39 % 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 aren not related in a simple way. whole: 0.33 (0.21), residues: 1634 helix: 1.76 (0.22), residues: 587 sheet: 0.40 (0.27), residues: 357 loop : -1.27 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 16 TYR 0.023 0.001 TYR B 11 PHE 0.012 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 covalent geometry : bond 0.00309 (14618) covalent geometry : angle 0.54260 (19929) hydrogen bonds : bond 0.04371 ( 612) hydrogen bonds : angle 4.20764 ( 1715) Misc. bond : bond 0.00031 ( 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 362 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 330 time to evaluate : 0.597 Fit side-chains REVERT: A 225 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8570 (mt0) REVERT: A 291 LYS cc_start: 0.8231 (mmtm) cc_final: 0.7999 (mmtm) REVERT: A 351 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8636 (tttm) REVERT: A 373 ASP cc_start: 0.7981 (t0) cc_final: 0.7590 (t0) REVERT: A 413 ASN cc_start: 0.7793 (t0) cc_final: 0.7426 (t0) REVERT: A 540 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.8186 (mtt) REVERT: A 742 ARG cc_start: 0.7945 (ttm-80) cc_final: 0.7691 (ttm-80) REVERT: B 96 ILE cc_start: 0.8086 (tp) cc_final: 0.7776 (tp) REVERT: B 205 ASP cc_start: 0.8028 (t0) cc_final: 0.7601 (t0) REVERT: C 21 ARG cc_start: 0.7041 (ptm160) cc_final: 0.6306 (ptm160) REVERT: C 32 ASN cc_start: 0.8022 (m-40) cc_final: 0.7778 (m-40) REVERT: C 95 MET cc_start: 0.3628 (mmp) cc_final: 0.2569 (mmp) REVERT: C 184 MET cc_start: 0.8460 (mmp) cc_final: 0.8051 (mmp) REVERT: C 224 LYS cc_start: 0.7686 (ptpp) cc_final: 0.7402 (ptpp) REVERT: C 336 ASP cc_start: 0.8122 (m-30) cc_final: 0.7746 (m-30) REVERT: C 395 LEU cc_start: 0.7589 (mp) cc_final: 0.7264 (mt) REVERT: C 422 LYS cc_start: 0.8125 (tptp) cc_final: 0.7689 (tptp) outliers start: 32 outliers final: 17 residues processed: 338 average time/residue: 0.6713 time to fit residues: 248.0601 Evaluate side-chains 344 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 324 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 209 THR 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 351 LYS Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 688 THR 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 175 THR Chi-restraints excluded: chain C residue 22 PHE 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: 2.9990 chunk 14 optimal weight: 0.9990 chunk 131 optimal weight: 30.0000 chunk 60 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN A 801 GLN C 397 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.164996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.126004 restraints weight = 21263.190| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.08 r_work: 0.3406 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3257 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 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 = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3257 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 14620 Z= 0.267 Angle : 0.625 11.168 19929 Z= 0.332 Chirality : 0.047 0.383 2208 Planarity : 0.005 0.056 2391 Dihedral : 15.419 135.905 2277 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.35 % Favored : 95.41 % Rotamer: Outliers : 2.24 % Allowed : 16.77 % Favored : 80.99 % 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 aren not related in a simple way. whole: 0.20 (0.21), residues: 1634 helix: 1.56 (0.22), residues: 593 sheet: 0.48 (0.27), residues: 363 loop : -1.39 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 16 TYR 0.024 0.002 TYR B 11 PHE 0.016 0.002 PHE A 560 TRP 0.016 0.002 TRP A 470 HIS 0.007 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00649 (14618) covalent geometry : angle 0.62549 (19929) hydrogen bonds : bond 0.05972 ( 612) hydrogen bonds : angle 4.39726 ( 1715) Misc. bond : bond 0.00102 ( 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 365 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 331 time to evaluate : 0.579 Fit side-chains REVERT: A 225 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8555 (mt0) REVERT: A 291 LYS cc_start: 0.8246 (mmtm) cc_final: 0.8007 (mmtm) REVERT: A 310 VAL cc_start: 0.8549 (p) cc_final: 0.8337 (t) REVERT: A 351 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8633 (tttm) REVERT: A 373 ASP cc_start: 0.7992 (t0) cc_final: 0.7633 (t0) REVERT: A 413 ASN cc_start: 0.7817 (t0) cc_final: 0.7427 (t0) REVERT: A 540 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.8238 (mtt) REVERT: A 742 ARG cc_start: 0.7913 (ttm-80) cc_final: 0.7667 (ttm-80) REVERT: A 979 ILE cc_start: 0.8452 (mm) cc_final: 0.8202 (mp) REVERT: B 1 MET cc_start: 0.8487 (mmt) cc_final: 0.8274 (tpt) REVERT: B 96 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7856 (tp) REVERT: B 205 ASP cc_start: 0.8089 (t0) cc_final: 0.7674 (t0) REVERT: C 21 ARG cc_start: 0.7157 (ptm160) cc_final: 0.6364 (ptm160) REVERT: C 32 ASN cc_start: 0.8112 (m-40) cc_final: 0.7859 (m-40) REVERT: C 160 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.7061 (tm) REVERT: C 184 MET cc_start: 0.8436 (mmp) cc_final: 0.8004 (mmp) REVERT: C 224 LYS cc_start: 0.7731 (ptpp) cc_final: 0.7451 (ptpp) REVERT: C 336 ASP cc_start: 0.8158 (m-30) cc_final: 0.7779 (m-30) REVERT: C 373 ASN cc_start: 0.7329 (m-40) cc_final: 0.7053 (m110) REVERT: C 397 ASN cc_start: 0.8080 (t0) cc_final: 0.7811 (t0) REVERT: C 422 LYS cc_start: 0.8136 (tptp) cc_final: 0.7768 (tptp) outliers start: 34 outliers final: 20 residues processed: 338 average time/residue: 0.6493 time to fit residues: 239.8169 Evaluate side-chains 348 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 323 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 209 THR 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 351 LYS Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 732 ILE 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 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 96 ILE Chi-restraints excluded: chain B residue 130 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 90 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 63 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN A 214 GLN A 801 GLN B 109 ASN ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.167009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.128317 restraints weight = 21468.632| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.00 r_work: 0.3447 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.19 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 | |-----------------------------------------------------------------------------| r_final: 0.3291 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14620 Z= 0.147 Angle : 0.568 9.599 19929 Z= 0.300 Chirality : 0.042 0.335 2208 Planarity : 0.004 0.052 2391 Dihedral : 15.273 137.112 2277 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.92 % Favored : 95.84 % Rotamer: Outliers : 2.05 % Allowed : 17.36 % Favored : 80.59 % 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 aren not related in a simple way. whole: 0.26 (0.21), residues: 1634 helix: 1.70 (0.22), residues: 587 sheet: 0.39 (0.28), residues: 354 loop : -1.32 (0.22), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 16 TYR 0.025 0.001 TYR B 11 PHE 0.012 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 covalent geometry : bond 0.00345 (14618) covalent geometry : angle 0.56824 (19929) hydrogen bonds : bond 0.04570 ( 612) hydrogen bonds : angle 4.25536 ( 1715) Misc. bond : bond 0.00038 ( 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 : 0.680 Fit side-chains REVERT: A 207 MET cc_start: 0.8932 (mtp) cc_final: 0.8705 (mtp) REVERT: A 225 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8568 (mt0) REVERT: A 291 LYS cc_start: 0.8242 (mmtm) cc_final: 0.8007 (mmtm) REVERT: A 351 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8621 (tttm) REVERT: A 373 ASP cc_start: 0.7979 (t0) cc_final: 0.7565 (t0) REVERT: A 413 ASN cc_start: 0.7788 (t0) cc_final: 0.7403 (t0) REVERT: A 540 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.8163 (mtt) REVERT: A 742 ARG cc_start: 0.7916 (ttm-80) cc_final: 0.7660 (ttm-80) REVERT: B 96 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7807 (tp) REVERT: B 205 ASP cc_start: 0.8036 (t0) cc_final: 0.7628 (t0) REVERT: C 21 ARG cc_start: 0.7133 (ptm160) cc_final: 0.6369 (ptm160) REVERT: C 184 MET cc_start: 0.8457 (mmp) cc_final: 0.8022 (mmp) REVERT: C 224 LYS cc_start: 0.7681 (ptpp) cc_final: 0.7413 (ptpp) REVERT: C 336 ASP cc_start: 0.8200 (m-30) cc_final: 0.7791 (m-30) REVERT: C 374 ASN cc_start: 0.7202 (p0) cc_final: 0.6741 (p0) REVERT: C 422 LYS cc_start: 0.8116 (tptp) cc_final: 0.7743 (tptp) outliers start: 31 outliers final: 21 residues processed: 339 average time/residue: 0.6297 time to fit residues: 233.5459 Evaluate side-chains 351 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 326 