Starting phenix.real_space_refine on Wed Mar 4 15:21:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rhi_24462/03_2026/7rhi_24462.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rhi_24462/03_2026/7rhi_24462.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rhi_24462/03_2026/7rhi_24462.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rhi_24462/03_2026/7rhi_24462.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rhi_24462/03_2026/7rhi_24462.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rhi_24462/03_2026/7rhi_24462.map" } resolution = 3.31 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 82 5.16 5 C 9602 2.51 5 N 2396 2.21 5 O 2633 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14717 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3688 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3561 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 14, 'TRANS': 419} Chain breaks: 1 Chain: "C" Number of atoms: 3688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3688 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 3688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3688 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.52, per 1000 atoms: 0.24 Number of scatterers: 14717 At special positions: 0 Unit cell: (97.223, 98.04, 120.099, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 82 16.00 P 4 15.00 O 2633 8.00 N 2396 7.00 C 9602 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=0, symmetry=0 Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 461.7 milliseconds 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3372 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 11 sheets defined 66.6% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 162 through 189 removed outlier: 3.575A pdb=" N TYR A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) Proline residue: A 175 - end of helix removed outlier: 5.240A pdb=" N ILE A 184 " --> pdb=" O TRP A 180 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.516A pdb=" N GLN A 193 " --> pdb=" O PHE A 189 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 221 Processing helix chain 'A' and resid 232 through 243 removed outlier: 3.548A pdb=" N ASN A 243 " --> pdb=" O LYS A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 253 removed outlier: 3.924A pdb=" N LYS A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 258 removed outlier: 3.696A pdb=" N LEU A 258 " --> pdb=" O PRO A 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 255 through 258' Processing helix chain 'A' and resid 259 through 264 Processing helix chain 'A' and resid 267 through 276 removed outlier: 4.164A pdb=" N ILE A 270 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU A 272 " --> pdb=" O GLU A 269 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASN A 273 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 292 removed outlier: 3.746A pdb=" N MET A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 326 Processing helix chain 'A' and resid 344 through 361 Processing helix chain 'A' and resid 371 through 388 Processing helix chain 'A' and resid 388 through 404 Processing helix chain 'A' and resid 404 through 424 Processing helix chain 'A' and resid 427 through 444 Processing helix chain 'A' and resid 449 through 454 removed outlier: 3.648A pdb=" N VAL A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 470 removed outlier: 3.675A pdb=" N ASN A 468 " --> pdb=" O GLU A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 477 removed outlier: 3.869A pdb=" N LYS A 476 " --> pdb=" O ASP A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 578 through 586 removed outlier: 3.639A pdb=" N ALA A 584 " --> pdb=" O ASP A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 603 removed outlier: 3.560A pdb=" N LYS A 598 " --> pdb=" O MET A 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 680 removed outlier: 3.654A pdb=" N VAL B 657 " --> pdb=" O ASN B 653 " (cutoff:3.500A) Proline residue: B 675 - end of helix Processing helix chain 'B' and resid 687 through 708 Processing helix chain 'B' and resid 709 through 713 removed outlier: 3.582A pdb=" N LEU B 713 " --> pdb=" O GLN B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 735 Processing helix chain 'B' and resid 735 through 745 removed outlier: 3.831A pdb=" N LYS B 739 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 768 Proline residue: B 764 - end of helix removed outlier: 3.751A pdb=" N LYS B 768 " --> pdb=" O ARG B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 782 Processing helix chain 'B' and resid 786 through 817 removed outlier: 3.511A pdb=" N ARG B 790 " --> pdb=" O ALA B 786 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 844 Processing helix chain 'B' and resid 854 through 887 removed outlier: 3.614A pdb=" N SER B 873 " --> pdb=" O VAL B 869 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR B 887 " --> pdb=" O VAL B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 907 Processing helix chain 'B' and resid 910 through 928 removed outlier: 3.702A pdb=" N ARG B 916 " --> pdb=" O SER B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 933 through 938 Processing helix chain 'B' and resid 941 through 953 removed outlier: 3.631A pdb=" N ASP