Starting phenix.real_space_refine on Wed Mar 4 15:24:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rhh_24461/03_2026/7rhh_24461.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rhh_24461/03_2026/7rhh_24461.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/7rhh_24461/03_2026/7rhh_24461.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rhh_24461/03_2026/7rhh_24461.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rhh_24461/03_2026/7rhh_24461.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rhh_24461/03_2026/7rhh_24461.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= 0.000 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 8 residue(s): 0.01s 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: 2.93, per 1000 atoms: 0.20 Number of scatterers: 14717 At special positions: 0 Unit cell: (98.857, 100.491, 120.916, 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: 1.32 Conformation dependent library (CDL) restraints added in 540.8 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: 83 helices and 12 sheets defined 67.8% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 162 through 189 removed outlier: 3.545A pdb=" N TYR A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 174 " --> pdb=" O PHE A 170 " (cutoff:3.500A) Proline residue: A 175 - end of helix removed outlier: 5.130A pdb=" N ILE A 184 " --> pdb=" O TRP A 180 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.513A pdb=" N GLN A 193 " --> pdb=" O PHE A 189 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 219 removed outlier: 3.889A pdb=" N ILE A 202 " --> pdb=" O GLU A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 242 removed outlier: 3.520A pdb=" N LEU A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 253 removed outlier: 3.929A pdb=" N LYS A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 258 through 264 removed outlier: 4.133A pdb=" N LYS A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 276 removed outlier: 3.515A pdb=" N ARG A 271 " --> pdb=" O PRO A 268 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 272 " --> pdb=" O GLU A 269 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ASN A 273 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 292 removed outlier: 3.832A pdb=" N MET A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR A 290 " --> pdb=" O GLN A 286 " (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 removed outlier: 3.523A pdb=" N ASN A 404 " --> pdb=" O ILE A 400 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 458 through 470 removed outlier: 3.640A pdb=" N ASN A 468 " --> pdb=" O GLU A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 477 Processing helix chain 'A' and resid 486 through 495 removed outlier: 3.895A pdb=" N GLU A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU A 493 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS A 494 " --> pdb=" O GLU A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 587 removed outlier: 4.066A pdb=" N GLU A 587 " --> pdb=" O GLU A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 591 No H-bonds generated for 'chain 'A' and resid 589 through 591' Processing helix chain 'A' and resid 592 through 605 removed outlier: 4.032A pdb=" N MET A 604 " --> pdb=" O LYS A 600 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS A 605 " --> pdb=" O GLN A 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 680 removed outlier: 3.927A 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 removed outlier: 3.527A pdb=" N TRP B 691 " --> pdb=" O ASN B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 713 Processing helix chain 'B' and resid 724 through 735 Processing helix chain 'B' and resid 735 through 745 removed outlier: 3.701A pdb=" N LYS B 739 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 768 removed outlier: 3.586A pdb=" N ARG B 762 " --> pdb=" O PRO B 759 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU B 763 " --> pdb=" O LEU B 760 " (cutoff:3.500A) Proline residue: B 764 - end of helix removed outlier: 3.754A pdb=" N LYS B 768 " --> pdb=" O ARG B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 783 removed outlier: 3.824A pdb=" N LEU B 783 " --> pdb=" O LEU B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 817 Processing helix chain 'B' and resid 832 through 844 removed outlier: 3.641A pdb=" N ILE B 844 " --> pdb=" O VAL B 840 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 887 removed outlier: 3.722A pdb=" N PHE B 870 " --> pdb=" O PHE B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 907 removed outlier: 3.523A pdb=" N TYR B 907 " --> pdb=" O TYR B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 928 Processing helix chain 'B' and resid 933 through 940 removed outlier: 3.810A pdb=" N GLN B 939 " --> pdb=" O GLU B 935 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 940 " --> pdb=" O LEU B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 960 removed outlier: 5.645A pdb=" N ASN B 955 " --> pdb=" O ASP B 951 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ILE B 956 