Starting phenix.real_space_refine on Fri Jul 3 15:14:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rhj_24463/07_2026/7rhj_24463.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rhj_24463/07_2026/7rhj_24463.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rhj_24463/07_2026/7rhj_24463.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rhj_24463/07_2026/7rhj_24463.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7rhj_24463/07_2026/7rhj_24463.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rhj_24463/07_2026/7rhj_24463.cif" model { file = "/net/cci-nas-00/data/ceres_data/7rhj_24463/07_2026/7rhj_24463.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rhj_24463/07_2026/7rhj_24463.cif" } resolution = 2.88 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= 0.006 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 83 5.16 5 C 9618 2.51 5 N 2397 2.21 5 O 2636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14738 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: 3553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3553 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 14, 'TRANS': 418} 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: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {'5H0': 1, 'PCG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.40, per 1000 atoms: 0.16 Number of scatterers: 14738 At special positions: 0 Unit cell: (99.002, 97.324, 119.977, 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 83 16.00 P 4 15.00 O 2636 8.00 N 2397 7.00 C 9618 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: 1.01 Conformation dependent library (CDL) restraints added in 531.8 milliseconds 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3370 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 12 sheets defined 67.7% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 162 through 189 removed outlier: 3.506A pdb=" N TYR A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) Proline residue: A 175 - end of helix removed outlier: 5.080A pdb=" N ILE A 184 " --> pdb=" O TRP A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.704A 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 Processing helix chain 'A' and resid 243 through 253 removed outlier: 3.991A pdb=" N LYS A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 261 Processing helix chain 'A' and resid 267 through 276 removed outlier: 3.789A pdb=" N ILE A 270 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG A 271 " --> pdb=" O PRO A 268 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ASN A 273 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG A 274 " --> pdb=" O ARG A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 292 removed outlier: 3.777A pdb=" N MET A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 3.750A 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: 3.642A 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 Processing helix chain 'A' and resid 470 through 476 removed outlier: 3.739A pdb=" N LYS A 476 " --> pdb=" O ASP A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 493 removed outlier: 3.955A pdb=" N LEU A 493 " --> pdb=" O VAL A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 550 removed outlier: 3.807A pdb=" N ILE A 549 " --> pdb=" O GLY A 545 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 545 through 550' Processing helix chain 'A' and resid 578 through 586 Processing helix chain 'A' and resid 588 through 605 removed outlier: 3.503A pdb=" N ILE A 602 " --> pdb=" O LYS A 598 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS A 605 " --> pdb=" O GLN A 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 680 Proline residue: B 675 - end of helix Processing helix chain 'B' and resid 687 through 709 removed outlier: 3.576A pdb=" N TRP B 691 " --> pdb=" O ASN B 687 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE B 709 " --> pdb=" O ASP B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 726 through 735 removed outlier: 3.642A pdb=" N TYR B 732 " --> pdb=" O MET B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 735 through 745 removed outlier: 3.721A 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: 3.637A pdb=" N LYS B 768 " --> pdb=" O ARG B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 783 removed outlier: 3.559A pdb=" N SER B 781 " --> pdb=" O SER B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 817 Processing helix chain 'B' and resid 830 through 844 Processing helix chain 'B' and resid 854 through 887 Processing helix chain 'B' and resid 887 through 907 Processing helix chain 'B' and resid 910 through 928 Processing helix chain 'B' and resid 932 through 940 removed outlier: 4.181A pdb=" N LEU B 936 " --> pdb=" O ASP B 932 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN B 939 " --> pdb=" O GLU B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 959 removed outlier: 7.185A pdb=" N ASN B 955 " --> pdb=" O ASP B 951 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ILE B 956 " --> pdb=" O VAL B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 978 removed outlier: 3.589A pdb=" N ILE B 971 " --> pdb=" O ASP B 967 " (cutoff:3.500A) Processing helix chain 'B' and resid 1030 through 1035 removed outlier: 3.780A pdb=" N LEU B1034 " --> pdb=" O GLU B1030 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA B1035 " --> pdb=" O ILE B1031 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1030 through 1035' Processing helix chain 'B' and resid 1061 through 1067 Processing helix chain 'B' and resid 1069 through 1083 Processing helix chain 'C' and resid 162 through 189 removed outlier: 3.543A pdb=" N TYR C 166 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Proline residue: C 175 - end of helix removed outlier: 4.984A pdb=" N ILE C 184 " --> pdb=" O TRP C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 196 removed outlier: 3.758A pdb=" N TYR C 196 " --> pdb=" O LEU C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 219 Processing helix chain 'C' and resid 232 through 243 removed outlier: 3.535A pdb=" N ASN C 243 " --> pdb=" O LYS C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 253 removed outlier: 3.984A pdb=" N LYS C 247 " --> pdb=" O ASN