B 951 " --> pdb=" O ASP B 947 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN B 953 " --> pdb=" O ALA B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 959 Processing helix chain 'B' and resid 967 through 975 removed outlier: 3.874A pdb=" N ILE B 971 " --> pdb=" O ASP B 967 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE B 972 " --> pdb=" O ARG B 968 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 975 " --> pdb=" O ILE B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 1030 through 1034 removed outlier: 3.513A pdb=" N LEU B1033 " --> pdb=" O GLU B1030 " (cutoff:3.500A) Processing helix chain 'B' and resid 1061 through 1067 removed outlier: 3.930A pdb=" N ILE B1065 " --> pdb=" O ASP B1061 " (cutoff:3.500A) Processing helix chain 'B' and resid 1069 through 1084 Processing helix chain 'C' and resid 162 through 189 removed outlier: 3.519A pdb=" N TYR C 166 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Proline residue: C 175 - end of helix removed outlier: 3.671A pdb=" N VAL C 183 " --> pdb=" O ASN C 179 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ILE C 184 " --> pdb=" O TRP C 180 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA C 185 " --> pdb=" O THR C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 196 removed outlier: 3.516A pdb=" N GLN C 193 " --> pdb=" O PHE C 189 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR C 196 " --> pdb=" O LEU C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 219 removed outlier: 3.576A pdb=" N ILE C 202 " --> pdb=" O GLU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 242 Processing helix chain 'C' and resid 243 through 253 removed outlier: 3.855A pdb=" N LYS C 247 " --> pdb=" O ASN C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 258 removed outlier: 4.618A pdb=" N ASP C 257 " --> pdb=" O ILE C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 264 Processing helix chain 'C' and resid 269 through 276 removed outlier: 3.522A pdb=" N LEU C 272 " --> pdb=" O GLU C 269 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASN C 273 " --> pdb=" O ILE C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 292 removed outlier: 4.205A pdb=" N MET C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR C 290 " --> pdb=" O GLN C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 326 Processing helix chain 'C' and resid 344 through 361 Processing helix chain 'C' and resid 371 through 404 Processing helix chain 'C' and resid 407 through 424 Processing helix chain 'C' and resid 427 through 444 Processing helix chain 'C' and resid 449 through 454 Processing helix chain 'C' and resid 458 through 470 Processing helix chain 'C' and resid 470 through 477 removed outlier: 3.867A pdb=" N LYS C 475 " --> pdb=" O LEU C 471 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LYS C 476 " --> pdb=" O ASP C 472 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL C 477 " --> pdb=" O THR C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 492 Processing helix chain 'C' and resid 578 through 586 removed outlier: 3.508A pdb=" N GLU C 583 " --> pdb=" O ASP C 579 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA C 584 " --> pdb=" O ASP C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 605 removed outlier: 3.964A pdb=" N LYS C 592 " --> pdb=" O TYR C 588 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR C 593 " --> pdb=" O PRO C 589 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET C 594 " --> pdb=" O ASP C 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 189 removed outlier: 3.613A pdb=" N TYR D 166 " --> pdb=" O GLY D 162 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N CYS D 171 " --> pdb=" O ASN D 167 " (cutoff:3.500A) Proline residue: D 175 - end of helix removed outlier: 3.623A pdb=" N VAL D 183 " --> pdb=" O ASN D 179 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ILE D 184 " --> pdb=" O TRP D 180 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA D 185 " --> pdb=" O THR D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 196 removed outlier: 3.655A pdb=" N TYR D 196 " --> pdb=" O LEU D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 221 Processing helix chain 'D' and resid 232 through 243 removed outlier: 3.651A pdb=" N ASN D 243 " --> pdb=" O LYS D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 253 removed outlier: 3.879A pdb=" N LYS D 247 " --> pdb=" O ASN D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 258 removed outlier: 3.799A pdb=" N LEU D 258 " --> pdb=" O PRO D 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 255 through 258' Processing helix chain 'D' and resid 259 through 264 Processing helix chain 'D' and resid 267 through 276 removed outlier: 4.041A pdb=" N ILE D 270 " --> pdb=" O TYR D 267 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG D 271 " --> pdb=" O PRO D 268 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASN D 273 " --> pdb=" O ILE D 270 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG D 274 " --> pdb=" O ARG D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 290 removed outlier: 3.760A pdb=" N MET D 281 " --> pdb=" O ARG D 277 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR D 290 " --> pdb=" O GLN