Starting phenix.real_space_refine on Fri Jul 3 18:44:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k9v_62200/07_2026/9k9v_62200.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k9v_62200/07_2026/9k9v_62200.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k9v_62200/07_2026/9k9v_62200.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k9v_62200/07_2026/9k9v_62200.map" model { file = "/net/cci-nas-00/data/ceres_data/9k9v_62200/07_2026/9k9v_62200.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k9v_62200/07_2026/9k9v_62200.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2165 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 29 5.49 5 S 70 5.16 5 C 8806 2.51 5 N 2301 2.21 5 O 2663 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13869 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 8106 Classifications: {'peptide': 990} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 952} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1762 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 2} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 204} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 3389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3389 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 10, 'TRANS': 405} Chain breaks: 1 Chain: "P" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 345 Classifications: {'DNA': 17} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 16} Chain: "E" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 267 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Time building chain proxies: 2.65, per 1000 atoms: 0.19 Number of scatterers: 13869 At special positions: 0 Unit cell: (110.5, 124.95, 145.35, 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 70 16.00 P 29 15.00 O 2663 8.00 N 2301 7.00 C 8806 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: 1.03 Conformation dependent library (CDL) restraints added in 548.3 milliseconds 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3110 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 20 sheets defined 39.6% alpha, 20.2% beta 12 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 108 through 118 Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 209 through 220 removed outlier: 3.588A pdb=" N ILE A 213 " --> pdb=" O THR A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 253 Processing helix chain 'A' and resid 267 through 280 Processing helix chain 'A' and resid 331 through 339 removed outlier: 3.534A pdb=" N GLU A 339 " --> pdb=" O ILE A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 380 through 389 Processing helix chain 'A' and resid 439 through 446 removed outlier: 3.539A pdb=" N MET A 443 " --> pdb=" O ASP A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 474 removed outlier: 3.701A pdb=" N CYS A 466 " --> pdb=" O ASP A 462 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLN A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 487 Processing helix chain 'A' and resid 489 through 493 Processing helix chain 'A' and resid 502 through 514 Processing helix chain 'A' and resid 552 through 562 Processing helix chain 'A' and resid 564 through 566 No H-bonds generated for 'chain 'A' and resid 564 through 566' Processing helix chain 'A' and resid 576 through 591 Processing helix chain 'A' and resid 622 through 643 Processing helix chain 'A' and resid 646 through 665 Processing helix chain 'A' and resid 666 through 672 removed outlier: 3.590A pdb=" N GLY A 672 " --> pdb=" O TYR A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 703 Processing helix chain 'A' and resid 763 through 781 Processing helix chain 'A' and resid 837 through 854 removed outlier: 3.735A pdb=" N ASN A 841 " --> pdb=" O LYS A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 883 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.710A pdb=" N MET A 891 " --> pdb=" O GLU A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 918 removed outlier: 4.042A pdb=" N TYR A 909 " --> pdb=" O ASN A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 949 No H-bonds generated for 'chain 'A' and resid 947 through 949' Processing helix chain 'A' and resid 967 through 982 removed outlier: 4.003A pdb=" N TYR A 971 " --> pdb=" O PHE A 967 