C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 258 No H-bonds generated for 'chain 'C' and resid 256 through 258' Processing helix chain 'C' and resid 259 through 264 Processing helix chain 'C' and resid 267 through 276 removed outlier: 3.990A pdb=" N ILE C 270 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG C 271 " --> pdb=" O PRO C 268 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ASN C 273 " --> pdb=" O ILE C 270 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG C 274 " --> pdb=" O ARG C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 292 removed outlier: 3.732A pdb=" N MET C 281 " --> pdb=" O ARG C 277 " (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 424 removed outlier: 4.971A pdb=" N ALA C 406 " --> pdb=" O ASN C 402 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ARG C 407 " --> pdb=" O MET C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 444 Processing helix chain 'C' and resid 458 through 470 removed outlier: 3.633A pdb=" N GLU C 464 " --> pdb=" O LYS C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 476 removed outlier: 3.699A pdb=" N LYS C 476 " --> pdb=" O ASP C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 495 removed outlier: 4.069A pdb=" N GLU C 490 " --> pdb=" O GLY C 486 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL C 492 " --> pdb=" O LEU C 488 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LEU C 493 " --> pdb=" O VAL C 489 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LYS C 494 " --> pdb=" O GLU C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 550 removed outlier: 4.381A pdb=" N ILE C 549 " --> pdb=" O GLY C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 586 Processing helix chain 'C' and resid 588 through 604 removed outlier: 4.311A pdb=" N GLU C 596 " --> pdb=" O LYS C 592 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN C 601 " --> pdb=" O GLU C 597 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE C 602 " --> pdb=" O LYS C 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 189 Proline residue: D 175 - end of helix removed outlier: 5.073A pdb=" N ILE D 184 " --> pdb=" O TRP D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 196 removed outlier: 3.597A pdb=" N GLN D 193 " --> pdb=" O PHE D 189 " (cutoff:3.500A) removed outlier: 3.656A 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 242 Processing helix chain 'D' and resid 243 through 253 removed outlier: 3.790A pdb=" N LYS D 247 " --> pdb=" O ASN D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 257 No H-bonds generated for 'chain 'D' and resid 255 through 257' Processing helix chain 'D' and resid 258 through 264 removed outlier: 3.967A pdb=" N LYS D 262 " --> pdb=" O LEU D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 276 removed outlier: 3.927A pdb=" N ILE D 270 " --> pdb=" O TYR D 267 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASN D 273 " --> pdb=" O ILE D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 292 removed outlier: 3.764A pdb=" N MET D 281 " --> pdb=" O ARG D 277 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU D 289 " --> pdb=" O PHE D 285 " (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: 4.123A pdb=" N PHE D 389 " --> pdb=" O GLY D 385 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA D 390 " --> pdb=" O VAL D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 425 Processing helix chain 'D' and resid 427 through 444 Processing helix chain 'D' and resid 449 through 455 removed outlier: 3.545A pdb=" N VAL D 453 " --> pdb=" O ASP D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 470 removed outlier: 3.518A pdb=" N HIS D 470 " --> pdb=" O ALA D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 475 Processing helix chain 'D' and resid 486 through 491 Processing helix chain 'D' and resid 545 through 550 removed outlier: 4.149A pdb=" N ILE D 549 " --> pdb=" O GLY D 545 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 545 through 550' Processing helix chain 'D' and resid 577 through 586 Processing helix chain 'D' and resid 588 through 605 removed outlier: 3.502A pdb=" N LYS D 592 " --> pdb=" O TYR D 588 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS D 598 " --> pdb=" O MET D 594 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS D 605 " --> pdb=" O GLN D 601 " (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 removed outlier: 6.905A pdb=" N LYS A 566 " --> pdb=" O VAL A 526 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N VAL A 526 " --> pdb=" O LYS A 566 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ILE A 568 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N LEU A 524 " --> pdb=" O ILE A 568 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N TYR A 570 " --> pdb=" O GLY A 522 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLY A 522 " --> pdb=" O TYR A 570 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ASP A 572 " --> pdb=" O LYS A 520 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LEU A 524 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N VAL A 537 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL A 526 " --> pdb=" O PHE A 535 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 505 through 507 removed outlier: 6.899A pdb=" N ILE A 565 " --> pdb=" O ILE A 506 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LYS A 566 " --> pdb=" O VAL A 526 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N VAL A 526 " --> pdb=" O LYS A 566 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ILE A 568 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N LEU A 524 " --> pdb=" O ILE A 568 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N TYR A 570 " --> pdb=" O GLY A 522 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLY A 522 " --> pdb=" O TYR A 570 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ASP A 572 " --> pdb=" O LYS A 520 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 715 through 716 removed outlier: 3.603A pdb=" N PHE B 715 " --> pdb=" O ILE B 721 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 979 through 983 removed outlier: 6.918A pdb=" N VAL B1047 " --> pdb=" O VAL B1009 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N VAL B1009 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N