Starting phenix.real_space_refine on Wed Mar 4 16:08:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rhj_24463/03_2026/7rhj_24463.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rhj_24463/03_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_24463/03_2026/7rhj_24463.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rhj_24463/03_2026/7rhj_24463.map" model { file = "/net/cci-nas-00/data/ceres_data/7rhj_24463/03_2026/7rhj_24463.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rhj_24463/03_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.72, per 1000 atoms: 0.25 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: 1.27 Conformation dependent library (CDL) restraints added in 539.9 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: 2.49 Time building geometry restraints manager: 1.69 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: 8732 29.03 - 58.07: 269 58.07 - 87.10: 16 87.10 - 116.14: 2 116.14 - 145.17: 15 Dihedral angle restraints: 9034 sinusoidal: 3773 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 9031 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: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.910 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 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 : 15.050 145.171 5664 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 covalent geometry : bond 0.00464 (15099) covalent geometry : angle 0.80015 (20478) hydrogen bonds : bond 0.12441 ( 888) hydrogen bonds : angle 5.96342 ( 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 : 0.567 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: 0.6030 time to fit residues: 143.7408 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 : 0.600 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3807 r_free = 0.3807 target = 0.157755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.120087 restraints weight = 17491.089| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.94 r_work: 0.2996 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1265 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= 0.162 Angle : 0.548 12.666 20478 Z= 0.285 Chirality : 0.041 0.167 2282 Planarity : 0.004 0.064 2521 Dihedral : 12.661 152.622 2139 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.81 % Allowed : 8.80 % Favored : 89.39 % 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: 0.78 (0.19), residues: 1773 helix: 1.18 (0.15), residues: 1081 sheet: -1.16 (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 0.019 0.002 TYR D 349 PHE 0.025 0.001 PHE D 410 TRP 0.020 0.002 TRP A 442 HIS 0.004 0.001 HIS B 803 Details of bonding type rmsd covalent geometry : bond 0.00367 (15099) covalent geometry : angle 0.54790 (20478) hydrogen bonds : bond 0.04307 ( 888) hydrogen bonds : angle 4.54901 ( 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 216 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 0.625 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: 0.9093 (mmm) cc_final: 0.8822 (mmm) REVERT: A 234 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8090 (tm) REVERT: A 341 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8179 (mm-30) REVERT: A 423 PHE cc_start: 0.7901 (t80) cc_final: 0.7548 (t80) REVERT: B 665 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7584 (mmm) REVERT: B 694 MET cc_start: 0.8159 (mmm) cc_final: 0.7847 (tpp) REVERT: B 699 ASP cc_start: 0.7604 (m-30) cc_final: 0.7341 (m-30) REVERT: B 974 MET cc_start: 0.7196 (ppp) cc_final: 0.6787 (ppp) REVERT: C 415 ASP cc_start: 0.8263 (m-30) cc_final: 0.8048 (m-30) REVERT: C 498 GLN cc_start: 0.7206 (mt0) cc_final: 0.6959 (mt0) REVERT: D 498 GLN cc_start: 0.6814 (tt0) cc_final: 0.6305 (tp40) REVERT: D 580 ASP cc_start: 0.6872 (m-30) cc_final: 0.5895 (t0) outliers start: 29 outliers final: 12 residues processed: 200 average time/residue: 0.5454 time to fit residues: 121.6861 Evaluate side-chains 187 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 172 time to evaluate : 0.550 ------------------------------------------------------------------------------- 