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU A 982 " --> pdb=" O GLU A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 998 Processing helix chain 'B' and resid 19 through 31 removed outlier: 4.215A pdb=" N SER B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N GLN B 25 " --> pdb=" O PRO B 21 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 26 " --> pdb=" O VAL B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 38 removed outlier: 3.540A pdb=" N LEU B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 86 through 101 Processing helix chain 'B' and resid 133 through 150 removed outlier: 5.472A pdb=" N LYS B 139 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ILE B 140 " --> pdb=" O TYR B 136 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS B 150 " --> pdb=" O GLN B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 170 removed outlier: 3.612A pdb=" N LYS B 169 " --> pdb=" O ASN B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 192 removed outlier: 3.820A pdb=" N HIS B 187 " --> pdb=" O ALA B 184 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN B 188 " --> pdb=" O ARG B 185 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N PHE B 189 " --> pdb=" O ASP B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 205 removed outlier: 3.613A pdb=" N ILE B 197 " --> pdb=" O ARG B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 214 Processing helix chain 'C' and resid 4 through 19 Processing helix chain 'C' and resid 24 through 42 Processing helix chain 'C' and resid 57 through 61 Processing helix chain 'C' and resid 107 through 121 removed outlier: 3.600A pdb=" N SER C 120 " --> pdb=" O LYS C 116 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASP C 121 " --> pdb=" O VAL C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 158 removed outlier: 4.197A pdb=" N ILE C 151 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYS C 153 " --> pdb=" O VAL C 149 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU C 154 " --> pdb=" O ASN C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 189 Processing helix chain 'C' and resid 249 through 256 Processing helix chain 'C' and resid 285 through 298 removed outlier: 3.506A pdb=" N LYS C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 324 Processing helix chain 'C' and resid 330 through 341 removed outlier: 3.541A pdb=" N SER C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 350 removed outlier: 3.604A pdb=" N ILE C 348 " --> pdb=" O VAL C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 361 Processing helix chain 'C' and resid 364 through 373 removed outlier: 3.626A pdb=" N ASN C 373 " --> pdb=" O ILE C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 396 Processing helix chain 'C' and resid 397 through 425 removed outlier: 4.325A pdb=" N ASN C 408 " --> pdb=" O TYR C 404 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N GLN C 409 " --> pdb=" O GLY C 405 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER C 412 " --> pdb=" O ASN C 408 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 134 removed outlier: 8.313A pdb=" N TYR A 140 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N PHE A 31 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N CYS A 142 " --> pdb=" O PHE A 31 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ARG A 33 " --> pdb=" O CYS A 142 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N PHE A 17 " --> pdb=" O GLU A 10 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N GLU A 10 " --> pdb=" O PHE A 17 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TYR A 19 " --> pdb=" O TRP A 8 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N TRP A 8 " --> pdb=" O TYR A 19 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LYS A 21 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N CYS A 124 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER A 126 " --> pdb=" O LYS A 151 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LYS A 151 " --> pdb=" O SER A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 43 removed outlier: 3.790A pdb=" N GLY A 61 " --> pdb=" O MET A 88 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N LEU A 90 " --> pdb=" O PRO A 59 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N