HIS B1049 " --> pdb=" O VAL B1007 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N VAL B1007 " --> pdb=" O HIS B1049 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N PHE B1051 " --> pdb=" O GLY B1005 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLY B1005 " --> pdb=" O PHE B1051 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASN B1053 " --> pdb=" O GLN B1003 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL B1020 " --> pdb=" O VAL B1009 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 979 through 983 removed outlier: 6.918A pdb=" N VAL B1047 " --> pdb=" O VAL B1009 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N VAL B1009 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N HIS B1049 " --> pdb=" O VAL B1007 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N VAL B1007 " --> pdb=" O HIS B1049 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N PHE B1051 " --> pdb=" O GLY B1005 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLY B1005 " --> pdb=" O PHE B1051 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASN B1053 " --> pdb=" O GLN B1003 " (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 'C' and resid 534 through 538 removed outlier: 4.227A pdb=" N VAL C 536 " --> pdb=" O VAL C 526 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LYS C 523 " --> pdb=" O ILE C 568 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE C 568 " --> pdb=" O LYS C 523 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN C 564 " --> pdb=" O VAL C 527 " (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 496 through 500 removed outlier: 6.444A pdb=" N ASP D 572 " --> pdb=" O LYS D 520 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 505 through 507 removed outlier: 6.430A pdb=" N ILE D 565 " --> pdb=" O ILE D 506 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASN D 564 " --> pdb=" O VAL D 527 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL D 526 " --> pdb=" O VAL D 536 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N VAL D 536 " --> pdb=" O VAL D 526 " (cutoff:3.500A) 904 hydrogen bonds defined for protein. 2622 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: 2.13 Time building geometry restraints manager: 1.42 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: 4534 1.34 - 1.47: 3822 1.47 - 1.59: 6594 1.59 - 1.71: 9 1.71 - 1.84: 140 Bond restraints: 15099 Sorted by residual: bond pdb=" O1A PCG D 802 " pdb=" PA PCG D 802 " ideal model delta sigma weight residual 1.582 1.477 0.105 2.00e-02 2.50e+03 2.74e+01 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 2.61e+01 bond pdb=" O1A PCG A 701 " pdb=" PA PCG A 701 " ideal model delta sigma weight residual 1.582 1.480 0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" O1A PCG B1301 " pdb=" PA PCG B1301 " ideal model delta sigma weight residual 1.582 1.480 0.102 2.00e-02 2.50e+03 2.60e+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 1.38e+01 ... (remaining 15094 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 20037 2.28 - 4.55: 345 4.55 - 6.83: 58 6.83 - 9.10: 33 9.10 - 11.38: 5 Bond angle restraints: 20478 Sorted by residual: angle pdb=" CA PRO C 497 " pdb=" N PRO C 497 " pdb=" CD PRO C 497 " ideal model delta sigma weight residual 112.00 105.56 6.44 1.40e+00 5.10e-01 2.11e+01 angle pdb=" C LYS B1059 " pdb=" N LYS B1060 " pdb=" CA LYS B1060 " ideal model delta sigma weight residual 121.54 129.79 -8.25 1.91e+00 2.74e-01 1.86e+01 angle pdb=" N GLU D 464 " pdb=" CA GLU D 464 " pdb=" CB GLU D 464 " ideal model delta sigma weight residual 110.41 117.10 -6.69 1.68e+00 3.54e-01 1.59e+01 angle pdb=" N GLU B 780 " pdb=" CA GLU B 780 " pdb=" CB GLU B 780 " ideal model delta sigma weight residual 110.39 117.11 -6.72 1.75e+00 3.27e-01 1.47e+01 angle pdb=" C ALA D 463 " pdb=" N GLU D 464 " pdb=" CA GLU D 464 " ideal model delta sigma weight residual 121.58 114.12 7.46 1.95e+00 2.63e-01 1.46e+01 ... (remaining 20473 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.03: 8712 29.03 - 58.07: 265 58.07 - 87.10: 16 87.10 - 116.14: 2 116.14 - 145.17: 15 Dihedral angle restraints: 9010 sinusoidal: 3749 harmonic: 5261 Sorted by residual: dihedral pdb=" C3' PCG D 802 " pdb=" O3' PCG D 802 " pdb=" PA PCG D 802 " pdb=" O1A PCG D 802 " ideal model delta sinusoidal sigma weight residual 151.41 -63.42 -145.17 1 3.00e+01 1.11e-03 1.94e+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 -66.37 -142.22 1 3.00e+01 1.11e-03 1.91e+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 -66.72 -141.87 1 3.00e+01 1.11e-03 1.91e+01 ... (remaining 9007 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.135: 2251 0.135 - 0.269: 27 0.269 - 0.404: 0 0.404 - 0.538: 0 0.538 - 0.673: 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 1.13e+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 -3.37 -0.67 2.00e-01 2.50e+01 1.12e+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 -3.37 -0.67 2.00e-01 2.50e+01 1.12e+01 ... (remaining 2279 not shown) Planarity restraints: 2521 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 763 " 0.048 5.00e-02 4.00e+02 7.28e-02 8.48e+00 pdb=" N PRO B 764 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 764 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 764 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET C 281 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.53e+00 pdb=" C MET C 281 " -0.041 2.00e-02 2.50e+03 pdb=" O MET C 281 " 0.015 2.00e-02 2.50e+03 pdb=" N PHE C 282 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE D 254 " -0.039 5.00e-02 4.00e+02 5.74e-02 5.26e+00 pdb=" N PRO D 255 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO D 255 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 255 " -0.032 5.00e-02 4.00e+02 ... (remaining 2518 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3521 2.79 - 3.32: 14486 3.32 - 3.84: 26521 3.84 - 4.37: 30349 4.37 - 4.90: 51429 Nonbonded interactions: 126306 Sorted by model distance: nonbonded pdb=" O LEU C 169 " pdb=" OG1 THR C 173 " model vdw 2.261 3.040 nonbonded pdb=" OD1 ASN B 776 " pdb=" OH TYR B 789 " model vdw 2.262 3.040 nonbonded pdb=" O LEU D 169 " pdb=" OG1 THR D 173 " model vdw 2.262 3.040 nonbonded pdb=" OE2 GLU A 515 " pdb=" OH TYR A 517 " model vdw 2.269 3.040 nonbonded pdb=" O LEU A 169 " pdb=" OG1 THR A 173 " model vdw 2.271 3.040 ... (remaining 126301 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 156 through 605) selection = (chain 'C' and resid 156 through 605) selection = (chain 'D' and resid 156 through 605) } 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: 2.