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 143 ASP Chi-restraints excluded: chain A residue 209 THR 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 351 LYS Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 688 THR 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 A residue 982 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain C residue 22 PHE 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: 2.9990 chunk 146 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 44 optimal weight: 0.2980 chunk 137 optimal weight: 0.9990 chunk 142 optimal weight: 20.0000 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 162 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN A 801 GLN A 816 ASN C 397 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.166132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.127149 restraints weight = 24414.347| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.32 r_work: 0.3411 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- 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 = 0.49 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 | |-----------------------------------------------------------------------------| r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 14620 Z= 0.184 Angle : 0.601 10.511 19929 Z= 0.317 Chirality : 0.044 0.410 2208 Planarity : 0.004 0.052 2391 Dihedral : 15.365 136.497 2277 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.28 % Favored : 95.47 % Rotamer: Outliers : 1.98 % Allowed : 18.42 % Favored : 79.60 % 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 aren not related in a simple way. whole: 0.24 (0.21), residues: 1634 helix: 1.67 (0.22), residues: 587 sheet: 0.50 (0.28), residues: 355 loop : -1.40 (0.21), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 16 TYR 0.027 0.001 TYR B 11 PHE 0.013 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 covalent geometry : bond 0.00440 (14618) covalent geometry : angle 0.60106 (19929) hydrogen bonds : bond 0.05110 ( 612) hydrogen bonds : angle 4.31424 ( 1715) Misc. bond : bond 0.00060 ( 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: 30 poor density : 328 time to evaluate : 0.432 Fit side-chains REVERT: A 225 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.8619 (mt0) REVERT: A 291 LYS cc_start: 0.8259 (mmtm) cc_final: 0.8011 (mmtm) REVERT: A 351 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8644 (tttm) REVERT: A 373 ASP cc_start: 0.8032 (t0) cc_final: 0.7623 (t0) REVERT: A 413 ASN cc_start: 0.7804 (t0) cc_final: 0.7405 (t0) REVERT: A 540 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8265 (mtt) REVERT: A 742 ARG cc_start: 0.7986 (ttm-80) cc_final: 0.7735 (ttm-80) REVERT: A 792 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7997 (mm-30) REVERT: B 96 ILE cc_start: 0.8140 (OUTLIER) cc_final: 0.7826 (tp) REVERT: B 205 ASP cc_start: 0.8121 (t0) cc_final: 0.7705 (t0) REVERT: C 9 ASN cc_start: 0.8049 (t0) cc_final: 0.7479 (m-40) REVERT: C 21 ARG cc_start: 0.7192 (ptm160) cc_final: 0.6407 (ptm160) REVERT: C 184 MET cc_start: 0.8425 (mmp) cc_final: 0.7984 (mmp) REVERT: C 224 LYS cc_start: 0.7733 (ptpp) cc_final: 0.7461 (ptpp) REVERT: C 336 ASP cc_start: 0.8222 (m-30) cc_final: 0.7811 (m-30) REVERT: C 374 ASN cc_start: 0.7164 (p0) cc_final: 0.6823 (p0) REVERT: C 395 LEU cc_start: 0.7533 (mp) cc_final: 0.6966 (mt) REVERT: C 397 ASN cc_start: 0.7954 (t0) cc_final: 0.7724 (t0) REVERT: C 422 LYS cc_start: 0.8167 (tptp) cc_final: 0.7776 (tptp) outliers start: 30 outliers final: 21 residues processed: 335 average time/residue: 0.6368 time to fit residues: 232.9316 Evaluate side-chains 350 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 325 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 209 THR 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 351 LYS Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 589 GLN 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 A residue 982 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain C residue 22 PHE 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: 0.2980 chunk 39 optimal weight: 1.9990 chunk 98 optimal weight: 0.3980 chunk 158 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 155 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 204 ASN A 801 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.167908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.129020 restraints weight = 