GLU A 92 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ALA A 57 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N ILE A 516 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ARG A 64 " --> pdb=" O ILE A 516 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL A 518 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE A 66 " --> pdb=" O VAL A 518 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 222 through 223 removed outlier: 6.458A pdb=" N LEU A 222 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N VAL A 237 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N THR A 201 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N CYS A 239 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ILE A 203 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N SER A 184 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU A 165 " --> pdb=" O VAL A 260 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 285 through 287 Processing sheet with id=AA5, first strand: chain 'A' and resid 300 through 302 Processing sheet with id=AA6, first strand: chain 'A' and resid 355 through 362 removed outlier: 7.068A pdb=" N MET A 357 " --> pdb=" O ASP A 373 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ASP A 373 " --> pdb=" O MET A 357 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N THR A 369 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG A 407 " --> pdb=" O VAL A 418 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 732 through 734 removed outlier: 3.566A pdb=" N PHE A 743 " --> pdb=" O LEU A 707 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N SER A 747 " --> pdb=" O GLU A 758 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLU A 758 " --> pdb=" O SER A 747 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N TYR A 749 " --> pdb=" O PHE A 756 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL A 545 " --> pdb=" O VAL A 794 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL A 794 " --> pdb=" O VAL A 545 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE A 547 " --> pdb=" O GLU A 792 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LEU A 798 " --> pdb=" O THR A 807 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N THR A 807 " --> pdb=" O LEU A 798 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 568 through 574 removed outlier: 6.489A pdb=" N LEU A 568 " --> pdb=" O ASP A 616 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASP A 616 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY A 570 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLU A 611 " --> pdb=" O CYS A 601 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 892 through 895 removed outlier: 4.386A pdb=" N TYR A 929 " --> pdb=" O ILE A 954 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 892 through 895 Processing sheet with id=AB2, first strand: chain 'B' and resid 2 through 4 Processing sheet with id=AB3, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.858A pdb=" N CYS B 125 " --> pdb=" O SER B 43 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 116 through 120 removed outlier: 7.578A pdb=" N VAL B 62 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N TRP B 119 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL B 64 " --> pdb=" O TRP B 119 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N CYS B 63 " --> pdb=" O TYR B 156 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LEU B 155 " --> pdb=" O ILE B 177 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 107 through 108 Processing sheet with id=AB6, first strand: chain 'C' and resid 70 through 71 removed outlier: 3.839A pdb=" N THR C 174 " --> pdb=" O ILE C 71 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 166 through 169 removed outlier: 3.867A pdb=" N GLN C 208 " --> pdb=" O TYR C 199 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 95 through 97 removed outlier: 6.477A pdb=" N ILE C 124 " --> pdb=" O SER C 143 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N SER C 143 " --> pdb=" O ILE C 124 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N PHE C 126 " --> pdb=" O ALA C 141 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ALA C 141 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ARG C 128 " --> pdb=" O GLU C 