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: 1.9990 chunk 19 optimal weight: 2.9990 chunk 64 optimal weight: 0.4980 chunk 160 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 128 optimal weight: 9.9990 chunk 127 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 496 GLN B 689 HIS D 226 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.157709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.120194 restraints weight = 17655.094| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.11 r_work: 0.2979 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15099 Z= 0.140 Angle : 0.503 8.853 20478 Z= 0.263 Chirality : 0.039 0.184 2282 Planarity : 0.004 0.059 2521 Dihedral : 12.513 153.234 2139 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.50 % Allowed : 10.42 % Favored : 87.08 % 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: 1.08 (0.19), residues: 1773 helix: 1.46 (0.15), residues: 1089 sheet: -1.28 (0.62), residues: 59 loop : -0.29 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 220 TYR 0.017 0.001 TYR C 543 PHE 0.018 0.001 PHE D 410 TRP 0.020 0.002 TRP D 168 HIS 0.004 0.001 HIS B 803 Details of bonding type rmsd covalent geometry : bond 0.00315 (15099) covalent geometry : angle 0.50283 (20478) hydrogen bonds : bond 0.04056 ( 888) hydrogen bonds : angle 4.34240 ( 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 223 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 183 time to evaluate : 0.608 Fit side-chains TARDY: cannot create tardy model for: "VAL C 156 " (corrupted residue). Skipping it. REVERT: A 182 MET cc_start: 0.9054 (mmm) cc_final: 0.8778 (mmm) REVERT: A 234 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8094 (tm) REVERT: A 341 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8241 (mm-30) REVERT: A 415 ASP cc_start: 0.8248 (m-30) cc_final: 0.7848 (m-30) REVERT: A 423 PHE cc_start: 0.7977 (t80) cc_final: 0.7750 (t80) REVERT: A 433 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7521 (ttp80) REVERT: A 594 MET cc_start: 0.6106 (tmm) cc_final: 0.5761 (mtt) REVERT: B 651 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7647 (mm) REVERT: B 665 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7776 (mmm) REVERT: B 694 MET cc_start: 0.8171 (mmm) cc_final: 0.7853 (tpt) REVERT: B 699 ASP cc_start: 0.7582 (m-30) cc_final: 0.7364 (m-30) REVERT: B 947 ASP cc_start: 0.7188 (OUTLIER) cc_final: 0.6410 (m-30) REVERT: B 970 MET cc_start: 0.6200 (ttt) cc_final: 0.5928 (ttt) REVERT: B 974 MET cc_start: 0.7160 (ppp) cc_final: 0.6712 (ppp) REVERT: B 994 GLU cc_start: 0.7386 (tt0) cc_final: 0.6343 (pt0) REVERT: B 1078 LYS cc_start: 0.5811 (tttt) cc_final: 0.5161 (pptt) REVERT: C 289 GLU cc_start: 0.8517 (tt0) cc_final: 0.8013 (pt0) REVERT: C 498 GLN cc_start: 0.7260 (mt0) cc_final: 0.6871 (mt0) REVERT: D 464 GLU cc_start: 0.6283 (OUTLIER) cc_final: 0.5979 (tp30) REVERT: D 580 ASP cc_start: 0.6706 (m-30) cc_final: 0.5897 (t0) outliers start: 40 outliers final: 13 residues processed: 205 average time/residue: 0.5653 time to fit residues: 128.9817 Evaluate side-chains 189 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 0.582 ------------------------------------------------------------------------------- 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 651 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 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 464 GLU Chi-restraints excluded: chain D residue 467 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 53 optimal weight: 0.6980 chunk 95 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 38 optimal weight: 10.0000 chunk 128 optimal weight: 20.0000 chunk 39 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 496 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.157032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.119625 restraints weight = 17645.642| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.10 r_work: 0.2981 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1699 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= 0.133 Angle : 0.490 