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 11.510 Find NCS groups from input model: 0.250 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:7.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.127 15099 Z= 0.220 Angle : 0.800 11.378 20478 Z= 0.393 Chirality : 0.054 0.673 2282 Planarity : 0.005 0.073 2521 Dihedral : 15.043 145.171 5640 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.12 % Allowed : 0.62 % Favored : 99.25 % 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: -0.03 (0.19), residues: 1773 helix: 0.38 (0.15), residues: 1087 sheet: -1.36 (0.66), residues: 54 loop : -0.39 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 407 TYR 0.019 0.001 TYR B 865 PHE 0.018 0.002 PHE C 285 TRP 0.022 0.002 TRP A 442 HIS 0.006 0.001 HIS C 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.22 (15099) covalent geometry : angle 0.80015 / 0.39 (20478) hydrogen bonds : bond 0.12441 / 7.82 ( 888) hydrogen bonds : angle 5.96342 / 4.39 ( 2622) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 214 time to evaluate : 0.545 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "VAL C 156 " (corrupted residue). Skipping it. REVERT: B 970 MET cc_start: 0.6197 (ttt) cc_final: 0.5979 (ttt) REVERT: D 451 LYS cc_start: 0.6809 (mmtt) cc_final: 0.6596 (mmmt) REVERT: D 498 GLN cc_start: 0.6527 (tt0) cc_final: 0.6185 (tp40) outliers start: 2 outliers final: 1 residues processed: 216 average time/residue: 0.5154 time to fit residues: 122.9772 Evaluate side-chains 162 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 161 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 547 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 GLN A 496 GLN B 689 HIS B 939 GLN D 243 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.157600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.119965 restraints weight = 17481.452| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.94 r_work: 0.2992 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 15099 Z= 0.161 Angle : 0.548 12.765 20478 Z= 0.285 Chirality : 0.040 0.168 2282 Planarity : 0.004 0.063 2521 Dihedral : 12.690 153.243 2115 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.81 % Allowed : 8.93 % Favored : 89.26 % 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: 0.79 (0.19), residues: 1773 helix: 1.19 (0.15), residues: 1081 sheet: -1.14 (0.68), residues: 51 loop : -0.36 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 407 TYR 0.020 0.002 TYR D 349 PHE 0.024 0.002 PHE D 410 TRP 0.021 0.002 TRP A 442 HIS 0.005 0.001 HIS B 803 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (15099) covalent geometry : angle 0.54768 / 0.28 (20478) hydrogen bonds : bond 0.04261 / 2.76 ( 888) hydrogen bonds : angle 4.52753 / 3.31 ( 2622) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 192 time to evaluate : 0.593 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "VAL C 156 " (corrupted residue). Skipping it. REVERT: A 182 MET cc_start: 0.9089 (mmm) cc_final: 0.8814 (mmm) REVERT: A 234 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8089 (tm) REVERT: A 341 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8222 (mm-30) REVERT: A 423 PHE cc_start: 0.7932 (t80) cc_final: 0.7590 (t80) REVERT: B 665 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7624 (mmm) REVERT: B 694 MET cc_start: 0.8179 (mmm) cc_final: 0.7869 (tpp) REVERT: B 699 ASP cc_start: 0.7593 (m-30) cc_final: 0.7334 (m-30) REVERT: B 974 MET cc_start: 0.7219 (ppp) cc_final: 0.6762 (ppp) REVERT: C 415 ASP cc_start: 0.8273 (m-30) cc_final: 0.8069 (m-30) REVERT: C 498 GLN cc_start: 0.7185 (mt0) cc_final: 0.6972 (mt0) REVERT: D 498 GLN cc_start: 0.6816 (tt0) cc_final: 0.6318 (tp40) REVERT: D 580 ASP cc_start: 0.6856 (m-30) cc_final: 0.5911 (t0) outliers start: 29 outliers final: 12 residues processed: 204 average time/residue: 0.4621 time to fit residues: 105.3541 Evaluate side-chains 186 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 171 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 930 MET Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 547 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 92 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 160 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 chunk 127 optimal weight: 0.0980 chunk 28 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 63 optimal weight: 0.5980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 GLN B 689 HIS D 226 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.158501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.121082 restraints weight = 17681.212| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.11 r_work: 0.2990 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15099 Z= 0.124 Angle : 0.492 8.869 20478 Z= 0.257 Chirality : 0.039 0.184 2282 Planarity : 0.003 0.058 2521 Dihedral : 12.514 152.769 2115 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.43 % Allowed : 10.67 % Favored : 86.89 % 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: 1.13 (0.19), residues: 1773 helix: 1.49 (0.15), residues: 1089 sheet: -1.22 (0.62), residues: 59 loop : -0.28 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 220 TYR 0.019 0.001 TYR C 543 PHE 0.019 0.001 PHE D 410 TRP 0.019 0.001 TRP D 168 HIS 0.003 0.001 HIS B 803 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (15099) covalent geometry : angle 0.49235 / 0.26 (20478) hydrogen bonds : bond 0.03967 / 2.55 ( 888) hydrogen bonds : angle 4.29922 / 3.15 ( 2622) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 180 time to evaluate : 0.452 Fit side-chains TARDY: cannot create tardy model for: "VAL C 156 " (corrupted residue). Skipping it. REVERT: A 182 MET cc_start: 0.9039 (mmm) cc_final: 0.8818 (mmm) REVERT: A 234 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8098 (tm) REVERT: A 341 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8225 (mm-30) REVERT: A 415 ASP