139 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU C 139 " --> pdb=" O ARG C 128 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 233 through 239 removed outlier: 3.717A pdb=" N ILE C 234 " --> pdb=" O ASP C 226 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER C 222 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 302 through 303 removed outlier: 3.823A pdb=" N TYR C 302 " --> pdb=" O SER C 309 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 375 through 380 removed outlier: 3.642A pdb=" N ASN C 386 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLU C 380 " --> pdb=" O VAL C 384 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N VAL C 384 " --> pdb=" O GLU C 380 " (cutoff:3.500A) 573 hydrogen bonds defined for protein. 1620 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 26 hydrogen bonds 52 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 2.84 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3914 1.33 - 1.45: 2483 1.45 - 1.57: 7668 1.57 - 1.69: 57 1.69 - 1.81: 107 Bond restraints: 14229 Sorted by residual: bond pdb=" N LEU A 76 " pdb=" CA LEU A 76 " ideal model delta sigma weight residual 1.458 1.501 -0.043 1.14e-02 7.69e+03 1.42e+01 bond pdb=" N ILE A 72 " pdb=" CA ILE A 72 " ideal model delta sigma weight residual 1.459 1.503 -0.044 1.25e-02 6.40e+03 1.24e+01 bond pdb=" C3' DA P 20 " pdb=" C2' DA P 20 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DA E 23 " pdb=" C2' DA E 23 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DT E 25 " pdb=" C2' DT E 25 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.55e+00 ... (remaining 14224 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 18953 1.98 - 3.97: 353 3.97 - 5.95: 43 5.95 - 7.93: 4 7.93 - 9.91: 2 Bond angle restraints: 19355 Sorted by residual: angle pdb=" O THR A 71 " pdb=" C THR A 71 " pdb=" N ILE A 72 " ideal model delta sigma weight residual 123.30 117.11 6.19 1.19e+00 7.06e-01 2.71e+01 angle pdb=" N TYR A 74 " pdb=" CA TYR A 74 " pdb=" C TYR A 74 " ideal model delta sigma weight residual 112.93 107.23 5.70 1.12e+00 7.97e-01 2.59e+01 angle pdb=" CA THR A 71 " pdb=" C THR A 71 " pdb=" N ILE A 72 " ideal model delta sigma weight residual 116.29 122.37 -6.08 1.30e+00 5.92e-01 2.19e+01 angle pdb=" N3 DT P 15 " pdb=" C4 DT P 15 " pdb=" O4 DT P 15 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT E 25 " pdb=" C4 DT E 25 " pdb=" O4 DT E 25 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 ... (remaining 19350 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.03: 8140 29.03 - 58.06: 355 58.06 - 87.09: 24 87.09 - 116.12: 1 116.12 - 145.15: 1 Dihedral angle restraints: 8521 sinusoidal: 3701 harmonic: 4820 Sorted by residual: dihedral pdb=" CA THR A 209 " pdb=" C THR A 209 " pdb=" N GLU A 210 " pdb=" CA GLU A 210 " ideal model delta harmonic sigma weight residual -180.00 -159.26 -20.74 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA GLU B 20 " pdb=" C GLU B 20 " pdb=" N PRO B 21 " pdb=" CA PRO B 21 " ideal model delta harmonic sigma weight residual 180.00 -159.52 -20.48 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" C4' DA P 20 " pdb=" C3' DA P 20 " pdb=" O3' DA P 20 " pdb=" P DA P 21 " ideal model delta sinusoidal sigma weight residual 220.00 74.85 145.15 1 3.50e+01 8.16e-04 1.43e+01 ... (remaining 8518 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1594 0.045 - 0.090: 414 0.090 - 0.135: 125 0.135 - 0.180: 9 0.180 - 0.225: 2 Chirality restraints: 2144 Sorted by residual: chirality pdb=" CB VAL A 365 " pdb=" CA VAL A 365 " pdb=" CG1 VAL A 365 " pdb=" CG2 VAL A 365 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CG LEU A 578 " pdb=" CB LEU A 578 " pdb=" CD1 LEU A 578 " pdb=" CD2 LEU A 578 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CB ILE A 690 " pdb=" CA ILE A 690 " pdb=" CG1 ILE A 690 " pdb=" CG2 ILE A 690 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.43e-01 ... (remaining 2141 not shown) Planarity restraints: 2357 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 9 " 0.052 5.00e-02 4.00e+02 7.92e-02 1.00e+01 pdb=" N PRO B 10 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO B 10 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 10 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 79 " -0.039 