7.344 20478 Z= 0.256 Chirality : 0.039 0.179 2282 Planarity : 0.003 0.057 2521 Dihedral : 12.460 153.098 2137 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.37 % Allowed : 12.36 % Favored : 85.27 % 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: 1.31 (0.20), residues: 1773 helix: 1.65 (0.15), residues: 1089 sheet: -1.00 (0.66), residues: 51 loop : -0.26 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 220 TYR 0.020 0.001 TYR A 543 PHE 0.015 0.001 PHE C 298 TRP 0.021 0.001 TRP A 442 HIS 0.004 0.001 HIS B 803 Details of bonding type rmsd covalent geometry : bond 0.00299 (15099) covalent geometry : angle 0.48986 (20478) hydrogen bonds : bond 0.03916 ( 888) hydrogen bonds : angle 4.26258 ( 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 221 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 183 time to evaluate : 0.576 Fit side-chains TARDY: cannot create tardy model for: "VAL C 156 " (corrupted residue). Skipping it. REVERT: A 182 MET cc_start: 0.9063 (mmm) cc_final: 0.8820 (mmm) REVERT: A 234 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8114 (tm) REVERT: A 341 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8279 (mm-30) REVERT: A 415 ASP cc_start: 0.8255 (m-30) cc_final: 0.7909 (m-30) REVERT: A 423 PHE cc_start: 0.7995 (t80) cc_final: 0.7745 (t80) REVERT: A 433 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7554 (ttp80) REVERT: A 592 LYS cc_start: 0.6805 (tppt) cc_final: 0.6033 (tptt) REVERT: A 594 MET cc_start: 0.6136 (OUTLIER) cc_final: 0.5753 (mtm) REVERT: B 665 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7814 (mmm) REVERT: B 694 MET cc_start: 0.8160 (mmm) cc_final: 0.7809 (tpt) REVERT: B 699 ASP cc_start: 0.7623 (m-30) cc_final: 0.7411 (m-30) REVERT: B 739 LYS cc_start: 0.6216 (tmmt) cc_final: 0.5861 (mtmm) REVERT: B 947 ASP cc_start: 0.7168 (OUTLIER) cc_final: 0.6515 (m-30) REVERT: B 974 MET cc_start: 0.7232 (ppp) cc_final: 0.6810 (ppp) REVERT: B 1078 LYS cc_start: 0.6059 (tttt) cc_final: 0.5329 (pptt) REVERT: C 182 MET cc_start: 0.9035 (mmm) cc_final: 0.8790 (mmm) REVERT: C 226 GLN cc_start: 0.7464 (mm-40) cc_final: 0.7249 (mm110) REVERT: C 411 GLN cc_start: 0.8254 (mm-40) cc_final: 0.7777 (tp-100) REVERT: C 498 GLN cc_start: 0.7306 (mt0) cc_final: 0.6946 (mt0) REVERT: C 516 MET cc_start: 0.6856 (OUTLIER) cc_final: 0.6437 (ppp) REVERT: C 543 TYR cc_start: 0.8249 (p90) cc_final: 0.8028 (p90) REVERT: D 451 LYS cc_start: 0.7147 (mmtt) cc_final: 0.6750 (mmmt) REVERT: D 464 GLU cc_start: 0.6372 (OUTLIER) cc_final: 0.6074 (tp30) REVERT: D 498 GLN cc_start: 0.6889 (tt0) cc_final: 0.6250 (tp40) REVERT: D 580 ASP cc_start: 0.6645 (m-30) cc_final: 0.5891 (t0) outliers start: 38 outliers final: 13 residues processed: 203 average time/residue: 0.5682 time to fit residues: 128.5722 Evaluate side-chains 193 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 172 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 575 CYS Chi-restraints excluded: chain A residue 594 MET 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 782 ILE Chi-restraints excluded: chain B residue 930 MET Chi-restraints excluded: chain B residue 947 ASP 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 Chi-restraints excluded: chain D residue 464 GLU 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: 0.9990 chunk 78 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 chunk 174 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 129 optimal weight: 8.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 496 GLN ** B 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3783 r_free = 0.3783 target = 0.155825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.119005 restraints weight = 17396.090| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.17 r_work: 0.2951 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1938 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= 0.184 Angle : 0.530 7.013 20478 Z= 0.277 Chirality : 0.041 0.174 2282 Planarity : 0.004 0.058 2521 Dihedral : 12.503 154.520 2137 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.00 % Allowed : 12.61 % Favored : 84.39 % 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: 1.25 (0.19), residues: 1773 helix: 1.58 (0.15), residues: 1090 sheet: -1.06 (0.61), residues: 59 loop : -0.25 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 347 TYR 0.019 0.002 TYR C 351 PHE 0.018 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 covalent geometry : bond 0.00424 (15099) covalent geometry : angle 0.52989 (20478) hydrogen bonds : bond 0.04190 ( 888) hydrogen bonds : angle 4.38322 ( 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 227 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 179 time to evaluate : 0.570 Fit side-chains REVERT: A 182 MET cc_start: 0.9113 (mmm) cc_final: 0.8831 (mmm) REVERT: A 234 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8071 (tm) REVERT: A 341 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.7849 (mp0) REVERT: A 399 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8200 (mtp) REVERT: A 415 ASP cc_start: 0.8198 (m-30) cc_final: 0.7822 (m-30) REVERT: A 423 PHE cc_start: 0.7971 (t80) cc_final: 0.7717 (t80) REVERT: B 651 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7648 (mm) REVERT: B 665 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.7854 (mmm) REVERT: B 739 LYS cc_start: 0.6331 (tmmt) cc_final: 0.5780 (mtmm) REVERT: B 947 ASP cc_start: 0.7263 (OUTLIER) cc_final: 0.6505 (m-30) REVERT: B 994 GLU cc_start: 0.7570 (tt0) cc_final: 0.6484 (pt0) REVERT: B 1078 LYS cc_start: 0.5993 (tttt) cc_final: 0.5286 (pptt) REVERT: C 226 GLN cc_start: 0.7510 (mm-40) cc_final: 0.7304 (mm110) REVERT: C 415 ASP cc_start: 0.8170 (m-30) cc_final: 0.7961 (m-30) REVERT: C 498 GLN cc_start: 0.7260 (mt0) cc_final: 0.6551 (mt0) REVERT: C 516 MET cc_start: 0.6767 (OUTLIER) cc_final: 0.6512 (ppp) REVERT: C 543 TYR cc_start: 0.8246 (p90) cc_final: 0.7988 (p90) REVERT: D 451 LYS cc_start: 0.7164 (mmtt) cc_final: 0.6728 (mmmt) REVERT: D 459 ASP cc_start: 0.6934 (m-30) cc_final: 0.6715 (m-30) REVERT: D 498 GLN cc_start: 0.6890 (tt0) cc_final: 0.6241 (tp40) REVERT: D 572 ASP cc_start: 0.7732 (OUTLIER) cc_final: 0.7247 (m-30) REVERT: D 580 ASP cc_start: 0.6739 (m-30) cc_final: 0.5918 (t0) outliers start: 48 outliers final: 15 residues processed: 207 average time/residue: 0.5658 time to fit residues: 129.9586 Evaluate side-chains 193 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 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 B residue 651 LEU 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 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 Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 572 ASP 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: 3.9990 chunk 31 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 110 optimal weight: 0.6980 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 496 GLN ** B 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 816 GLN ** B 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 411 GLN D 226 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.153719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.116340 restraints weight = 17383.700| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.13 r_work: 0.2886 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 15099 Z= 0.240 Angle : 0.587 9.982 20478 Z= 0.304 Chirality : 0.043 0.173 2282 Planarity : 0.004 0.060 2521 Dihedral : 12.618 156.000 2137 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.37 % Allowed : 13.36 % Favored : 83.27 % 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: 1.14 (0.19), residues: 1773 helix: 1.48 (0.15), residues: 1084 sheet: -0.88 (0.62), residues: 57 loop : -0.27 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 347 TYR 0.021 0.002 TYR C 351 PHE 0.021 0.002 PHE D 298 TRP 0.027 0.002 TRP A 442 HIS 0.007 0.001 HIS B 803 Details of bonding type rmsd covalent geometry : bond 0.00560 (15099) covalent geometry : angle 0.58692 (20478) hydrogen bonds : bond 0.04508 ( 888) hydrogen bonds : angle 4.54716 ( 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 223 