cc_start: 0.8248 (m-30) cc_final: 0.7858 (m-30) REVERT: A 423 PHE cc_start: 0.7951 (t80) cc_final: 0.7613 (t80) REVERT: A 433 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7427 (ttp80) REVERT: A 594 MET cc_start: 0.6096 (tmm) cc_final: 0.5759 (mtt) REVERT: B 665 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7708 (mmm) REVERT: B 694 MET cc_start: 0.8187 (mmm) cc_final: 0.7855 (tpt) REVERT: B 947 ASP cc_start: 0.7169 (OUTLIER) cc_final: 0.6387 (m-30) REVERT: B 970 MET cc_start: 0.6180 (ttt) cc_final: 0.5890 (ttt) REVERT: B 974 MET cc_start: 0.7156 (ppp) cc_final: 0.6709 (ppp) REVERT: B 1078 LYS cc_start: 0.5814 (tttt) cc_final: 0.5172 (pptt) REVERT: C 289 GLU cc_start: 0.8518 (tt0) cc_final: 0.8017 (pt0) REVERT: C 430 MET cc_start: 0.7970 (tpp) cc_final: 0.7714 (tpp) REVERT: C 498 GLN cc_start: 0.7244 (mt0) cc_final: 0.6880 (mt0) REVERT: D 474 LEU cc_start: 0.7130 (mt) cc_final: 0.6253 (pp) REVERT: D 498 GLN cc_start: 0.6757 (tt0) cc_final: 0.6244 (tp40) REVERT: D 580 ASP cc_start: 0.6707 (m-30) cc_final: 0.5905 (t0) outliers start: 39 outliers final: 13 residues processed: 200 average time/residue: 0.5140 time to fit residues: 114.6275 Evaluate side-chains 190 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 172 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 947 ASP Chi-restraints excluded: chain B residue 980 SER Chi-restraints excluded: chain B residue 997 ARG Chi-restraints excluded: chain B residue 999 MET Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 516 MET Chi-restraints excluded: chain D residue 320 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 53 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 128 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 GLN ** B 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.155168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.117663 restraints weight = 17552.503| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.97 r_work: 0.2910 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15099 Z= 0.197 Angle : 0.542 8.062 20478 Z= 0.285 Chirality : 0.041 0.174 2282 Planarity : 0.004 0.060 2521 Dihedral : 12.569 154.667 2113 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.81 % Allowed : 11.67 % Favored : 85.52 % 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: 1.09 (0.19), residues: 1773 helix: 1.43 (0.15), residues: 1097 sheet: -1.10 (0.61), residues: 59 loop : -0.27 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 291 TYR 0.021 0.002 TYR C 351 PHE 0.019 0.002 PHE D 298 TRP 0.023 0.002 TRP A 442 HIS 0.006 0.001 HIS B 803 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 (15099) covalent geometry : angle 0.54172 / 0.28 (20478) hydrogen bonds : bond 0.04321 / 2.81 ( 888) hydrogen bonds : angle 4.44627 / 3.24 ( 2622) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 174 time to evaluate : 0.489 Fit side-chains REVERT: A 234 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8075 (tm) REVERT: A 244 LEU cc_start: 0.8650 (tt) cc_final: 0.8387 (tp) REVERT: A 341 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.7894 (mp0) REVERT: A 399 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.7979 (mtp) REVERT: A 415 ASP cc_start: 0.8201 (m-30) cc_final: 0.7816 (m-30) REVERT: A 423 PHE cc_start: 0.7974 (t80) cc_final: 0.7717 (t80) REVERT: A 433 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7995 (mtm180) REVERT: A 594 MET cc_start: 0.6213 (OUTLIER) cc_final: 0.5873 (mtm) REVERT: B 651 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7647 (mm) REVERT: B 665 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.7874 (mmm) REVERT: B 739 LYS cc_start: 0.6315 (tmmt) cc_final: 0.5785 (mtmm) REVERT: B 947 ASP cc_start: 0.7269 (OUTLIER) cc_final: 0.6451 (m-30) REVERT: B 974 MET cc_start: 0.7230 (ppp) cc_final: 0.6680 (ppp) REVERT: B 998 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6823 (pt0) REVERT: B 1078 LYS cc_start: 0.5951 (tttt) cc_final: 0.5260 (pptt) REVERT: C 430 MET cc_start: 0.7921 (tpp) cc_final: 0.7601 (tpp) REVERT: C 498 GLN cc_start: 0.7328 (mt0) cc_final: 0.6952 (mt0) REVERT: C 516 MET cc_start: 0.6925 (OUTLIER) cc_final: 0.6554 (ppp) REVERT: D 451 LYS cc_start: 0.7160 (mmtt) cc_final: 0.6734 (mmmt) REVERT: D 459 ASP cc_start: 0.6984 (m-30) cc_final: 0.6760 (m-30) REVERT: D 580 ASP cc_start: 0.6756 (m-30) cc_final: 0.5912 (t0) outliers start: 45 outliers final: 12 residues processed: 199 average time/residue: 0.4656 time to fit residues: 102.8658 Evaluate side-chains 188 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 166 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 947 ASP Chi-restraints excluded: chain B residue 980 SER Chi-restraints excluded: chain B residue 998 GLU Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 516 MET Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 467 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 80 optimal weight: 7.9990 chunk 78 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 174 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 GLN B 653 ASN ** B 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 GLN ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.155839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.118695 restraints weight = 17359.336| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.06 r_work: 0.2961 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15099 Z= 0.149 Angle : 0.515 7.125 20478 Z= 0.268 Chirality : 0.040 0.183 2282 Planarity : 0.004 0.056 2521 Dihedral : 12.515 153.993 2113 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.87 % Allowed : 13.17 % Favored : 83.96 % 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: 1.21 (0.19), residues: 1773 helix: 1.55 (0.15), residues: 1095 sheet: -1.07 (0.60), residues: 59 loop : -0.27 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 220 TYR 0.018 0.001 TYR C 543 PHE 0.015 0.001 PHE C 298 TRP 0.022 0.002 TRP A 442 HIS 0.004 0.001 HIS B 803 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (15099) covalent geometry : angle 0.51465 / 0.27 (20478) hydrogen bonds : bond 0.04057 / 2.63 ( 888) hydrogen bonds : angle 4.36313 / 3.18 ( 2622) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 170 time to evaluate : 0.579 Fit