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL B 960 " --> pdb=" O ILE B 956 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 976 removed outlier: 3.804A pdb=" N LYS B 976 " --> pdb=" O PHE B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 1029 through 1033 Processing helix chain 'B' and resid 1062 through 1067 Processing helix chain 'B' and resid 1069 through 1084 Processing helix chain 'C' and resid 162 through 189 removed outlier: 3.566A pdb=" N TYR C 166 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Proline residue: C 175 - end of helix removed outlier: 3.546A pdb=" N THR C 181 " --> pdb=" O MET C 177 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL C 183 " --> pdb=" O ASN C 179 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ILE C 184 " --> pdb=" O TRP C 180 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA C 185 " --> pdb=" O THR C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 196 removed outlier: 3.616A pdb=" N TYR C 196 " --> pdb=" O LEU C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 221 Processing helix chain 'C' and resid 232 through 243 removed outlier: 3.567A pdb=" N ASN C 243 " --> pdb=" O LYS C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 253 removed outlier: 3.914A pdb=" N LYS C 247 " --> pdb=" O ASN C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 264 removed outlier: 3.968A pdb=" N LYS C 262 " --> pdb=" O LEU C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 276 removed outlier: 3.856A pdb=" N ILE C 270 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASN C 273 " --> pdb=" O ILE C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 292 removed outlier: 3.770A pdb=" N MET C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) removed outlier: 3.510A 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 404 through 425 Processing helix chain 'C' and resid 427 through 444 Processing helix chain 'C' and resid 449 through 455 removed outlier: 3.722A pdb=" N VAL C 453 " --> pdb=" O ASP C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 470 Processing helix chain 'C' and resid 470 through 475 removed outlier: 3.772A pdb=" N LYS C 475 " --> pdb=" O LEU C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 492 Processing helix chain 'C' and resid 493 through 495 No H-bonds generated for 'chain 'C' and resid 493 through 495' Processing helix chain 'C' and resid 545 through 550 removed outlier: 4.560A pdb=" N ILE C 549 " --> pdb=" O GLY C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 588 removed outlier: 3.993A pdb=" N GLU C 587 " --> pdb=" O GLU C 583 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR C 588 " --> pdb=" O ALA C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 605 removed outlier: 3.594A pdb=" N MET C 594 " --> pdb=" O ASP C 590 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS C 605 " --> pdb=" O GLN C 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 189 removed outlier: 3.669A pdb=" N TYR D 166 " --> pdb=" O GLY D 162 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N CYS D 171 " --> pdb=" O ASN D 167 " (cutoff:3.500A) Proline residue: D 175 - end of helix removed outlier: 3.673A pdb=" N VAL D 183 " --> pdb=" O ASN D 179 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ILE D 184 " --> pdb=" O TRP D 180 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA D 185 " --> pdb=" O THR D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 196 removed outlier: 3.651A 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: 3.530A pdb=" N ASN D 243 " --> pdb=" O LYS D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 253 removed outlier: 4.058A pdb=" N LYS D 247 " --> pdb=" O ASN D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 258 No H-bonds generated for 'chain 'D' and resid 256 through 258' Processing helix chain 'D' and resid 259 through 264 Processing helix chain 'D' and resid 267 through 272 removed outlier: 3.990A pdb=" N ILE D 270 " --> pdb=" O TYR D 267 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG D 271 " --> pdb=" O PRO D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 276 Processing helix chain 'D' and resid 277 through 292 removed outlier: 4.329A pdb=" N MET D 281 " --> pdb=" O ARG D 277 " (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: 3.730A pdb=" N PHE D 389 " --> pdb=" O GLY D 385 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ALA D 390 " --> pdb=" O VAL D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 424 Processing helix chain 'D' and resid 427 through 444 Processing helix chain 'D' and resid 449 through 454 Processing helix chain 'D' and resid 455 through 457 No H-bonds generated for 'chain 'D' and resid 455 through 457' Processing helix chain 'D' and resid 458 through 470 Processing helix chain 'D' and resid 470 through 476 removed outlier: 3.867A pdb=" N LYS D 475 " --> pdb=" O LEU D 471 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS D 476 " --> pdb=" O ASP D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 492 removed outlier: 3.988A