D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 326 Processing helix chain 'D' and resid 344 through 361 Processing helix chain 'D' and resid 371 through 402 removed outlier: 4.055A pdb=" N PHE D 389 " --> pdb=" O GLY D 385 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA D 390 " --> pdb=" O VAL D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 424 removed outlier: 3.784A pdb=" N PHE D 423 " --> pdb=" O GLN D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 444 Processing helix chain 'D' and resid 449 through 455 removed outlier: 3.669A pdb=" N VAL D 453 " --> pdb=" O ASP D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 470 Processing helix chain 'D' and resid 470 through 475 Processing helix chain 'D' and resid 486 through 492 removed outlier: 4.466A pdb=" N GLU D 490 " --> pdb=" O GLY D 486 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU D 491 " --> pdb=" O LEU D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 586 removed outlier: 3.534A pdb=" N LEU D 581 " --> pdb=" O SER D 577 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR D 586 " --> pdb=" O MET D 582 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 604 removed outlier: 4.002A pdb=" N LYS D 592 " --> pdb=" O TYR D 588 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR D 593 " --> pdb=" O PRO D 589 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 224 through 225 Processing sheet with id=AA2, first strand: chain 'A' and resid 496 through 500 Processing sheet with id=AA3, first strand: chain 'A' and resid 504 through 505 removed outlier: 3.535A pdb=" N ASP A 504 " --> pdb=" O SER A 567 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASN A 564 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE A 568 " --> pdb=" O LYS A 523 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LYS A 523 " --> pdb=" O ILE A 568 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL A 536 " --> pdb=" O VAL A 526 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 715 through 717 removed outlier: 3.800A pdb=" N PHE B 715 " --> pdb=" O ILE B 722 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 979 through 983 removed outlier: 3.718A pdb=" N ARG B 979 " --> pdb=" O ILE B1056 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASN B1053 " --> pdb=" O GLN B1003 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 987 through 990 removed outlier: 6.445A pdb=" N TYR B 988 " --> pdb=" O ALA B1048 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA B1048 " --> pdb=" O TYR B 988 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL B1020 " --> pdb=" O VAL B1009 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 224 through 225 Processing sheet with id=AA8, first strand: chain 'C' and resid 496 through 500 Processing sheet with id=AA9, first strand: chain 'D' and resid 224 through 225 Processing sheet with id=AB1, first strand: chain 'D' and resid 495 through 500 removed outlier: 6.058A pdb=" N PHE D 574 " --> pdb=" O ILE D 519 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ILE D 519 " --> pdb=" O PHE D 574 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 505 through 507 removed outlier: 6.428A pdb=" N TYR D 505 " --> pdb=" O SER D 567 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N SER D 567 " --> pdb=" O TYR D 505 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS D 507 " --> pdb=" O ILE D 565 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU D 524 " --> pdb=" O VAL D 537 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL D 537 " --> pdb=" O LEU D 524 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL D 526 " --> pdb=" O PHE D 535 " (cutoff:3.500A) 855 hydrogen bonds defined for protein. 2472 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.71 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4540 1.34 - 1.46: 3479 1.46 - 1.58: 6911 1.58 - 1.70: 8 1.70 - 1.82: 138 Bond restraints: 15076 Sorted by residual: bond pdb=" O1A PCG C 701 " pdb=" PA PCG C 701 " ideal model delta sigma weight residual 1.582 1.479 0.103 2.00e-02 2.50e+03 2.67e+01 bond pdb=" O1A PCG A 701 " pdb=" PA PCG A 701 " ideal model delta sigma weight residual 1.582 1.479 0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" O1A PCG D 701 " pdb=" PA PCG D 701 " ideal model delta sigma weight residual 1.582 1.479 0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" O1A PCG B1301 " pdb=" PA PCG B1301 " ideal model delta sigma weight residual 1.582 1.481 0.101 2.00e-02 2.50e+03 2.58e+01 bond pdb=" C1' PCG C 701 " pdb=" O4' PCG C 701 " ideal model delta sigma weight residual 1.409 1.483 -0.074 2.00e-02 2.50e+03 1.37e+01 ... (remaining 15071 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 19883 1.85 - 3.71: 417 3.71 - 5.56: 78 5.56 - 7.41: 42 7.41 - 9.26: 26 Bond angle restraints: 20446 Sorted by residual: angle pdb=" N TYR A 260 " pdb=" CA TYR A 260 " pdb=" C TYR A 260 " ideal model delta sigma weight residual 112.23 107.79 4.44 1.26e+00 6.30e-01 1.24e+01 angle pdb=" CA VAL C 526 " pdb=" CB VAL C 526 " pdb=" CG1 VAL C 526 " ideal model delta sigma weight residual 110.40 115.88 -5.48 1.70e+00 3.46e-01 1.04e+01 angle pdb=" C TYR C 267 " pdb=" N PRO C 268 " pdb=" CA PRO C 268 " ideal model delta sigma weight residual 120.83 