5.00e-02 4.00e+02 5.96e-02 5.69e+00 pdb=" N PRO C 80 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 288 " -0.035 5.00e-02 4.00e+02 5.29e-02 4.48e+00 pdb=" N PRO A 289 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 289 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 289 " -0.029 5.00e-02 4.00e+02 ... (remaining 2354 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1492 2.75 - 3.29: 13251 3.29 - 3.82: 22377 3.82 - 4.36: 25298 4.36 - 4.90: 44004 Nonbonded interactions: 106422 Sorted by model distance: nonbonded pdb=" OG SER C 196 " pdb=" O VAL C 210 " model vdw 2.212 3.040 nonbonded pdb=" OE1 GLN C 409 " pdb=" OG SER C 412 " model vdw 2.228 3.040 nonbonded pdb=" NZ LYS C 383 " pdb=" OD1 ASP C 419 " model vdw 2.257 3.120 nonbonded pdb=" O LYS A 803 " pdb=" NZ LYS A 826 " model vdw 2.271 3.120 nonbonded pdb=" OD1 ASN C 304 " pdb=" OG SER C 309 " model vdw 2.272 3.040 ... (remaining 106417 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.010 Normalize map: mean=0, sd=1: 2.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.250 Find NCS groups from input model: 0.060 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:9.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 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 : 0.003 0.044 14229 Z= 0.220 Angle : 0.624 9.914 19355 Z= 0.391 Chirality : 0.044 0.225 2144 Planarity : 0.005 0.079 2357 Dihedral : 15.072 145.151 5411 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.71 % Favored : 95.16 % Rotamer: Outliers : 0.20 % Allowed : 0.47 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.33 (0.21), residues: 1612 helix: 1.38 (0.22), residues: 572 sheet: 0.47 (0.31), residues: 293 loop : -0.79 (0.22), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 287 TYR 0.017 0.001 TYR A 74 PHE 0.027 0.002 PHE C 152 TRP 0.012 0.001 TRP A 8 HIS 0.005 0.001 HIS B 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.22 (14229) covalent geometry : angle 0.62414 / 0.39 (19355) hydrogen bonds : bond 0.14477 / 9.36 ( 595) hydrogen bonds : angle 6.29019 / 4.53 ( 1672) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 298 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 399 GLU cc_start: 0.6690 (mm-30) cc_final: 0.6298 (mm-30) REVERT: A 837 LYS cc_start: 0.7845 (tptt) cc_final: 0.7641 (tptt) REVERT: B 146 GLN cc_start: 0.7110 (mt0) cc_final: 0.6819 (mt0) REVERT: C 95 MET cc_start: -0.1021 (ppp) cc_final: -0.1355 (tpp) REVERT: C 152 PHE cc_start: 0.8083 (m-80) cc_final: 0.7528 (m-10) REVERT: C 304 ASN cc_start: 0.6921 (m110) cc_final: 0.6673 (m110) REVERT: C 391 ASN cc_start: 0.6518 (t0) cc_final: 0.5998 (t0) REVERT: C 393 ASN cc_start: 0.8015 (p0) cc_final: 0.7150 (p0) REVERT: C 421 LYS cc_start: 0.7245 (tppp) cc_final: 0.6837 (tppp) outliers start: 3 outliers final: 0 residues processed: 299 average time/residue: 0.4978 time to fit residues: 164.0718 Evaluate side-chains 268 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 703 ASN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 897 HIS B 151 HIS C 321 ASN C 396 ASN ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.193304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.151869 restraints weight = 20600.803| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 2.52 r_work: 0.3836 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 14229 Z= 0.325 Angle : 0.751 10.290 19355 Z= 0.402 Chirality : 0.051 0.314 2144 Planarity : 0.006 0.075 2357 Dihedral : 13.171 150.029 2118 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.40 % Favored : 94.42 % Rotamer: Outliers : 1.67 % Allowed : 11.87 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.28 (0.20), residues: 1612 helix: 0.83 (0.21), residues: 588 sheet: 0.21 (0.30), residues: 295 loop : -1.19 (0.21), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 207 TYR 0.027 0.002 TYR A 806 PHE 0.032 0.003 PHE C 152 TRP 0.024 0.003 TRP A 8 HIS 0.015 0.002 HIS B 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00748 / 0.32 (14229) covalent geometry : angle 0.75084 / 0.40 (19355) hydrogen bonds : bond 0.06876 / 4.65 ( 595) hydrogen bonds : angle 5.04714 / 3.55 ( 1672) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 293 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 292 LYS