pdb=" N LEU D 491 " --> pdb=" O LEU D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 586 removed outlier: 3.601A pdb=" N MET D 582 " --> pdb=" O LYS D 578 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU D 583 " --> pdb=" O ASP D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 604 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 505 through 507 removed outlier: 6.832A pdb=" N ILE A 565 " --> pdb=" O ILE A 506 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ASN A 564 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL A 527 " --> pdb=" O ASN A 564 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LYS A 523 " --> pdb=" O ILE A 568 " (cutoff:3.500A) removed outlier: 4.159A 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: 3.809A 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: 6.579A 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: 3.663A pdb=" N ASP B 987 " --> pdb=" O ALA B1048 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL B1046 " --> pdb=" O VAL B 989 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN B1045 " --> pdb=" O LEU B1010 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N VAL B1007 " --> pdb=" O THR B1021 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N THR B1021 " --> pdb=" O VAL B1007 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL B1009 " --> pdb=" O LEU B1019 " (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 removed outlier: 7.201A pdb=" N ASP C 572 " --> pdb=" O LYS C 520 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS C 520 " --> pdb=" O ASP C 572 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 505 through 507 removed outlier: 6.548A pdb=" N ILE C 565 " --> pdb=" O ILE C 506 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 224 through 225 Processing sheet with id=AB2, first strand: chain 'D' and resid 495 through 500 removed outlier: 3.616A pdb=" N GLN D 496 " --> pdb=" O CYS D 575 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 504 through 507 removed outlier: 6.212A pdb=" N TYR D 505 " --> pdb=" O SER D 567 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N SER D 567 " --> pdb=" O TYR D 505 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ASN D 564 " --> pdb=" O VAL D 527 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL D 536 " --> pdb=" O VAL D 526 " (cutoff:3.500A) 877 hydrogen bonds defined for protein. 2547 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: 2.52 Time building geometry restraints manager: 1.75 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: 4538 1.34 - 1.46: 3283 1.46 - 1.58: 7109 1.58 - 1.70: 8 1.70 - 1.81: 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 1.480 0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" O1A PCG D 701 " pdb=" PA PCG D 701 " ideal model delta sigma weight residual 1.582 1.480 0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" O1A PCG A 701 " pdb=" PA PCG A 701 " ideal model delta sigma weight residual 1.582 1.481 0.101 2.00e-02 2.50e+03 2.57e+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 2.56e+01 bond pdb=" C1' PCG D 701 " pdb=" O4' PCG D 701 " ideal model delta sigma weight residual 1.409 1.483 -0.074 2.00e-02 2.50e+03 1.35e+01 ... (remaining 15071 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 19960 1.82 - 3.65: 362 3.65 - 5.47: 59 5.47 - 7.29: 37 7.29 - 9.12: 28 Bond angle restraints: 20446 Sorted by residual: angle pdb=" N ILE C 363 " pdb=" CA ILE C 363 " pdb=" C ILE C 363 " ideal model delta sigma weight residual 113.53 108.67 4.86 9.80e-01 1.04e+00 2.46e+01 angle pdb=" C ASP B 649 " pdb=" N PRO B 650 " pdb=" CA PRO B 650 " ideal model delta sigma weight residual 119.05 124.16 -5.11 1.11e+00 8.12e-01 2.12e+01 angle pdb=" N PHE B 709 " pdb=" CA PHE B 709 " pdb=" C PHE B 709 " ideal model delta sigma weight residual 112.04 117.74 -5.70 1.44e+00 4.82e-01 1.57e+01 angle pdb=" N ASN D 468 " pdb=" CA ASN D 468 " pdb=" C ASN D 468 " ideal model delta sigma weight residual 111.28 115.56 -4.28 1.09e+00 8.42e-01 1.54e+01 angle pdb=" N TYR B 656 " pdb=" CA TYR B 656 " pdb=" C TYR B 656 " ideal model delta sigma weight residual 111.36 107.13 4.23 1.09e+00 8.42e-01 1.50e+01 ... (remaining 20441 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.91: 8725 28.91 - 57.82: 247 57.82 - 86.74: 17 86.74 - 115.65: 5 115.65 - 144.56: 14 Dihedral angle restraints: 9008 sinusoidal: 3744 harmonic: 5264 Sorted by residual: dihedral pdb=" C3' PCG D 701 " pdb=" O3' PCG D 701 " pdb=" PA PCG D 701 " pdb=" O1A PCG D 701 " ideal model delta sinusoidal sigma weight residual 151.41 -64.03 -144.56 1 3.00e+01 1.11e-03 1.94e+01 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 -64.68 -143.91 1 3.00e+01 1.11e-03 1.93e+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 -65.35 -143.24 1 3.00e+01 1.11e-03 1.92e+01 ... (remaining 9005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.135: 2260 0.135 - 0.270: 18 0.270 - 0.405: 0 0.405 - 0.540: 0 0.540 - 0.675: 4 Chirality restraints: 2282 Sorted by residual: 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 -3.37 -0.67 2.00e-01 2.50e+01 1.14e+01 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 1.13e+01 chirality pdb=" PA PCG D 701 " pdb=" O2A PCG D 701 " pdb=" O3' PCG D 701 " pdb=" O5' PCG D 701 " both_signs ideal model delta sigma weight residual True 2.70 -3.37 -0.67 2.00e-01 2.50e+01 1.13e+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 6.94e-02 7.71e+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 GLN A 496 " -0.046 5.00e-02 4.00e+02 6.82e-02 7.45e+00 pdb=" N PRO A 497 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 497 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 497 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 588 " -0.032 5.00e-02 4.00e+02 4.93e-02 3.90e+00 pdb=" N PRO A 589 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 589 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 589 " -0.027 5.00e-02 4.00e+02 ... (remaining 2515 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2510 2.76 - 3.30: 14527 3.30 - 3.83: 25704 3.83 - 4.37: 29760 4.37 - 4.90: 50821 Nonbonded interactions: 123322 Sorted by model distance: nonbonded pdb=" O THR C 357 " pdb=" OG1 THR C 361 " model vdw 2.231 3.040 nonbonded pdb=" O PHE B 703 " pdb=" OG1 THR B 707 " model vdw 2.262 3.040 nonbonded pdb=" O LEU D 169 " pdb=" OG1 THR D 173 " model vdw 2.263 3.040 nonbonded pdb=" OG SER B 647 " pdb=" OE1 GLN B 714 " model vdw 2.274 3.040 nonbonded pdb=" OD1 ASN B 776 " pdb=" OH TYR B 789 " model vdw 2.292 3.040 ... (remaining 123317 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: 1.660 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: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.550 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 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 0.102 15076 Z= 0.197 Angle : 0.705 9.118 20446 Z= 0.339 Chirality : 0.051 0.675 2282 Planarity : 0.005 0.069 2518 Dihedral : 14.927 144.561 5636 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.06 % Allowed : 0.44 % Favored : 99.50 % 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: 0.69 (0.19), residues: 1774 helix: 0.89 (0.15), residues: 1098 sheet: 0.25 (0.58), residues: 62 loop : -0.11 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1077 TYR 0.021 0.001 TYR B 769 PHE 0.022 0.001 PHE A 382 TRP 0.028 0.001 TRP A 442 HIS 0.004 0.001 HIS C 422 Details of bonding type rmsd covalent geometry : bond 0.00415 (15076) covalent geometry : angle 0.70518 (20446) hydrogen bonds : bond 0.15255 ( 877) hydrogen bonds : angle 5.58075 ( 2547) *********************** 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 174 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 173 time to evaluate : 0.566 Fit side-chains REVERT: C 208 ASP cc_start: 0.7817 (m-30) cc_final: 0.7496 (m-30) REVERT: C 579 ASP cc_start: 0.6666 (p0) cc_final: 0.6426 (p0) outliers start: 1 outliers final: 0 residues processed: 174 average time/residue: 0.0962 time to fit residues: 26.9595 Evaluate side-chains 137 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.574 ------------------------------------------------------------------------------- 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: 5.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 687 ASN B 714 GLN B1040 ASN B1053 ASN D 601 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.111995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.087713 restraints weight = 25207.865| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.50 r_work: 0.3026 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15076 Z= 0.171 Angle : 0.512 5.778 20446 Z= 0.269 Chirality : 0.040 0.183 2282 Planarity : 0.004 0.058 2518 Dihedral : 12.804 155.667 2107 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.94 % Allowed : 5.74 % Favored : 93.33 % 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: 1.31 (0.20), residues: 1774 helix: 1.45 (0.15), residues: 1116 sheet: 0.45 (0.65), residues: 51 loop : -0.06 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 271 TYR 0.018 0.001 TYR C 351 PHE 0.019 0.001 PHE A 382 TRP 0.015 0.001 TRP A 442 HIS 0.003 0.001 HIS B1049 Details of bonding type rmsd covalent geometry : bond 0.00398 (15076) covalent geometry : angle 0.51170 (20446) hydrogen bonds : bond 0.03873 ( 877) hydrogen bonds : angle 4.08179 ( 2547) *********************** 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 162 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 0.498 Fit side-chains REVERT: B 730 ASN cc_start: 0.7853 (m-40) cc_final: 0.7458 (m-40) REVERT: C 208 ASP cc_start: 0.8581 (m-30) cc_final: 0.8289 (m-30) outliers start: 15 outliers final: 12 residues processed: 154 average time/residue: 0.0938 time to fit residues: 23.7842 Evaluate side-chains 153 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 1032 SER Chi-restraints excluded: chain B residue 1040 ASN Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 536 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 20 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 143 