117.66 3.17 1.02e+00 9.61e-01 9.68e+00 angle pdb=" O1A PCG B1301 " pdb=" PA PCG B1301 " pdb=" O3' PCG B1301 " ideal model delta sigma weight residual 100.83 110.09 -9.26 3.00e+00 1.11e-01 9.53e+00 angle pdb=" CA MET A 215 " pdb=" CB MET A 215 " pdb=" CG MET A 215 " ideal model delta sigma weight residual 114.10 120.21 -6.11 2.00e+00 2.50e-01 9.33e+00 ... (remaining 20441 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.24: 8677 29.24 - 58.49: 299 58.49 - 87.73: 16 87.73 - 116.98: 3 116.98 - 146.22: 13 Dihedral angle restraints: 9008 sinusoidal: 3744 harmonic: 5264 Sorted by residual: dihedral pdb=" C3' PCG C 701 " pdb=" O3' PCG C 701 " pdb=" PA PCG C 701 " pdb=" O1A PCG C 701 " ideal model delta sinusoidal sigma weight residual 151.41 -62.37 -146.22 1 3.00e+01 1.11e-03 1.95e+01 dihedral pdb=" C3' PCG A 701 " pdb=" O3' PCG A 701 " pdb=" PA PCG A 701 " pdb=" O1A PCG A 701 " ideal model delta sinusoidal sigma weight residual 151.41 -65.28 -143.31 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" C3' PCG B1301 " pdb=" O3' PCG B1301 " pdb=" PA PCG B1301 " pdb=" O1A PCG B1301 " ideal model delta sinusoidal sigma weight residual 151.41 -66.24 -142.35 1 3.00e+01 1.11e-03 1.91e+01 ... (remaining 9005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 2262 0.133 - 0.267: 16 0.267 - 0.400: 0 0.400 - 0.534: 0 0.534 - 0.667: 4 Chirality restraints: 2282 Sorted by residual: chirality pdb=" PA PCG B1301 " pdb=" O2A PCG B1301 " pdb=" O3' PCG B1301 " pdb=" O5' PCG B1301 " both_signs ideal model delta sigma weight residual True 2.70 -3.37 -0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" PA PCG A 701 " pdb=" O2A PCG A 701 " pdb=" O3' PCG A 701 " pdb=" O5' PCG A 701 " both_signs ideal model delta sigma weight residual True 2.70 -3.36 -0.66 2.00e-01 2.50e+01 1.10e+01 chirality pdb=" PA PCG C 701 " pdb=" O2A PCG C 701 " pdb=" O3' PCG C 701 " pdb=" O5' PCG C 701 " both_signs ideal model delta sigma weight residual True 2.70 -3.36 -0.66 2.00e-01 2.50e+01 1.08e+01 ... (remaining 2279 not shown) Planarity restraints: 2518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 763 " 0.046 5.00e-02 4.00e+02 6.93e-02 7.68e+00 pdb=" N PRO B 764 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO B 764 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 764 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 254 " -0.034 5.00e-02 4.00e+02 5.27e-02 4.44e+00 pdb=" N PRO D 255 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO D 255 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 255 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 259 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.57e+00 pdb=" C LEU A 259 " 0.033 2.00e-02 2.50e+03 pdb=" O LEU A 259 " -0.012 2.00e-02 2.50e+03 pdb=" N TYR A 260 " -0.011 2.00e-02 2.50e+03 ... (remaining 2515 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2492 2.76 - 3.30: 14437 3.30 - 3.83: 25908 3.83 - 4.37: 29534 4.37 - 4.90: 50856 Nonbonded interactions: 123227 Sorted by model distance: nonbonded pdb=" O THR D 357 " pdb=" OG1 THR D 361 " model vdw 2.230 3.040 nonbonded pdb=" O LEU D 169 " pdb=" OG1 THR D 173 " model vdw 2.235 3.040 nonbonded pdb=" O LEU A 169 " pdb=" OG1 THR A 173 " model vdw 2.247 3.040 nonbonded pdb=" OH TYR D 334 " pdb=" O PHE D 342 " model vdw 2.287 3.040 nonbonded pdb=" OG1 THR B 684 " pdb=" OD1 ASN B 687 " model vdw 2.295 3.040 ... (remaining 123222 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.080 Find NCS groups from input model: 0.210 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: 0.010 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 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 : 0.004 0.103 15076 Z= 0.205 Angle : 0.755 9.263 20446 Z= 0.354 Chirality : 0.052 0.667 2282 Planarity : 0.004 0.069 2518 Dihedral : 15.444 146.224 5636 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.18), residues: 1774 helix: 0.18 (0.14), residues: 1062 sheet: -0.05 (0.55), residues: 91 loop : -0.87 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 478 TYR 0.015 0.001 TYR B 837 PHE 0.027 0.002 PHE D 382 TRP 0.016 0.002 TRP A 168 HIS 0.005 0.001 HIS B 803 Details of bonding type rmsd covalent geometry : bond 0.00435 (15076) covalent geometry : angle 0.75531 (20446) hydrogen bonds : bond 0.15723 ( 855) hydrogen bonds : angle 5.89975 ( 2472) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.515 Fit side-chains REVERT: C 267 TYR cc_start: 0.8324 (m-80) cc_final: 0.8074 (m-80) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.0953 time to fit residues: 22.8631 Evaluate side-chains 116 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.3980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.1980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.129013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.101164 restraints weight = 23921.392| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.39 r_work: 0.3226 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15076 Z= 0.108 Angle : 0.480 6.583 20446 Z= 0.250 Chirality : 0.038 0.153 2282 Planarity : 0.004 0.048 2518 Dihedral : 12.683 153.726 2107 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.31 % Allowed : 5.99 % Favored : 93.