cc_start: 0.8294 (mtmt) cc_final: 0.7474 (mtmt) REVERT: A 371 ILE cc_start: 0.8534 (tp) cc_final: 0.8282 (tt) REVERT: A 492 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7902 (mtp) REVERT: A 515 THR cc_start: 0.8680 (t) cc_final: 0.8475 (m) REVERT: A 566 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7350 (pp20) REVERT: A 809 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7705 (mmm) REVERT: A 837 LYS cc_start: 0.8284 (tptt) cc_final: 0.8065 (tptt) REVERT: A 859 MET cc_start: 0.4455 (mpp) cc_final: 0.3091 (mpp) REVERT: C 16 LEU cc_start: 0.8862 (mt) cc_final: 0.8641 (mt) REVERT: C 82 TYR cc_start: 0.6769 (m-10) cc_final: 0.6535 (m-10) REVERT: C 152 PHE cc_start: 0.8194 (m-80) cc_final: 0.7798 (m-80) REVERT: C 180 LEU cc_start: 0.7126 (tm) cc_final: 0.6867 (tt) REVERT: C 304 ASN cc_start: 0.7294 (m110) cc_final: 0.6952 (m110) REVERT: C 350 ASN cc_start: 0.6836 (t0) cc_final: 0.6556 (t0) REVERT: C 375 MET cc_start: 0.7482 (ppp) cc_final: 0.6998 (ppp) REVERT: C 421 LYS cc_start: 0.7332 (tppp) cc_final: 0.7079 (mmmt) outliers start: 25 outliers final: 12 residues processed: 299 average time/residue: 0.5223 time to fit residues: 171.7201 Evaluate side-chains 295 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 280 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 809 MET Chi-restraints excluded: chain A residue 937 ASN Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain C residue 165 TYR Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 418 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 95 optimal weight: 0.7980 chunk 133 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 113 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 131 optimal weight: 10.0000 chunk 77 optimal weight: 0.7980 chunk 156 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 ASN A 576 ASN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 9 ASN C 339 ASN C 397 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.196111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.155157 restraints weight = 20760.832| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 2.55 r_work: 0.3875 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14229 Z= 0.155 Angle : 0.632 9.849 19355 Z= 0.336 Chirality : 0.045 0.267 2144 Planarity : 0.005 0.056 2357 Dihedral : 13.243 148.038 2118 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.16 % Favored : 95.72 % Rotamer: Outliers : 1.67 % Allowed : 15.01 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.09 (0.20), residues: 1612 helix: 1.05 (0.22), residues: 583 sheet: 0.16 (0.30), residues: 293 loop : -1.05 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 674 TYR 0.020 0.001 TYR A 162 PHE 0.021 0.002 PHE A 526 TRP 0.016 0.002 TRP A 470 HIS 0.006 0.001 HIS B 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (14229) covalent geometry : angle 0.63191 / 0.34 (19355) hydrogen bonds : bond 0.05294 / 3.54 ( 595) hydrogen bonds : angle 4.75222 / 3.35 ( 1672) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 286 time to evaluate : 0.497 Fit side-chains revert: symmetry clash REVERT: A 230 MET cc_start: 0.6752 (OUTLIER) cc_final: 0.5463 (ttt) REVERT: A 371 ILE cc_start: 0.8529 (tp) cc_final: 0.8287 (tt) REVERT: A 515 THR cc_start: 0.8650 (t) cc_final: 0.8449 (m) REVERT: A 585 GLN cc_start: 0.7985 (tp40) cc_final: 0.7544 (tm-30) REVERT: A 837 LYS cc_start: 0.8135 (tptt) cc_final: 0.7927 (tptt) REVERT: A 859 MET cc_start: 0.4255 (mpp) cc_final: 0.2917 (mpp) REVERT: B 143 LEU cc_start: 0.7256 (tt) cc_final: 0.6986 (tp) REVERT: C 82 TYR cc_start: 0.6760 (m-10) cc_final: 0.6531 (m-10) REVERT: C 152 PHE cc_start: 0.8043 (m-80) cc_final: 0.7674 (m-80) REVERT: C 177 ASP cc_start: 0.6752 (t0) cc_final: 0.6547 (t0) REVERT: C 180 LEU cc_start: 0.7109 (tm) cc_final: 0.6834 (tt) REVERT: C 304 ASN cc_start: 0.7252 (m110) cc_final: 0.6916 (m110) REVERT: C 339 ASN cc_start: 0.8606 (m110) cc_final: 0.8222 (p0) REVERT: C 350 ASN cc_start: 0.6845 (t0) cc_final: 0.6567 (t0) REVERT: C 375 MET cc_start: 0.7628 (ppp) cc_final: 0.6775 (ppp) REVERT: C 387 PHE cc_start: 0.8018 (p90) cc_final: 0.7719 (p90) REVERT: C 397 ASN cc_start: 0.8081 (t0) cc_final: 0.7829 (t160) REVERT: C 421 LYS cc_start: 0.7336 (tppp) cc_final: 0.6984 (mmtt) outliers