side-chains REVERT: A 234 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8071 (tm) REVERT: A 341 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7857 (mp0) REVERT: A 399 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8011 (mtp) REVERT: A 415 ASP cc_start: 0.8209 (m-30) cc_final: 0.7832 (m-30) REVERT: A 423 PHE cc_start: 0.7966 (t80) cc_final: 0.7690 (t80) REVERT: A 592 LYS cc_start: 0.6786 (tppt) cc_final: 0.6045 (tptt) REVERT: B 648 ILE cc_start: 0.8106 (OUTLIER) cc_final: 0.7902 (pt) REVERT: B 651 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7675 (mm) REVERT: B 665 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.7860 (mmm) REVERT: B 739 LYS cc_start: 0.6260 (tmmt) cc_final: 0.5761 (mtmm) REVERT: B 947 ASP cc_start: 0.7246 (OUTLIER) cc_final: 0.6452 (m-30) REVERT: B 1078 LYS cc_start: 0.6015 (tttt) cc_final: 0.5283 (pptt) REVERT: C 225 GLU cc_start: 0.7233 (pt0) cc_final: 0.6917 (tt0) REVERT: C 498 GLN cc_start: 0.7264 (mt0) cc_final: 0.6628 (mt0) REVERT: C 516 MET cc_start: 0.6776 (OUTLIER) cc_final: 0.6509 (ppp) REVERT: D 451 LYS cc_start: 0.7195 (mmtt) cc_final: 0.6774 (mmmt) REVERT: D 498 GLN cc_start: 0.6883 (tt0) cc_final: 0.6252 (tp40) REVERT: D 580 ASP cc_start: 0.6751 (m-30) cc_final: 0.5930 (t0) outliers start: 46 outliers final: 18 residues processed: 198 average time/residue: 0.5089 time to fit residues: 112.7835 Evaluate side-chains 189 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 947 ASP Chi-restraints excluded: chain B residue 980 SER Chi-restraints excluded: chain B residue 997 ARG Chi-restraints excluded: chain B residue 999 MET Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 516 MET Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 492 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 145 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 162 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 110 optimal weight: 0.4980 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 GLN ** B 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 GLN D 226 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.154869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.116840 restraints weight = 17425.494| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.14 r_work: 0.2898 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15099 Z= 0.181 Angle : 0.542 9.886 20478 Z= 0.281 Chirality : 0.041 0.173 2282 Planarity : 0.004 0.057 2521 Dihedral : 12.551 154.836 2113 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.25 % Allowed : 13.67 % Favored : 83.08 % 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: 1.17 (0.19), residues: 1773 helix: 1.51 (0.15), residues: 1090 sheet: -0.95 (0.61), residues: 57 loop : -0.28 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 407 TYR 0.019 0.002 TYR A 543 PHE 0.017 0.002 PHE D 298 TRP 0.026 0.002 TRP A 442 HIS 0.005 0.001 HIS B 803 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (15099) covalent geometry : angle 0.54239 / 0.28 (20478) hydrogen bonds : bond 0.04203 / 2.74 ( 888) hydrogen bonds : angle 4.44070 / 3.22 ( 2622) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 174 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: A 234 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8145 (tm) REVERT: A 244 LEU cc_start: 0.8661 (tt) cc_final: 0.8410 (tp) REVERT: A 341 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8008 (mp0) REVERT: A 399 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.8125 (mtp) REVERT: A 415 ASP cc_start: 0.8326 (m-30) cc_final: 0.7997 (m-30) REVERT: A 423 PHE cc_start: 0.8059 (t80) cc_final: 0.7778 (t80) REVERT: B 665 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.7979 (mmm) REVERT: B 739 LYS cc_start: 0.6476 (tmmt) cc_final: 0.5839 (mtmm) REVERT: B 947 ASP cc_start: 0.7303 (OUTLIER) cc_final: 0.6662 (m-30) REVERT: B 974 MET cc_start: 0.7225 (ppp) cc_final: 0.6780 (ppp) REVERT: B 998 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.7092 (pt0) REVERT: B 1078 LYS cc_start: 0.6023 (tttt) cc_final: 0.5305 (pptt) REVERT: C 225 GLU cc_start: 0.7263 (pt0) cc_final: 0.7015 (tt0) REVERT: C 411 GLN cc_start: 0.8262 (mm-40) cc_final: 0.8002 (tp-100) REVERT: C 498 GLN cc_start: 0.7308 (mt0) cc_final: 0.6582 (mt0) REVERT: C 516 MET cc_start: 0.6832 (OUTLIER) cc_final: 0.6602 (ppp) REVERT: D 451 LYS cc_start: 0.7240 (mmtt) cc_final: 0.6842 (mmmt) REVERT: D 498 GLN cc_start: 0.6990 (tt0) cc_final: 0.6368 (tp40) REVERT: D 572 ASP cc_start: 0.7864 (OUTLIER) cc_final: 0.7416 (m-30) REVERT: D 580 ASP cc_start: 0.6916 (m-30) cc_final: 0.6055 (t0) outliers start: 52 outliers final: 17 residues processed: 199 average time/residue: 0.4966 time to fit residues: 110.6727 Evaluate side-chains 195 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 930 MET Chi-restraints excluded: chain B residue 947 ASP Chi-restraints excluded: chain B residue 980 SER Chi-restraints excluded: chain B residue 997 ARG Chi-restraints excluded: chain B residue 998 GLU Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 516 MET Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 572 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 75 optimal weight: 0.9990 chunk 122 optimal weight: 0.0270 chunk 136 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 128 optimal weight: 20.0000 chunk 132 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 37 optimal weight: 7.9990 chunk 172 optimal weight: 0.7980 chunk 168 optimal weight: 6.