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 79 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 121 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 314 ASN B1040 ASN D 601 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.111774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.087447 restraints weight = 25417.636| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.51 r_work: 0.3022 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15076 Z= 0.135 Angle : 0.467 5.530 20446 Z= 0.246 Chirality : 0.039 0.193 2282 Planarity : 0.003 0.054 2518 Dihedral : 12.638 152.632 2107 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.31 % Allowed : 7.36 % Favored : 91.33 % 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: 1.78 (0.15), residues: 1103 sheet: 0.31 (0.63), residues: 51 loop : -0.05 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1041 TYR 0.018 0.001 TYR C 205 PHE 0.012 0.001 PHE A 382 TRP 0.017 0.001 TRP A 442 HIS 0.002 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00314 (15076) covalent geometry : angle 0.46726 (20446) hydrogen bonds : bond 0.03531 ( 877) hydrogen bonds : angle 3.89382 ( 2547) *********************** 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 168 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.581 Fit side-chains revert: symmetry clash REVERT: A 573 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8747 (pp) REVERT: B 730 ASN cc_start: 0.7886 (m-40) cc_final: 0.7483 (m-40) REVERT: C 208 ASP cc_start: 0.8578 (m-30) cc_final: 0.8274 (m-30) outliers start: 21 outliers final: 16 residues processed: 159 average time/residue: 0.0900 time to fit residues: 23.6979 Evaluate side-chains 157 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 701 ILE Chi-restraints excluded: chain B residue 956 ILE Chi-restraints excluded: chain B residue 1040 ASN Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 565 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 165 optimal weight: 0.6980 chunk 172 optimal weight: 2.9990 chunk 154 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 40 optimal weight: 30.0000 chunk 46 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 21 optimal weight: 0.4980 chunk 56 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN D 601 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.111948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.087677 restraints weight = 25218.698| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.51 r_work: 0.3028 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15076 Z= 0.120 Angle : 0.455 7.184 20446 Z= 0.238 Chirality : 0.038 0.153 2282 Planarity : 0.003 0.051 2518 Dihedral : 12.569 152.191 2107 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.37 % Allowed : 8.67 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.20), residues: 1774 helix: 1.93 (0.15), residues: 1101 sheet: 0.18 (0.63), residues: 53 loop : -0.03 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1042 TYR 0.014 0.001 TYR C 351 PHE 0.010 0.001 PHE D 298 TRP 0.014 0.001 TRP C 168 HIS 0.002 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00275 (15076) covalent geometry : angle 0.45492 (20446) hydrogen bonds : bond 0.03341 ( 877) hydrogen bonds : angle 3.81745 ( 2547) *********************** 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 169 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.574 Fit side-chains revert: symmetry clash REVERT: A 521 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7231 (pp20) REVERT: A 573 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8662 (pp) REVERT: B 730 ASN cc_start: 0.7903 (m-40) cc_final: 0.7555 (m-40) REVERT: B 1040 ASN cc_start: 0.5301 (OUTLIER) cc_final: 0.4788 (p0) REVERT: C 208 ASP cc_start: 0.8573 (m-30) cc_final: 0.8264 (m-30) outliers start: 22 outliers final: 19 residues processed: 159 average time/residue: 0.0971 time to fit residues: 25.2333 Evaluate side-chains 163 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 956 ILE Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 1040 ASN Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain C residue 586 THR Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 507 CYS Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 565 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 59 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 176 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 498 GLN B 731 ASN B1040 ASN D 411 GLN D 601 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.110421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.086099 restraints weight = 25282.565| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.50 r_work: 0.2994 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15076 Z= 0.146 Angle : 0.476 5.726 20446 Z= 0.249 Chirality : 0.039 0.152 2282 Planarity : 0.003 0.047 2518 Dihedral : 12.519 152.161 2107 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.56 % Allowed : 9.79 % Favored : 88.65 % 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: 1.67 (0.20), residues: 