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.19), residues: 1774 helix: 1.06 (0.15), residues: 1072 sheet: -0.21 (0.55), residues: 95 loop : -0.74 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 287 TYR 0.011 0.001 TYR B 837 PHE 0.022 0.001 PHE D 574 TRP 0.011 0.001 TRP A 168 HIS 0.004 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00228 (15076) covalent geometry : angle 0.47986 (20446) hydrogen bonds : bond 0.03779 ( 855) hydrogen bonds : angle 4.20987 ( 2472) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 130 time to evaluate : 0.472 Fit side-chains REVERT: A 305 MET cc_start: 0.8335 (ttp) cc_final: 0.8095 (ttm) REVERT: A 516 MET cc_start: 0.8490 (ptm) cc_final: 0.8271 (ptm) REVERT: C 267 TYR cc_start: 0.8586 (m-80) cc_final: 0.8273 (m-80) REVERT: C 465 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8453 (pt) outliers start: 5 outliers final: 3 residues processed: 133 average time/residue: 0.1069 time to fit residues: 22.3068 Evaluate side-chains 120 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 116 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain B residue 876 ILE Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 17 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 143 optimal weight: 0.0470 chunk 47 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 121 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 overall best weight: 1.9284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1008 GLN B1073 GLN C 314 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.125455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.097067 restraints weight = 24290.146| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.47 r_work: 0.3136 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15076 Z= 0.156 Angle : 0.495 6.106 20446 Z= 0.258 Chirality : 0.039 0.151 2282 Planarity : 0.003 0.041 2518 Dihedral : 12.527 152.281 2107 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.81 % Allowed : 8.30 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.20), residues: 1774 helix: 1.39 (0.15), residues: 1067 sheet: -0.46 (0.53), residues: 103 loop : -0.47 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 347 TYR 0.017 0.001 TYR A 349 PHE 0.025 0.002 PHE C 389 TRP 0.014 0.001 TRP A 168 HIS 0.004 0.001 HIS B 803 Details of bonding type rmsd covalent geometry : bond 0.00364 (15076) covalent geometry : angle 0.49520 (20446) hydrogen bonds : bond 0.03640 ( 855) hydrogen bonds : angle 4.06935 ( 2472) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 0.596 Fit side-chains REVERT: A 305 MET cc_start: 0.8458 (ttp) cc_final: 0.8093 (ttm) REVERT: A 578 LYS cc_start: 0.6719 (tptm) cc_final: 0.6197 (mtpp) REVERT: B 994 GLU cc_start: 0.6217 (mm-30) cc_final: 0.5931 (mm-30) REVERT: C 267 TYR cc_start: 0.8664 (m-80) cc_final: 0.8268 (m-80) outliers start: 13 outliers final: 10 residues processed: 134 average time/residue: 0.1053 time to fit residues: 22.2330 Evaluate side-chains 126 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain B residue 876 ILE Chi-restraints excluded: chain B residue 1020 VAL Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 165 optimal weight: 0.0870 chunk 172 optimal weight: 2.9990 chunk 154 optimal weight: 0.0170 chunk 28 optimal weight: 7.9990 chunk 40 optimal weight: 30.0000 chunk 46 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 21 optimal weight: 0.0870 chunk 56 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 overall best weight: 0.6376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.127444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.099654 restraints weight = 24083.176| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.41 r_work: 0.3184 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15076 Z= 0.096 Angle : 0.442 5.439 20446 Z= 0.230 Chirality : 0.038 0.150 2282 Planarity : 0.003 0.036 2518 Dihedral : 12.444 152.144 2107 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.25 % Allowed : 9.05 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.20), residues: 1774 helix: 1.65 (0.16), residues: 1065 sheet: 0.16 (0.56), residues: 91 loop : -0.51 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 424 TYR 0.011 0.001 TYR B 837 PHE 0.024 0.001 PHE C 389 TRP 0.013 0.001 TRP A 168 HIS 0.003 0.001 HIS B 803 Details of bonding type rmsd covalent geometry : bond 0.00209 (15076) covalent geometry : angle 0.44210 (20446) hydrogen bonds : bond 0.03292 ( 855) hydrogen bonds : angle 3.85758 ( 2472) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.589 Fit side-chains REVERT: A 251 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8253 (tt) REVERT: A 290 THR cc_start: 0.9011 (OUTLIER) cc_final: 0.8676 (m) REVERT: A 305 MET cc_start: 0.8423 (ttp) cc_final: 0.8111 (ttm) REVERT: A 573 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8551 (pp) REVERT: A 578 LYS cc_start: 0.6736 (tptm) cc_final: 0.6236 (mtpp) REVERT: B 994 GLU cc_start: 0.6090 (mm-30) cc_final: 0.5816 (mm-30) REVERT: C 267 TYR cc_start: 0.8592 (m-80) cc_final: 0.8242 (m-80) REVERT: C 498 GLN cc_start: 0.8368 (mt0) cc_final: 0.7964 (pt0) outliers start: 20 outliers final: 9 residues processed: 143 average time/residue: 0.1114 time to fit residues: 24.4945 Evaluate side-chains 132 