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 GLN ** B 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.157757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.120195 restraints weight = 17386.088| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.92 r_work: 0.2991 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15099 Z= 0.115 Angle : 0.502 8.235 20478 Z= 0.258 Chirality : 0.039 0.188 2282 Planarity : 0.003 0.052 2521 Dihedral : 12.456 153.276 2113 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.37 % Allowed : 15.17 % Favored : 82.46 % 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: 1.42 (0.20), residues: 1773 helix: 1.72 (0.15), residues: 1089 sheet: -0.92 (0.61), residues: 57 loop : -0.18 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 407 TYR 0.020 0.001 TYR D 420 PHE 0.013 0.001 PHE C 298 TRP 0.024 0.002 TRP A 442 HIS 0.003 0.001 HIS B 803 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (15099) covalent geometry : angle 0.50201 / 0.26 (20478) hydrogen bonds : bond 0.03811 / 2.46 ( 888) hydrogen bonds : angle 4.26560 / 3.10 ( 2622) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 172 time to evaluate : 0.525 Fit side-chains REVERT: A 234 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8081 (tm) REVERT: A 415 ASP cc_start: 0.8178 (m-30) cc_final: 0.7868 (m-30) REVERT: A 423 PHE cc_start: 0.7968 (t80) cc_final: 0.7594 (t80) REVERT: A 592 LYS cc_start: 0.6796 (tppt) cc_final: 0.6116 (tptt) REVERT: B 665 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.7859 (mmm) REVERT: B 739 LYS cc_start: 0.6335 (tmmt) cc_final: 0.5824 (mtmt) REVERT: B 947 ASP cc_start: 0.7204 (OUTLIER) cc_final: 0.6480 (m-30) REVERT: B 974 MET cc_start: 0.7101 (ppp) cc_final: 0.6858 (ppp) REVERT: C 225 GLU cc_start: 0.7181 (pt0) cc_final: 0.6945 (tt0) REVERT: C 498 GLN cc_start: 0.7147 (mt0) cc_final: 0.6524 (mt0) REVERT: D 237 ILE cc_start: 0.8474 (mm) cc_final: 0.8267 (mm) REVERT: D 451 LYS cc_start: 0.7159 (mmtt) cc_final: 0.6811 (mmmt) REVERT: D 498 GLN cc_start: 0.6913 (tt0) cc_final: 0.6246 (tp40) REVERT: D 516 MET cc_start: 0.7343 (OUTLIER) cc_final: 0.6946 (tmm) REVERT: D 580 ASP cc_start: 0.6802 (m-30) cc_final: 0.6000 (t0) outliers start: 38 outliers final: 15 residues processed: 192 average time/residue: 0.5067 time to fit residues: 109.0584 Evaluate side-chains 181 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 947 ASP Chi-restraints excluded: chain B residue 997 ARG Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 516 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 30 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 167 optimal weight: 8.9990 chunk 123 optimal weight: 9.9990 chunk 122 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 chunk 155 optimal weight: 0.7980 chunk 101 optimal weight: 0.9980 chunk 148 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 GLN ** B 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 GLN D 226 GLN D 243 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.157138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.120055 restraints weight = 17413.998| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.90 r_work: 0.2972 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15099 Z= 0.120 Angle : 0.508 8.587 20478 Z= 0.261 Chirality : 0.039 0.193 2282 Planarity : 0.003 0.052 2521 Dihedral : 12.432 153.343 2113 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.94 % Allowed : 15.79 % Favored : 82.27 % 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: 1.50 (0.20), residues: 1773 helix: 1.78 (0.15), residues: 1089 sheet: -0.76 (0.60), residues: 55 loop : -0.16 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 220 TYR 0.022 0.001 TYR A 543 PHE 0.013 0.001 PHE C 298 TRP 0.029 0.001 TRP A 442 HIS 0.004 0.001 HIS B 803 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (15099) covalent geometry : angle 0.50803 / 0.26 (20478) hydrogen bonds : bond 0.03784 / 2.45 ( 888) hydrogen bonds : angle 4.24201 / 3.09 ( 2622) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 174 time to evaluate : 0.460 Fit side-chains REVERT: A 234 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8103 (tm) REVERT: A 415 ASP cc_start: 0.8183 (m-30) cc_final: 0.7877 (m-30) REVERT: A 423 PHE cc_start: 0.7971 (t80) cc_final: 0.7595 (t80) REVERT: A 592 LYS cc_start: 0.6808 (tppt) cc_final: 0.6148 (tptt) REVERT: A 594 MET cc_start: 0.5991 (mtm) cc_final: 0.5620 (mmm) REVERT: B 665 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7802 (mmm) REVERT: B 694 MET cc_start: 0.8127 (mmm) cc_final: 0.7782 (tpt) REVERT: B 739 LYS cc_start: 0.6355 (tmmt) cc_final: 0.5803 (mtmm) REVERT: B 946 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7897 (tm) REVERT: C 225 GLU cc_start: 0.7203 (pt0) cc_final: 0.6960 (tt0) REVERT: C 411 GLN cc_start: 0.8173 (mm-40) cc_final: 0.7861 (tp-100) REVERT: C 498 GLN cc_start: 0.7119 (mt0) cc_final: 0.6486 (mt0) REVERT: D 451 LYS cc_start: 0.7173 (mmtt) cc_final: 0.6817 (mmmt) REVERT: D 498 GLN cc_start: 0.6909 (tt0) cc_final: 0.6228 (tp40) REVERT: D 516 MET cc_start: 0.7376 (OUTLIER) cc_final: 0.6971 (tmm) REVERT: D 580 ASP cc_start: 0.6861 (m-30) cc_final: 0.6040 (t0) outliers start: 31 outliers final: 17 residues processed: 187 average time/residue: 0.5030 time to fit residues: 105.3873 Evaluate side-chains 186 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 930 MET Chi-restraints excluded: chain B residue 946 LEU Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 403 MET Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 516 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 6 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 chunk 154 optimal weight: 0.3980 chunk 51 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 157 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 GLN ** B 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 GLN D 226 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.157976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.121013 restraints weight = 17521.295| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.89 r_work: 0.3001 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15099 Z= 0.114 Angle : 0.506 9.722 20478 Z= 0.259 Chirality : 0.039 0.187 2282 Planarity : 0.003 0.051 2521 Dihedral : 12.399 153.212 2113 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.69 % Allowed : 16.35 % Favored : 81.96 % 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: 1.57 (0.20), residues: 1773 helix: 1.83 (0.15), residues: 1090 sheet: -0.97 (0.60), residues: 57 loop : -0.10 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 407 TYR 0.022 0.001 TYR C 543 PHE 0.025 0.001 PHE B 906 TRP 0.029 0.001 TRP A 442 HIS 0.003 0.001 HIS B 803 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (15099) covalent geometry : angle 0.50591 / 0.26 (20478) hydrogen bonds : bond 0.03696 / 2.39 ( 888) hydrogen bonds : angle 4.18681 / 3.05 ( 2622) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 0.604 Fit side-chains