1774 helix: 1.87 (0.15), residues: 1109 sheet: 0.15 (0.64), residues: 53 loop : -0.16 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1077 TYR 0.017 0.001 TYR C 351 PHE 0.012 0.001 PHE A 382 TRP 0.014 0.001 TRP C 168 HIS 0.003 0.001 HIS B 803 Details of bonding type rmsd covalent geometry : bond 0.00342 (15076) covalent geometry : angle 0.47577 (20446) hydrogen bonds : bond 0.03403 ( 877) hydrogen bonds : angle 3.81802 ( 2547) *********************** 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 167 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.611 Fit side-chains REVERT: A 521 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7097 (pp20) REVERT: A 573 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8724 (pp) REVERT: B 730 ASN cc_start: 0.7938 (m-40) cc_final: 0.7592 (m-40) REVERT: C 208 ASP cc_start: 0.8595 (m-30) cc_final: 0.8313 (m-30) REVERT: C 551 ASN cc_start: 0.7412 (m-40) cc_final: 0.7145 (m110) outliers start: 25 outliers final: 20 residues processed: 157 average time/residue: 0.0986 time to fit residues: 25.4525 Evaluate side-chains 155 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 956 ILE Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 1040 ASN Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain C residue 586 THR Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 507 CYS Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 565 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 120 optimal weight: 7.9990 chunk 148 optimal weight: 0.7980 chunk 168 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 144 optimal weight: 0.0970 chunk 164 optimal weight: 5.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN B1040 ASN D 601 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.110683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.086438 restraints weight = 25159.186| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.50 r_work: 0.3005 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15076 Z= 0.128 Angle : 0.462 6.453 20446 Z= 0.243 Chirality : 0.039 0.185 2282 Planarity : 0.003 0.045 2518 Dihedral : 12.488 152.358 2107 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.68 % Allowed : 10.54 % Favored : 87.77 % 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: 1.73 (0.20), residues: 1774 helix: 1.93 (0.15), residues: 1103 sheet: 0.02 (0.63), residues: 53 loop : -0.13 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1077 TYR 0.015 0.001 TYR C 351 PHE 0.015 0.001 PHE D 423 TRP 0.015 0.001 TRP C 168 HIS 0.002 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00298 (15076) covalent geometry : angle 0.46238 (20446) hydrogen bonds : bond 0.03305 ( 877) hydrogen bonds : angle 3.80186 ( 2547) *********************** 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 169 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 0.507 Fit side-chains REVERT: A 521 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7064 (pp20) REVERT: A 573 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8672 (pp) REVERT: B 730 ASN cc_start: 0.7956 (m-40) cc_final: 0.7591 (m-40) REVERT: C 208 ASP cc_start: 0.8601 (m-30) cc_final: 0.8313 (m-30) REVERT: C 551 ASN cc_start: 0.7519 (m-40) cc_final: 0.7264 (m110) outliers start: 27 outliers final: 23 residues processed: 159 average time/residue: 0.0963 time to fit residues: 25.0471 Evaluate side-chains 156 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 956 ILE Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 999 MET Chi-restraints excluded: chain B residue 1040 ASN Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain C residue 586 THR Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 507 CYS Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 565 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 170 optimal weight: 0.0030 chunk 110 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 174 optimal weight: 10.0000 chunk 141 optimal weight: 0.7980 chunk 149 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN D 601 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.111442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.087480 restraints weight = 25205.586| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.47 r_work: 0.3001 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1864 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= 0.098 Angle : 0.447 6.434 20446 Z= 0.234 Chirality : 0.038 0.154 2282 Planarity : 0.003 0.044 2518 Dihedral : 12.427 151.904 2107 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.50 % Allowed : 10.92 % Favored : 87.59 % 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: 1.86 (0.20), residues: 1774 helix: 2.04 (0.15), residues: 1103 sheet: -0.03 (0.64), residues: 53 loop : -0.09 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1077 TYR 0.018 0.001 TYR B 769 PHE 0.013 0.001 PHE D 423 TRP 0.014 0.001 TRP C 168 HIS 0.002 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00219 (15076) covalent geometry : angle 0.44716 (20446) hydrogen bonds : bond 0.03140 ( 877) hydrogen bonds : angle 3.72928 ( 2547) *********************** 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 169 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 0.523 Fit side-chains REVERT: A 521 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7074 (pp20) REVERT: A 573 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8575 (pp) REVERT: B 730 ASN cc_start: 0.7930 (m-40) cc_final: 0.7579 (m-40) REVERT: C 208 ASP cc_start: 0.8447 (m-30) cc_final: 0.8229 (m-30) REVERT: C 551 ASN cc_start: 0.7381 (m-40) cc_final: 0.7139 (m110) REVERT: D 516 MET cc_start: 0.8017 (ttt) cc_final: 0.7771 (ttt) REVERT: D 553 LYS cc_start: 0.3880 (tmtt) cc_final: 0.3557 (tptp) outliers start: 24 outliers final: 20 residues processed: 160 average time/residue: 0.0966 time to fit residues: 25.4872 Evaluate side-chains 158 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 956 ILE Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 995 ILE Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 511 ASP Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 507 CYS Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 565 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 23 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 8 optimal weight: 6.9990 chunk 14 optimal weight: 0.6980 chunk 143 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 120 optimal weight: 6.9990 chunk 163 optimal weight: 8.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN B1040 ASN D 601 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.110983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.086996 restraints weight = 25327.536| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.49 r_work: 0.3010 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15076 Z= 0.114 Angle : 0.456 6.111 20446 Z= 0.238 Chirality : 0.038 0.145 2282 Planarity : 0.003 0.044 2518 Dihedral : 12.410 152.079 2107 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.68 % Allowed : 11.10 % Favored : 87.21 % 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: 1.85 (0.20), residues: 1774 helix: 2.03 (0.15), residues: 1104 sheet: -0.09 (0.64), residues: 53 loop : -0.06 (0.26), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1077 TYR 0.013 0.001 TYR C 351 PHE 0.011 0.001 PHE D 423 TRP 0.018 0.001 TRP A 442 HIS 0.002 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00263 (15076) covalent geometry : angle 0.45649 (20446) hydrogen bonds : bond 0.03149 ( 877) hydrogen bonds : angle 3.72821 ( 2547) *********************** 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 167 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.566 Fit side-chains REVERT: A 521 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7082 (pp20) REVERT: A 573 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8592 (pp) REVERT: B 730 ASN cc_start: 0.7922 (m-40) cc_final: 0.7572 (m-40) REVERT: B 966 CYS cc_start: 0.7075 (m) cc_final: 0.6729 (m) REVERT: C 208 ASP cc_start: 0.8446 (m-30) cc_final: 0.8230 (m-30) REVERT: C 551 ASN cc_start: 0.7443 (m-40) cc_final: 0.7208 (m110) REVERT: D 553 LYS cc_start: 0.4000 (tmtt) cc_final: 0.3649 (tptp) outliers start: 27 outliers final: 22 residues processed: 157 average time/residue: 0.1010 time to fit residues: 25.7414 Evaluate side-chains 160 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 956 ILE Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 995 ILE Chi-restraints excluded: chain B residue 1040 ASN Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 511 ASP Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 507 CYS Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 565 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 2 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 172 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN B1040 ASN D 601 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.110996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.087017 restraints weight = 25344.881| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.49 r_work: 0.3001 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15076 Z= 0.113 Angle : 0.458 6.207 20446 Z= 0.238 Chirality : 0.038 0.144 2282 Planarity : 0.003 0.044 2518 Dihedral : 12.398 152.093 2107 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.87 % Allowed : 10.85 % 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: 1.87 (0.20), residues: 1774 helix: 2.03 (0.15), residues: 1103 sheet: -0.10 (0.65), residues: 53 loop : -0.04 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1041 TYR 0.018 0.001 TYR C 205 PHE 0.021 0.001 PHE D 423 TRP 0.027 0.001 TRP A 442 HIS 0.002 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00261 (15076) covalent geometry : angle 0.45775 (20446) hydrogen bonds : bond 0.03132 ( 877) hydrogen bonds : angle 3.73256 ( 2547) *********************** 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 170 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 0.615 Fit side-chains REVERT: A 521 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7066 (pp20) REVERT: A 573 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8566 (pp) REVERT: B 730 ASN cc_start: 0.7909 (m-40) cc_final: 0.7576 (m-40) REVERT: B 966 CYS cc_start: 0.7025 (m) cc_final: 0.6747 (m) REVERT: C 208 ASP cc_start: 0.8455 (m-30) cc_final: 0.8241 (m-30) REVERT: C 399 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.8340 (ttp) REVERT: C 551 ASN cc_start: 0.7453 (m-40) cc_final: 0.7226 (m110) REVERT: D 553 LYS cc_start: 0.4035 (tmtt) cc_final: 0.3675 (tptp) outliers start: 30 outliers final: 23 residues processed: 159 average time/residue: 0.1046 time to fit residues: 26.8374 Evaluate side-chains 163 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 843 LEU Chi-restraints excluded: chain B residue 956 ILE Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 995 ILE Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 511 ASP Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 507 CYS Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 565 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 25 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 68 optimal weight: 10.0000 chunk 135 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 129 optimal weight: 0.9990 chunk 154 optimal weight: 0.2980 chunk 47 optimal weight: 0.9990 chunk 142 optimal weight: 7.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN D 601 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.111820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.087983 restraints weight = 25353.469| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.49 r_work: 0.3021 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15076 Z= 0.099 Angle : 0.453 6.420 20446 Z= 0.236 Chirality : 0.038 0.145 2282 Planarity : 0.003 0.044 2518 Dihedral : 12.361 152.049 2107 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.56 % Allowed : 11.29 % Favored : 87.15 % 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: 1.94 (0.20), residues: 1774 helix: 2.08 (0.15), residues: 1104 sheet: -0.12 (0.64), residues: 53 loop : 0.01 (0.26), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1077 TYR 0.011 0.001 TYR C 351 PHE 0.019 0.001 PHE D 423 TRP 0.021 0.001 TRP A 442 HIS 0.002 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00222 (15076) covalent geometry : angle 0.45306 (20446) hydrogen bonds : bond 0.03060 ( 877) hydrogen bonds : angle 3.69673 ( 2547) ********************** 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 168 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.584 Fit side-chains REVERT: A 521 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7066 (pp20) REVERT: A 573 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8502 (pp) REVERT: B 730 ASN cc_start: 0.7899 (m-40) cc_final: 0.7567 (m-40) REVERT: C 208 ASP cc_start: 0.8463 (m-30) cc_final: 0.8258 (m-30) REVERT: C 399 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8342 (ttp) REVERT: C 551 ASN cc_start: 0.7456 (m-40) cc_final: 0.7226 (m110) REVERT: D 553 LYS cc_start: 0.4051 (tmtt) cc_final: 0.3705 (tptp) outliers start: 25 outliers final: 22 residues processed: 158 average time/residue: 0.0935 time to fit residues: 23.9224 Evaluate side-chains 158 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 956 ILE Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 995 ILE Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 511 ASP Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 507 CYS Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain D residue 565 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 105 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 73 optimal weight: 8.9990 chunk 118 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 147 optimal weight: 6.9990 chunk 173 optimal weight: 5.9990 chunk 171 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN C 496 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.112145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.088365 restraints weight = 25307.337| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.50 r_work: 0.3020 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1990 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= 0.098 Angle : 0.453 8.736 20446 Z= 0.235 Chirality : 0.038 0.145 2282 Planarity : 0.003 0.043 2518 Dihedral : 12.342 152.084 2107 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.56 % Allowed : 11.54 % Favored : 86.90 % 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: 2.00 (0.20), residues: 1774 helix: 2.12 (0.15), residues: 1104 sheet: 0.09 (0.65), residues: 51 loop : 0.03 (0.26), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1077 TYR 0.018 0.001 TYR C 205 PHE 0.018 0.001 PHE D 423 TRP 0.019 0.001 TRP A 442 HIS 0.002 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00220 (15076) covalent geometry : angle 0.45316 (20446) hydrogen bonds : bond 0.03017 ( 877) hydrogen bonds : angle 3.67539 ( 2547) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3244.66 seconds wall clock time: 56 minutes 32.88 seconds (3392.88 seconds total)