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain B residue 876 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 426 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 59 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 108 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 176 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 302 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.127436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.100127 restraints weight = 24183.350| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.54 r_work: 0.3163 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15076 Z= 0.099 Angle : 0.441 5.351 20446 Z= 0.228 Chirality : 0.038 0.148 2282 Planarity : 0.003 0.043 2518 Dihedral : 12.395 152.086 2107 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.25 % Allowed : 10.29 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.20), residues: 1774 helix: 1.71 (0.15), residues: 1084 sheet: 0.20 (0.56), residues: 91 loop : -0.45 (0.26), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 424 TYR 0.012 0.001 TYR B 893 PHE 0.019 0.001 PHE C 389 TRP 0.013 0.001 TRP A 168 HIS 0.003 0.001 HIS B 803 Details of bonding type rmsd covalent geometry : bond 0.00221 (15076) covalent geometry : angle 0.44149 (20446) hydrogen bonds : bond 0.03172 ( 855) hydrogen bonds : angle 3.74759 ( 2472) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.588 Fit side-chains REVERT: A 251 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8273 (tt) REVERT: A 290 THR cc_start: 0.9008 (OUTLIER) cc_final: 0.8629 (m) REVERT: A 305 MET cc_start: 0.8496 (ttp) cc_final: 0.8153 (ttm) REVERT: A 578 LYS cc_start: 0.6688 (tptm) cc_final: 0.6213 (mtpp) REVERT: B 994 GLU cc_start: 0.6093 (mm-30) cc_final: 0.5817 (mm-30) REVERT: C 498 GLN cc_start: 0.8388 (mt0) cc_final: 0.8008 (pt0) outliers start: 20 outliers final: 14 residues processed: 135 average time/residue: 0.1078 time to fit residues: 22.7037 Evaluate side-chains 137 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain B residue 876 ILE Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 437 TRP Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain D residue 526 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 0 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 chunk 156 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 148 optimal weight: 0.7980 chunk 168 optimal weight: 8.9990 chunk 54 optimal weight: 8.9990 chunk 43 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.123217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.094720 restraints weight = 24167.909| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.46 r_work: 0.3088 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 15076 Z= 0.198 Angle : 0.520 5.511 20446 Z= 0.271 Chirality : 0.041 0.183 2282 Planarity : 0.004 0.040 2518 Dihedral : 12.482 152.707 2107 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.93 % Favored : 97.01 % Rotamer: Outliers : 1.75 % Allowed : 10.85 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.20), residues: 1774 helix: 1.48 (0.15), residues: 1078 sheet: 0.21 (0.55), residues: 91 loop : -0.50 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 880 TYR 0.018 0.002 TYR A 349 PHE 0.021 0.002 PHE C 423 TRP 0.014 0.001 TRP A 168 HIS 0.005 0.001 HIS B 803 Details of bonding type rmsd covalent geometry : bond 0.00466 (15076) covalent geometry : angle 0.52003 (20446) hydrogen bonds : bond 0.03628 ( 855) hydrogen bonds : angle 4.00472 ( 2472) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.639 Fit side-chains REVERT: A 251 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8409 (tt) REVERT: A 290 THR cc_start: 0.9035 (OUTLIER) cc_final: 0.8662 (m) REVERT: A 305 MET cc_start: 0.8574 (ttp) cc_final: 0.8282 (ttm) REVERT: A 573 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8478 (pp) REVERT: B 875 MET cc_start: 0.8468 (mpp) cc_final: 0.8011 (mtt) REVERT: B 970 MET cc_start: 0.7784 (ttp) cc_final: 0.7567 (ttp) REVERT: B 994 GLU cc_start: 0.6324 (mm-30) cc_final: 0.6014 (mm-30) REVERT: C 573 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8385 (pp) outliers start: 28 outliers final: 20 residues processed: 142 average time/residue: 0.1101 time to fit residues: 24.4759 Evaluate side-chains 139 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 876 ILE Chi-restraints excluded: chain B residue 937 MET Chi-restraints excluded: chain B residue 1020 VAL Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 437 TRP Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 170 optimal weight: 6.9990 chunk 110 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 174 optimal weight: 0.7980 chunk 141 optimal weight: 10.0000 chunk 149 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 72 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 955 ASN B1073 GLN D 302 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.126075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.097563 restraints weight = 23914.742| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.44 r_work: 0.3161 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15076 Z= 0.103 Angle : 0.455 7.008 20446 Z= 0.235 Chirality : 0.038 0.146 2282 Planarity : 0.003 0.033 