start: 25 outliers final: 10 residues processed: 294 average time/residue: 0.4581 time to fit residues: 149.0649 Evaluate side-chains 281 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 270 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 165 TYR Chi-restraints excluded: chain C residue 418 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 18 optimal weight: 0.9980 chunk 123 optimal weight: 9.9990 chunk 92 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 128 optimal weight: 10.0000 chunk 120 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 ASN A 181 ASN A 263 ASN A 576 ASN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 841 ASN ** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 ASN C 9 ASN ** C 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 396 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.193726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.152960 restraints weight = 20726.093| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 2.50 r_work: 0.3863 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14229 Z= 0.188 Angle : 0.638 8.607 19355 Z= 0.340 Chirality : 0.045 0.232 2144 Planarity : 0.005 0.059 2357 Dihedral : 13.386 149.931 2118 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.90 % Favored : 94.98 % Rotamer: Outliers : 2.67 % Allowed : 16.14 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.16 (0.20), residues: 1612 helix: 1.01 (0.22), residues: 587 sheet: 0.08 (0.31), residues: 286 loop : -1.09 (0.21), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 346 TYR 0.060 0.002 TYR C 165 PHE 0.019 0.002 PHE A 930 TRP 0.017 0.002 TRP A 470 HIS 0.008 0.001 HIS B 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.19 (14229) covalent geometry : angle 0.63756 / 0.34 (19355) hydrogen bonds : bond 0.05266 / 3.53 ( 595) hydrogen bonds : angle 4.71112 / 3.32 ( 1672) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 287 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 ILE cc_start: 0.8536 (tp) cc_final: 0.8312 (tt) REVERT: A 515 THR cc_start: 0.8638 (t) cc_final: 0.8430 (m) REVERT: A 809 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.7555 (mtm) REVERT: A 837 LYS cc_start: 0.8186 (tptt) cc_final: 0.7983 (tptt) REVERT: A 967 PHE cc_start: 0.7923 (OUTLIER) cc_final: 0.7639 (m-10) REVERT: B 14 THR cc_start: 0.7779 (OUTLIER) cc_final: 0.7461 (p) REVERT: B 23 MET cc_start: 0.4716 (OUTLIER) cc_final: 0.4075 (tmm) REVERT: B 143 LEU cc_start: 0.7287 (tt) cc_final: 0.7005 (tp) REVERT: B 148 ILE cc_start: 0.8318 (tt) cc_final: 0.8104 (tt) REVERT: C 11 LYS cc_start: 0.8176 (pttm) cc_final: 0.7966 (mptt) REVERT: C 16 LEU cc_start: 0.8840 (mt) cc_final: 0.8608 (mt) REVERT: C 82 TYR cc_start: 0.6836 (m-10) cc_final: 0.6605 (m-10) REVERT: C 152 PHE cc_start: 0.8075 (m-80) cc_final: 0.7497 (m-80) REVERT: C 160 LEU cc_start: 0.8019 (tt) cc_final: 0.7798 (tm) REVERT: C 177 ASP cc_start: 0.6813 (t0) cc_final: 0.6601 (t0) REVERT: C 180 LEU cc_start: 0.7136 (tm) cc_final: 0.6872 (tt) REVERT: C 304 ASN cc_start: 0.7145 (m110) cc_final: 0.6811 (m110) REVERT: C 344 VAL cc_start: 0.7509 (OUTLIER) cc_final: 0.7275 (p) REVERT: C 347 LYS cc_start: 0.8052 (mmpt) cc_final: 0.7575 (mmtm) REVERT: C 350 ASN cc_start: 0.6896 (t0) cc_final: 0.6603 (t0) REVERT: C 375 MET cc_start: 0.7659 (ppp) cc_final: 0.7288 (ppp) REVERT: C 387 PHE cc_start: 0.8015 (p90) cc_final: 0.7673 (p90) REVERT: C 421 LYS cc_start: 0.7381 (tppp) cc_final: 0.6858 (tmtt) outliers start: 40 outliers final: 14 residues processed: 300 average time/residue: 0.4526 time to fit residues: 150.2159 Evaluate side-chains 296 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 277 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 809 MET Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 967 PHE Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain C residue 165 TYR Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 418 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 53 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 72 optimal weight: 0.4980 chunk 157 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 19 optimal weight: 0.2980 chunk 1 optimal weight: 0.0270 overall best weight: 0.4840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 ASN A 