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 169 time to evaluate : 0.644 Fit side-chains REVERT: A 234 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8050 (tm) REVERT: A 244 LEU cc_start: 0.8666 (tt) cc_final: 0.8390 (tp) REVERT: A 341 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.7917 (mp0) REVERT: A 399 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.8281 (mtp) REVERT: A 415 ASP cc_start: 0.8210 (m-30) cc_final: 0.7845 (m-30) REVERT: A 423 PHE cc_start: 0.8022 (t80) cc_final: 0.7721 (t80) REVERT: B 665 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.7863 (mmm) REVERT: B 739 LYS cc_start: 0.6322 (tmmt) cc_final: 0.5643 (mtmm) REVERT: B 946 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7858 (tm) REVERT: B 974 MET cc_start: 0.7114 (ppp) cc_final: 0.6325 (pp-130) REVERT: B 978 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7255 (mp) REVERT: B 994 GLU cc_start: 0.7655 (tt0) cc_final: 0.6571 (pt0) REVERT: B 998 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6940 (pt0) REVERT: B 1078 LYS cc_start: 0.6017 (tttt) cc_final: 0.5342 (pptt) REVERT: C 403 MET cc_start: 0.8170 (OUTLIER) cc_final: 0.7935 (mtp) REVERT: C 411 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7869 (mm-40) REVERT: C 498 GLN cc_start: 0.7160 (mt0) cc_final: 0.6459 (mt0) REVERT: C 516 MET cc_start: 0.6783 (OUTLIER) cc_final: 0.6563 (ppp) REVERT: C 543 TYR cc_start: 0.8237 (p90) cc_final: 0.7959 (p90) REVERT: D 498 GLN cc_start: 0.6927 (tt0) cc_final: 0.6264 (tp40) REVERT: D 572 ASP cc_start: 0.7775 (OUTLIER) cc_final: 0.7274 (m-30) REVERT: D 580 ASP cc_start: 0.6879 (m-30) cc_final: 0.6015 (t0) outliers start: 54 outliers final: 19 residues processed: 196 average time/residue: 0.5560 time to fit residues: 120.9490 Evaluate side-chains 192 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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 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 A residue 575 CYS Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 731 ASN Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 930 MET Chi-restraints excluded: chain B residue 946 LEU Chi-restraints excluded: chain B residue 978 LEU Chi-restraints excluded: chain B residue 997 ARG Chi-restraints excluded: chain B residue 998 GLU Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 411 GLN 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: 2.9990 chunk 122 optimal weight: 4.9990 chunk 136 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 128 optimal weight: 20.0000 chunk 132 optimal weight: 10.0000 chunk 89 optimal weight: 0.7980 chunk 37 optimal weight: 7.9990 chunk 172 optimal weight: 0.7980 chunk 168 optimal weight: 3.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 496 GLN B 653 ASN ** B 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 GLN C 411 GLN D 226 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.155645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.119149 restraints weight = 17326.647| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.13 r_work: 0.2931 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2185 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= 0.143 Angle : 0.524 8.470 20478 Z= 0.271 Chirality : 0.040 0.184 2282 Planarity : 0.004 0.056 2521 Dihedral : 12.516 154.024 2137 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.75 % Allowed : 15.17 % Favored : 82.08 % 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: 1.25 (0.19), residues: 1773 helix: 1.59 (0.15), residues: 1089 sheet: -0.89 (0.62), residues: 57 loop : -0.28 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 220 TYR 0.014 0.001 TYR C 351 PHE 0.015 0.001 PHE C 298 TRP 0.026 0.002 TRP A 442 HIS 0.004 0.001 HIS B 803 Details of bonding type rmsd covalent geometry : bond 0.00324 (15099) covalent geometry : angle 0.52410 (20478) hydrogen bonds : bond 0.04074 ( 888) hydrogen bonds : angle 4.38170 ( 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 207 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 163 time to evaluate : 0.585 Fit side-chains