2518 Dihedral : 12.380 151.817 2107 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.62 % Allowed : 11.10 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.20), residues: 1774 helix: 1.68 (0.15), residues: 1088 sheet: 0.19 (0.55), residues: 91 loop : -0.44 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 997 TYR 0.012 0.001 TYR B 893 PHE 0.027 0.001 PHE C 389 TRP 0.014 0.001 TRP C 168 HIS 0.003 0.001 HIS B 803 Details of bonding type rmsd covalent geometry : bond 0.00232 (15076) covalent geometry : angle 0.45521 (20446) hydrogen bonds : bond 0.03242 ( 855) hydrogen bonds : angle 3.80630 ( 2472) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.655 Fit side-chains REVERT: A 251 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8278 (tt) REVERT: A 290 THR cc_start: 0.8993 (t) cc_final: 0.8604 (m) REVERT: A 305 MET cc_start: 0.8559 (ttp) cc_final: 0.8296 (ttm) REVERT: A 573 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8390 (pp) REVERT: A 578 LYS cc_start: 0.6743 (tptm) cc_final: 0.6050 (mtpp) REVERT: A 582 MET cc_start: 0.7052 (mmt) cc_final: 0.6780 (mmt) REVERT: A 604 MET cc_start: 0.6405 (mmm) cc_final: 0.6197 (mmp) REVERT: B 970 MET cc_start: 0.7770 (ttp) cc_final: 0.7538 (ttp) REVERT: B 994 GLU cc_start: 0.6126 (mm-30) cc_final: 0.5834 (mm-30) REVERT: C 498 GLN cc_start: 0.8381 (mt0) cc_final: 0.7987 (pt0) REVERT: C 573 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8280 (pp) REVERT: D 511 ASP cc_start: 0.6336 (t0) cc_final: 0.6051 (m-30) REVERT: D 521 GLU cc_start: 0.8516 (tt0) cc_final: 0.8135 (tt0) outliers start: 26 outliers final: 18 residues processed: 139 average time/residue: 0.1080 time to fit residues: 23.7763 Evaluate side-chains 135 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 876 ILE Chi-restraints excluded: chain B residue 1020 VAL Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 437 TRP Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 496 GLN Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 23 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 120 optimal weight: 0.7980 chunk 163 optimal weight: 7.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.126050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.097420 restraints weight = 23981.386| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.50 r_work: 0.3150 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15076 Z= 0.107 Angle : 0.457 7.204 20446 Z= 0.234 Chirality : 0.038 0.152 2282 Planarity : 0.003 0.034 2518 Dihedral : 12.352 151.674 2107 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.75 % Allowed : 11.23 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.20), residues: 1774 helix: 1.77 (0.15), residues: 1089 sheet: 0.23 (0.55), residues: 91 loop : -0.37 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 997 TYR 0.012 0.001 TYR B 893 PHE 0.035 0.001 PHE D 574 TRP 0.014 0.001 TRP A 168 HIS 0.004 0.001 HIS B 803 Details of bonding type rmsd covalent geometry : bond 0.00243 (15076) covalent geometry : angle 0.45725 (20446) hydrogen bonds : bond 0.03171 ( 855) hydrogen bonds : angle 3.73724 ( 2472) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.495 Fit side-chains REVERT: A 251 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8238 (tt) REVERT: A 290 THR cc_start: 0.8981 (OUTLIER) cc_final: 0.8576 (m) REVERT: A 305 MET cc_start: 0.8598 (ttp) cc_final: 0.8317 (ttm) REVERT: A 578 LYS cc_start: 0.6749 (tptm) cc_final: 0.6137 (mtpp) REVERT: B 970 MET cc_start: 0.7740 (ttp) cc_final: 0.7501 (ttp) REVERT: B 994 GLU cc_start: 0.6267 (mm-30) cc_final: 0.5948 (mm-30) REVERT: C 498 GLN cc_start: 0.8330 (mt0) cc_final: 0.7964 (pt0) REVERT: C 573 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8227 (pp) REVERT: D 511 ASP cc_start: 0.6395 (t0) cc_final: 0.6008 (m-30) REVERT: D 521 GLU cc_start: 0.8486 (tt0) cc_final: 0.8040 (tt0) outliers start: 28 outliers final: 21 residues processed: 139 average time/residue: 0.1067 time to fit residues: 23.2497 Evaluate side-chains 139 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 876 ILE Chi-restraints excluded: chain B residue 1020 VAL Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 437 TRP Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 2 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 172 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 822 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.125814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.097233 restraints weight = 23996.211| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.47 r_work: 0.3148 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15076 Z= 0.114 Angle : 0.465 7.261 20446 Z= 0.238 Chirality : 0.038 0.152 2282 Planarity : 0.003 0.033 2518 Dihedral : 12.347 151.735 2107 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.56 % Allowed : 11.67 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.20), residues: 1774 helix: 1.79 (0.15), residues: 1088 sheet: 0.28 (0.55), residues: 91 loop : -0.35 (0.27), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 997 TYR 0.012 0.001 TYR A 349 PHE 0.034 0.001 PHE D 574 TRP 0.014 0.001 TRP A 168 HIS 0.004 0.001 HIS B 822 Details of bonding type rmsd covalent geometry : bond 0.00263 (15076) covalent geometry : angle 0.46463 (20446) hydrogen bonds : bond 0.03178 ( 855) hydrogen bonds : angle 3.73470 ( 2472) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 0.415 Fit side-chains REVERT: A 251 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8246 (tt) REVERT: A 290 THR cc_start: 0.8975 (OUTLIER) cc_final: 0.8569 (m) REVERT: A 305 MET cc_start: 0.8604 (ttp) cc_final: 0.8317 (ttm) REVERT: A 578 LYS cc_start: 0.6704 (tptm) cc_final: 0.6024 (mtpp) REVERT: A 582 MET cc_start: 0.7091 (mmt) cc_final: 0.6812 (mmt) REVERT: B 970 MET cc_start: 0.7769 (ttp) cc_final: 0.7515 (ttp) REVERT: B 994 GLU cc_start: 0.6322 (mm-30) cc_final: 0.6005 (mm-30) REVERT: C 498 GLN cc_start: 0.8337 (mt0) cc_final: 0.7985 (pt0) REVERT: C 573 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8242 (pp) REVERT: D 511 ASP cc_start: 0.6435 (t0) cc_final: 0.6045 (m-30) REVERT: D 521 GLU cc_start: 0.8459 (tt0) cc_final: 0.8015 (tt0) outliers start: 25 outliers final: 21 residues processed: 132 average time/residue: 0.1109 time to fit residues: 22.7965 Evaluate side-chains 139 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 876 ILE Chi-restraints excluded: chain B residue 1020 VAL Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 437 TRP Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 25 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 68 optimal weight: 0.0040 chunk 135 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 108 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 129 optimal weight: 9.9990 chunk 154 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 302 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.126876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.098365 restraints weight = 24087.971| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.39 r_work: 0.3184 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15076 Z= 0.097 Angle : 0.447 7.385 20446 Z= 0.229 Chirality : 0.038 0.146 2282 Planarity : 0.003 0.033 2518 Dihedral : 12.304 151.521 2107 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.50 % Allowed : 11.73 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.20), residues: 1774 helix: 1.88 (0.15), residues: 1086 sheet: 0.36 (0.55), residues: 91 loop : -0.26 (0.27), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1077 TYR 0.012 0.001 TYR B 893 PHE 0.030 0.001 PHE D 574 TRP 0.015 0.001 TRP A 168 HIS 0.006 0.001 HIS B 822 Details of bonding type rmsd covalent geometry : bond 0.00216 (15076) covalent geometry : angle 0.44672 (20446) hydrogen bonds : bond 0.03062 ( 855) hydrogen bonds : angle 3.66232 ( 2472) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.481 Fit side-chains REVERT: A 251 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8254 (tt) REVERT: A 290 THR cc_start: 0.8942 (OUTLIER) cc_final: 0.8545 (m) REVERT: A 305 MET cc_start: 0.8515 (ttp) cc_final: 0.8228 (ttm) REVERT: A 578 LYS cc_start: 0.6709 (tptm) cc_final: 0.6056 (mtpp) REVERT: A 582 MET cc_start: 0.7150 (mmt) cc_final: 0.6836 (mmt) REVERT: B 970 MET cc_start: 0.7833 (ttp) cc_final: 0.7599 (ttp) REVERT: B 994 GLU cc_start: 0.6252 (mm-30) cc_final: 0.5927 (mm-30) REVERT: C 498 GLN cc_start: 0.8235 (mt0) cc_final: 0.7908 (pt0) REVERT: C 573 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8146 (pp) REVERT: D 511 ASP cc_start: 0.6402 (t0) cc_final: 0.6017 (m-30) REVERT: D 521 GLU cc_start: 0.8385 (tt0) cc_final: 0.7920 (tt0) outliers start: 24 outliers final: 17 residues processed: 136 average time/residue: 0.1085 time to fit residues: 23.0851 Evaluate side-chains 139 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain B residue 876 ILE Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 437 TRP Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 506 ILE Chi-restraints excluded: chain D residue 526 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 105 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 118 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 171 optimal weight: 0.0570 overall best weight: 0.8502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 302 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.126730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.098722 restraints weight = 24044.258| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.42 r_work: 0.3168 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15076 Z= 0.101 Angle : 0.453 7.471 20446 Z= 0.233 Chirality : 0.038 0.147 2282 Planarity : 0.003 0.033 2518 Dihedral : 12.299 151.756 2107 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.50 % Allowed : 11.85 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.20), residues: 1774 helix: 1.91 (0.15), residues: 1087 sheet: 0.38 (0.55), residues: 91 loop : -0.26 (0.27), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 997 TYR 0.012 0.001 TYR D 205 PHE 0.031 0.001 PHE D 574 TRP 0.014 0.001 TRP A 168 HIS 0.004 0.001 HIS B 822 Details of bonding type rmsd covalent geometry : bond 0.00229 (15076) covalent geometry : angle 0.45317 (20446) hydrogen bonds : bond 0.03063 ( 855) hydrogen bonds : angle 3.65108 ( 2472) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3371.39 seconds wall clock time: 58 minutes 34.76 seconds (3514.76 seconds total)