TARDY: cannot create tardy model for: "VAL C 156 " (corrupted residue). Skipping it. REVERT: A 234 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8112 (tm) REVERT: A 415 ASP cc_start: 0.8184 (m-30) cc_final: 0.7904 (m-30) REVERT: A 423 PHE cc_start: 0.7957 (t80) cc_final: 0.7589 (t80) REVERT: A 592 LYS cc_start: 0.6819 (tppt) cc_final: 0.6170 (tptt) REVERT: A 594 MET cc_start: 0.5993 (mtm) cc_final: 0.5667 (tmm) REVERT: B 694 MET cc_start: 0.8059 (mmm) cc_final: 0.7720 (tpt) REVERT: B 739 LYS cc_start: 0.6358 (tmmt) cc_final: 0.5796 (mtmm) REVERT: B 1033 LEU cc_start: 0.7562 (mt) cc_final: 0.7331 (mm) REVERT: C 182 MET cc_start: 0.9034 (mmm) cc_final: 0.8736 (mmm) REVERT: C 225 GLU cc_start: 0.7163 (pt0) cc_final: 0.6936 (tt0) REVERT: C 411 GLN cc_start: 0.8140 (mm-40) cc_final: 0.7806 (tp-100) REVERT: C 498 GLN cc_start: 0.7074 (mt0) cc_final: 0.6481 (mt0) REVERT: D 226 GLN cc_start: 0.7431 (OUTLIER) cc_final: 0.7009 (tp40) REVERT: D 451 LYS cc_start: 0.7198 (mmtt) cc_final: 0.6794 (mmmt) REVERT: D 498 GLN cc_start: 0.6891 (tt0) cc_final: 0.6195 (tp40) REVERT: D 516 MET cc_start: 0.7363 (OUTLIER) cc_final: 0.6972 (tmm) REVERT: D 580 ASP cc_start: 0.6830 (m-30) cc_final: 0.6052 (t0) outliers start: 27 outliers final: 16 residues processed: 176 average time/residue: 0.5190 time to fit residues: 102.4134 Evaluate side-chains 180 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 161 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 930 MET Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 516 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 7 optimal weight: 10.0000 chunk 42 optimal weight: 0.1980 chunk 29 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 166 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 GLN ** B 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.157988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.120744 restraints weight = 17394.711| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.91 r_work: 0.2983 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15099 Z= 0.117 Angle : 0.522 12.442 20478 Z= 0.265 Chirality : 0.039 0.188 2282 Planarity : 0.003 0.050 2521 Dihedral : 12.397 153.356 2113 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.56 % Allowed : 16.79 % Favored : 81.65 % 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: 1.57 (0.20), residues: 1773 helix: 1.84 (0.15), residues: 1084 sheet: -0.93 (0.61), residues: 57 loop : -0.09 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 407 TYR 0.022 0.001 TYR A 543 PHE 0.023 0.001 PHE B 906 TRP 0.031 0.001 TRP A 442 HIS 0.004 0.001 HIS B 803 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (15099) covalent geometry : angle 0.52201 / 0.26 (20478) hydrogen bonds : bond 0.03705 / 2.40 ( 888) hydrogen bonds : angle 4.19867 / 3.05 ( 2622) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 0.617 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "VAL C 156 " (corrupted residue). Skipping it. REVERT: A 234 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8052 (tm) REVERT: A 415 ASP cc_start: 0.8164 (m-30) cc_final: 0.7861 (m-30) REVERT: A 423 PHE cc_start: 0.7932 (t80) cc_final: 0.7559 (t80) REVERT: A 592 LYS cc_start: 0.6793 (tppt) cc_final: 0.6142 (tptt) REVERT: A 594 MET cc_start: 0.6026 (mtm) cc_final: 0.5657 (tmm) REVERT: B 694 MET cc_start: 0.8030 (mmm) cc_final: 0.7689 (tpt) REVERT: B 739 LYS cc_start: 0.6273 (tmmt) cc_final: 0.5706 (mtmm) REVERT: B 777 SER cc_start: 0.7936 (m) cc_final: 0.7605 (t) REVERT: B 974 MET cc_start: 0.7109 (ppp) cc_final: 0.6676 (pp-130) REVERT: B 1033 LEU cc_start: 0.7389 (mt) cc_final: 0.7139 (mm) REVERT: B 1078 LYS cc_start: 0.5961 (tttt) cc_final: 0.5243 (pptt) REVERT: C 182 MET cc_start: 0.9058 (mmm) cc_final: 0.8752 (mmm) REVERT: C 225 GLU cc_start: 0.7182 (pt0) cc_final: 0.6957 (tt0) REVERT: C 411 GLN cc_start: 0.8045 (mm-40) cc_final: 0.7764 (tp-100) REVERT: C 498 GLN cc_start: 0.7028 (mt0) cc_final: 0.6422 (mt0) REVERT: D 226 GLN cc_start: 0.7353 (OUTLIER) cc_final: 0.6916 (tp40) REVERT: D 407 ARG cc_start: 0.5481 (ttm170) cc_final: 0.5274 (ttt-90) REVERT: D 451 LYS cc_start: 0.7180 (mmtt) cc_final: 0.6752 (mmmt) REVERT: D 498 GLN cc_start: 0.6858 (tt0) cc_final: 0.6112 (tp40) REVERT: D 516 MET cc_start: 0.7324 (OUTLIER) cc_final: 0.6920 (tmm) REVERT: D 580 ASP cc_start: 0.6831 (m-30) cc_final: 0.6058 (t0) outliers start: 25 outliers final: 15 residues processed: 179 average time/residue: 0.5185 time to fit residues: 104.4163 Evaluate side-chains 181 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 930 MET Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 516 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 169 optimal weight: 0.9990 chunk 139 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 chunk 35 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 134 optimal weight: 0.5980 chunk 21 optimal weight: 0.0870 chunk 78 optimal weight: 0.9990 chunk 156 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 GLN ** B 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 GLN D 498 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.158372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.120993 restraints weight = 17388.873| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.89 r_work: 0.3007 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15099 Z= 0.111 Angle : 0.522 15.122 20478 Z= 0.263 Chirality : 0.039 0.187 2282 Planarity : 0.003 0.049 2521 Dihedral : 12.382 153.307 2113 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.31 % Allowed : 17.04 % Favored : 81.65 % 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: 1.59 (0.20), residues: 1773 helix: 1.85 (0.15), residues: 1084 sheet: -0.89 (0.61), residues: 57 loop : -0.09 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 220 TYR 0.023 0.001 TYR C 543 PHE 0.023 0.001 PHE B 906 TRP 0.030 0.001 TRP A 442 HIS 0.004 0.001 HIS C 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (15099) covalent geometry : angle 0.52196 / 0.26 (20478) hydrogen bonds : bond 0.03663 / 2.37 ( 888) hydrogen bonds : angle 4.18049 / 3.04 ( 2622) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4571.96 seconds wall clock time: 78 minutes 48.84 seconds (4728.84 seconds total)