REVERT: A 234 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8086 (tm) REVERT: A 341 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8372 (mm-30) REVERT: A 415 ASP cc_start: 0.8236 (m-30) cc_final: 0.7887 (m-30) REVERT: A 423 PHE cc_start: 0.8005 (t80) cc_final: 0.7725 (t80) REVERT: B 665 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.7877 (mmm) REVERT: B 739 LYS cc_start: 0.6432 (tmmt) cc_final: 0.5878 (ttmt) REVERT: B 998 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6963 (pt0) REVERT: C 226 GLN cc_start: 0.7413 (mm-40) cc_final: 0.7193 (mm110) REVERT: C 411 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7887 (tp-100) REVERT: C 498 GLN cc_start: 0.7183 (mt0) cc_final: 0.6552 (mt0) REVERT: C 516 MET cc_start: 0.6649 (OUTLIER) cc_final: 0.6445 (ppp) REVERT: C 543 TYR cc_start: 0.8236 (p90) cc_final: 0.7951 (p90) REVERT: D 237 ILE cc_start: 0.8531 (mm) cc_final: 0.8310 (mm) REVERT: D 451 LYS cc_start: 0.7178 (mmtt) cc_final: 0.6808 (mmmt) REVERT: D 498 GLN cc_start: 0.6923 (tt0) cc_final: 0.6271 (tp40) REVERT: D 516 MET cc_start: 0.7403 (OUTLIER) cc_final: 0.7006 (tmm) REVERT: D 580 ASP cc_start: 0.6908 (m-30) cc_final: 0.6078 (t0) outliers start: 44 outliers final: 15 residues processed: 190 average time/residue: 0.5374 time to fit residues: 114.1180 Evaluate side-chains 183 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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 341 GLU 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 731 ASN Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 997 ARG Chi-restraints excluded: chain B residue 998 GLU Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 411 GLN Chi-restraints excluded: chain C residue 499 VAL 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 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: 1.9990 chunk 54 optimal weight: 3.9990 chunk 167 optimal weight: 6.9990 chunk 123 optimal weight: 20.0000 chunk 122 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 chunk 101 optimal weight: 0.5980 chunk 148 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 496 GLN ** B 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 411 GLN D 226 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.156940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.119069 restraints weight = 17421.068| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.05 r_work: 0.2970 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2156 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= 0.127 Angle : 0.518 8.729 20478 Z= 0.265 Chirality : 0.039 0.179 2282 Planarity : 0.003 0.054 2521 Dihedral : 12.461 153.248 2137 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.18 % Allowed : 15.92 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.20), residues: 1773 helix: 1.70 (0.15), residues: 1088 sheet: -0.69 (0.61), residues: 55 loop : -0.23 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 220 TYR 0.020 0.001 TYR D 420 PHE 0.013 0.001 PHE C 298 TRP 0.028 0.002 TRP A 442 HIS 0.004 0.001 HIS B 803 Details of bonding type rmsd covalent geometry : bond 0.00287 (15099) covalent geometry : angle 0.51776 (20478) hydrogen bonds : bond 0.03917 ( 888) hydrogen bonds : angle 4.29504 ( 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 200 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 165 time to evaluate : 0.686 Fit side-chains REVERT: A 234 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8118 (tm) REVERT: A 341 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8328 (mm-30) REVERT: A 415 ASP cc_start: 0.8206 (m-30) cc_final: 0.7861 (m-30) REVERT: A 423 PHE cc_start: 0.8012 (t80) cc_final: 0.7737 (t80) REVERT: B 665 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.7828 (mmm) REVERT: B 739 LYS cc_start: 0.6464 (tmmt) cc_final: 0.5859 (mtmm) REVERT: C 226 GLN cc_start: 0.7500 (mm-40) cc_final: 0.7268 (mm110) REVERT: C 411 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7941 (tp-100) REVERT: C 498 GLN cc_start: 0.7197 (mt0) cc_final: 0.6551 (mt0) REVERT: C 543 TYR cc_start: 0.8234 (p90) cc_final: 0.7932 (p90) REVERT: D 451 LYS cc_start: 0.7204 (mmtt) cc_final: 0.6827 (mmmt) REVERT: D 498 GLN cc_start: 0.6932 (tt0) cc_final: 0.6285 (tp40) REVERT: D 516 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.7032 (tmm) REVERT: D 580 ASP cc_start: 0.6882 (m-30) cc_final: 0.6058 (t0) outliers start: 35 outliers final: 12 residues processed: 185 average time/residue: 0.5443 time to fit residues: 112.1701 Evaluate side-chains 178 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 0.571 ------------------------------------------------------------------------------- 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 341 GLU 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 C residue 202 ILE Chi-restraints excluded: chain C residue 411 GLN 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 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: 5.9990 chunk 31 optimal weight: 0.9990 chunk 87 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 154 optimal weight: 0.0070 chunk 51 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 157 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.7002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 496 GLN ** B 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 411 GLN D 226 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 = 0.3802 r_free = 0.3802 target = 0.157375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.119997 restraints weight = 17455.637| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.98 r_work: 0.2984 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2124 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 : 0.511 10.291 20478 Z= 0.260 Chirality : 0.039 0.184 2282 Planarity : 0.003 0.052 2521 Dihedral : 12.408 152.768 2137 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.69 % Allowed : 16.60 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.20), residues: 1773 helix: 1.80 (0.15), residues: 1088 sheet: -0.68 (0.61), residues: 55 loop : -0.18 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 413 TYR 0.019 0.001 TYR D 420 PHE 0.012 0.001 PHE B 870 TRP 0.027 0.001 TRP A 442 HIS 0.004 0.001 HIS B 803 Details of bonding type rmsd covalent geometry : bond 0.00253 (15099) covalent geometry : angle 0.51099 (20478) hydrogen bonds : bond 0.03780 ( 888) hydrogen bonds : angle 4.22524 ( 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 192 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 0.599 Fit side-chains REVERT: A 234 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8081 (tm) REVERT: A 415 ASP cc_start: 0.8169 (m-30) cc_final: 0.7855 (m-30) REVERT: A 423 PHE cc_start: 0.7968 (t80) cc_final: 0.7681 (t80) REVERT: B 665 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7796 (mmm) REVERT: B 739 LYS cc_start: 0.6354 (tmmt) cc_final: 0.5787 (mtmm) REVERT: B 1054 LEU cc_start: 0.8250 (pp) cc_final: 0.7599 (pt) REVERT: C 226 GLN cc_start: 0.7462 (mm-40) cc_final: 0.7211 (mm110) REVERT: C 411 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7723 (tp-100) REVERT: C 498 GLN cc_start: 0.7024 (mt0) cc_final: 0.6416 (mt0) REVERT: C 543 TYR cc_start: 0.8187 (p90) cc_final: 0.7898 (p90) REVERT: D 451 LYS cc_start: 0.7184 (mmtt) cc_final: 0.6795 (mmmt) REVERT: D 498 GLN cc_start: 0.6883 (tt0) cc_final: 0.6195 (tp40) REVERT: D 516 MET cc_start: 0.7331 (OUTLIER) cc_final: 0.6930 (tmm) REVERT: D 580 ASP cc_start: 0.6836 (m-30) cc_final: 0.6038 (t0) outliers start: 27 outliers final: 12 residues processed: 179 average time/residue: 0.5794 time to fit residues: 115.3145 Evaluate side-chains 173 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.552 ------------------------------------------------------------------------------- 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 C residue 202 ILE Chi-restraints excluded: chain C residue 411 GLN Chi-restraints excluded: chain D residue 281 MET Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 386 VAL 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: 0.0970 chunk 42 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 139 