22877.535| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.17 r_work: 0.3447 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3293 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 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 = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3293 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14620 Z= 0.131 Angle : 0.574 9.886 19929 Z= 0.301 Chirality : 0.042 0.410 2208 Planarity : 0.004 0.054 2391 Dihedral : 15.227 136.925 2277 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.92 % Favored : 95.84 % Rotamer: Outliers : 1.65 % Allowed : 18.35 % Favored : 80.00 % 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 aren not related in a simple way. whole: 0.30 (0.21), residues: 1634 helix: 1.83 (0.22), residues: 583 sheet: 0.33 (0.27), residues: 356 loop : -1.32 (0.21), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 577 TYR 0.027 0.001 TYR B 11 PHE 0.014 0.001 PHE A 992 TRP 0.015 0.001 TRP A 470 HIS 0.005 0.001 HIS A 839 Details of bonding type rmsd covalent geometry : bond 0.00300 (14618) covalent geometry : angle 0.57449 (19929) hydrogen bonds : bond 0.04188 ( 612) hydrogen bonds : angle 4.22507 ( 1715) Misc. bond : bond 0.00040 ( 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 354 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 329 time to evaluate : 0.602 Fit side-chains REVERT: A 291 LYS cc_start: 0.8216 (mmtm) cc_final: 0.7974 (mmtm) REVERT: A 351 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8630 (tttm) REVERT: A 373 ASP cc_start: 0.8001 (t0) cc_final: 0.7570 (t0) REVERT: A 413 ASN cc_start: 0.7746 (t0) cc_final: 0.7366 (t0) REVERT: A 540 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.8188 (mtt) REVERT: A 742 ARG cc_start: 0.7951 (ttm-80) cc_final: 0.7696 (ttm-80) REVERT: B 96 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7793 (tp) REVERT: B 205 ASP cc_start: 0.8049 (t0) cc_final: 0.7648 (t0) REVERT: C 9 ASN cc_start: 0.8004 (OUTLIER) cc_final: 0.7415 (m-40) REVERT: C 21 ARG cc_start: 0.7122 (ptm160) cc_final: 0.6415 (ptm160) REVERT: C 95 MET cc_start: 0.3340 (mmp) cc_final: 0.3118 (mmp) REVERT: C 184 MET cc_start: 0.8443 (mmp) cc_final: 0.8033 (mmp) REVERT: C 224 LYS cc_start: 0.7667 (ptpp) cc_final: 0.7402 (ptpp) REVERT: C 336 ASP cc_start: 0.8226 (m-30) cc_final: 0.7800 (m-30) REVERT: C 395 LEU cc_start: 0.7435 (mp) cc_final: 0.6909 (mt) REVERT: C 422 LYS cc_start: 0.8158 (tptp) cc_final: 0.7754 (tptp) outliers start: 25 outliers final: 18 residues processed: 336 average time/residue: 0.6647 time to fit residues: 244.3863 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 : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 688 THR 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 A residue 982 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain C residue 9 ASN Chi-restraints excluded: chain C residue 22 PHE 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: 0.8980 chunk 66 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN A 801 GLN C 397 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.167442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.128522 restraints weight = 22673.905| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.14 r_work: 0.3455 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- 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 = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3291 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14620 Z= 0.143 Angle : 0.588 10.374 19929 Z= 0.307 Chirality : 0.043 0.409 2208 Planarity : 0.004 0.054 2391 Dihedral : 15.268 135.987 2277 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.04 % Favored : 95.72 % Rotamer: Outliers : 1.72 % Allowed : 18.61 % Favored : 79.67 % 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 aren not related in a simple way. whole: 0.28 (0.21), residues: 1634 helix: 1.82 (0.22), residues: 583 sheet: 0.31 (0.27), residues: 356 loop : -1.33 (0.21), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 577 TYR 0.026 0.001 TYR B 11 PHE 0.014 0.001 PHE A 992 TRP 0.015 0.001 TRP A 470 HIS 0.006 0.001 HIS A 839 Details of bonding type rmsd covalent geometry : bond 0.00333 (14618) covalent geometry : angle 0.58838 (19929) hydrogen bonds : bond 0.04471 ( 612) hydrogen bonds : angle 4.24194 ( 1715) Misc. bond : bond 0.00051 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8918.97 seconds wall clock time: 151 minutes 55.78 seconds (9115.78 seconds total)