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 166 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 496 GLN ** B 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.157508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.120347 restraints weight = 17367.417| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.80 r_work: 0.3000 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15099 Z= 0.123 Angle : 0.523 12.454 20478 Z= 0.265 Chirality : 0.039 0.183 2282 Planarity : 0.003 0.052 2521 Dihedral : 12.393 153.018 2137 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.44 % Allowed : 17.35 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.20), residues: 1773 helix: 1.79 (0.15), residues: 1089 sheet: -0.65 (0.61), residues: 55 loop : -0.17 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 220 TYR 0.023 0.001 TYR A 543 PHE 0.024 0.001 PHE B 906 TRP 0.032 0.002 TRP A 442 HIS 0.004 0.001 HIS B 803 Details of bonding type rmsd covalent geometry : bond 0.00276 (15099) covalent geometry : angle 0.52346 (20478) hydrogen bonds : bond 0.03775 ( 888) hydrogen bonds : angle 4.23252 ( 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 181 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 0.633 Fit side-chains REVERT: A 234 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8112 (tm) REVERT: A 415 ASP cc_start: 0.8161 (m-30) cc_final: 0.7856 (m-30) REVERT: A 423 PHE cc_start: 0.7971 (t80) cc_final: 0.7686 (t80) REVERT: B 665 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7777 (mmm) REVERT: B 739 LYS cc_start: 0.6354 (tmmt) cc_final: 0.5780 (mtmm) REVERT: B 1054 LEU cc_start: 0.8253 (pp) cc_final: 0.7600 (pt) REVERT: C 226 GLN cc_start: 0.7536 (mm-40) cc_final: 0.7298 (mm110) REVERT: C 498 GLN cc_start: 0.7045 (mt0) cc_final: 0.6439 (mt0) REVERT: C 543 TYR cc_start: 0.8175 (p90) cc_final: 0.7881 (p90) REVERT: D 226 GLN cc_start: 0.7460 (OUTLIER) cc_final: 0.7051 (tp40) REVERT: D 451 LYS cc_start: 0.7181 (mmtt) cc_final: 0.6776 (mmmt) REVERT: D 498 GLN cc_start: 0.6886 (tt0) cc_final: 0.6208 (tp40) REVERT: D 580 ASP cc_start: 0.6862 (m-30) cc_final: 0.6112 (t0) outliers start: 23 outliers final: 13 residues processed: 172 average time/residue: 0.5609 time to fit residues: 107.5731 Evaluate side-chains 171 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 0.591 ------------------------------------------------------------------------------- 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 453 VAL 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 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 473 THR Chi-restraints excluded: chain D residue 492 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 169 optimal weight: 6.9990 chunk 139 optimal weight: 1.9990 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: 0.6980 chunk 21 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 496 GLN ** B 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.156892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.119016 restraints weight = 17386.358| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.02 r_work: 0.2963 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2176 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= 0.150 Angle : 0.543 15.126 20478 Z= 0.274 Chirality : 0.040 0.181 2282 Planarity : 0.004 0.054 2521 Dihedral : 12.416 153.674 2137 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.31 % Allowed : 17.48 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.20), residues: 1773 helix: 1.75 (0.15), residues: 1089 sheet: -0.63 (0.61), residues: 55 loop : -0.18 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 880 TYR 0.019 0.001 TYR D 420 PHE 0.022 0.001 PHE B 906 TRP 0.035 0.002 TRP A 442 HIS 0.005 0.001 HIS B 803 Details of bonding type rmsd covalent geometry : bond 0.00344 (15099) covalent geometry : angle 0.54321 (20478) hydrogen bonds : bond 0.03901 ( 888) hydrogen bonds : angle 4.27538 ( 2622) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5109.13 seconds wall clock time: 88 minutes 2.00 seconds (5282.00 seconds total)