181 ASN A 263 ASN A 576 ASN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.195421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.154760 restraints weight = 20670.090| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 2.50 r_work: 0.3890 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14229 Z= 0.132 Angle : 0.616 10.598 19355 Z= 0.326 Chirality : 0.043 0.224 2144 Planarity : 0.004 0.054 2357 Dihedral : 13.419 149.690 2118 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.09 % Favored : 95.78 % Rotamer: Outliers : 2.00 % Allowed : 18.28 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.05 (0.21), residues: 1612 helix: 1.17 (0.22), residues: 588 sheet: 0.02 (0.30), residues: 293 loop : -1.03 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 98 TYR 0.026 0.001 TYR A 468 PHE 0.026 0.002 PHE C 87 TRP 0.016 0.001 TRP A 470 HIS 0.006 0.001 HIS A 897 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (14229) covalent geometry : angle 0.61628 / 0.33 (19355) hydrogen bonds : bond 0.04509 / 2.99 ( 595) hydrogen bonds : angle 4.59215 / 3.22 ( 1672) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 295 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ASP cc_start: 0.7843 (t70) cc_final: 0.7552 (t0) REVERT: A 357 MET cc_start: 0.7319 (mpp) cc_final: 0.6851 (mpp) REVERT: A 371 ILE cc_start: 0.8531 (tp) cc_final: 0.8323 (tt) REVERT: A 398 ASP cc_start: 0.7502 (t0) cc_final: 0.7010 (t0) REVERT: A 515 THR cc_start: 0.8604 (t) cc_final: 0.8399 (m) REVERT: A 585 GLN cc_start: 0.7981 (tp40) cc_final: 0.7502 (tm-30) REVERT: A 837 LYS cc_start: 0.8123 (tptt) cc_final: 0.7914 (tptt) REVERT: B 14 THR cc_start: 0.7761 (OUTLIER) cc_final: 0.7434 (p) REVERT: B 23 MET cc_start: 0.4624 (OUTLIER) cc_final: 0.4041 (tmm) REVERT: B 148 ILE cc_start: 0.8228 (tt) cc_final: 0.8019 (tt) REVERT: C 16 LEU cc_start: 0.8821 (mt) cc_final: 0.8584 (mt) REVERT: C 82 TYR cc_start: 0.6755 (m-10) cc_final: 0.6544 (m-10) REVERT: C 87 PHE cc_start: 0.7436 (m-10) cc_final: 0.7104 (m-80) REVERT: C 152 PHE cc_start: 0.8005 (m-80) cc_final: 0.7420 (m-10) REVERT: C 160 LEU cc_start: 0.8024 (tt) cc_final: 0.7806 (tm) REVERT: C 180 LEU cc_start: 0.7113 (tm) cc_final: 0.6874 (tt) REVERT: C 304 ASN cc_start: 0.7053 (m110) cc_final: 0.6732 (m110) REVERT: C 344 VAL cc_start: 0.7516 (OUTLIER) cc_final: 0.7190 (p) REVERT: C 387 PHE cc_start: 0.7955 (p90) cc_final: 0.7618 (p90) REVERT: C 393 ASN cc_start: 0.8376 (p0) cc_final: 0.7990 (p0) REVERT: C 396 ASN cc_start: 0.8712 (p0) cc_final: 0.8458 (p0) REVERT: C 397 ASN cc_start: 0.8114 (t0) cc_final: 0.7902 (t0) REVERT: C 421 LYS cc_start: 0.7362 (tppp) cc_final: 0.6900 (tppp) outliers start: 30 outliers final: 15 residues processed: 305 average time/residue: 0.4674 time to fit residues: 157.7922 Evaluate side-chains 307 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 289 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain C residue 165 TYR Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 418 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 108 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 97 optimal weight: 0.5980 chunk 121 optimal weight: 0.7980 chunk 162 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 ASN A 263 ASN A 576 ASN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 ASN C 9 ASN C 351 GLN C 415 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.195081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.154300 restraints weight = 20639.016| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 2.53 r_work: 0.3877 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14229 Z= 0.148 Angle : 0.621 9.917 19355 Z= 0.329 Chirality : 0.044 0.273 2144 Planarity : 0.005 0.057 2357 Dihedral : 13.468 151.123 2118 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.53 % Favored : 95.35 % Rotamer: Outliers : 2.20 % Allowed : 19.01 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.07 (0.21), residues: 1612 helix: 1.14 (0.22), residues: 588 sheet: -0.01 (0.30), residues: 301 loop : -1.04 (0.22), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 98 TYR 0.027 0.001 TYR A 468 PHE 0.018 0.002 PHE C 377 TRP 0.016 0.002 TRP A 470 HIS 0.006 0.001 HIS A 897 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (14229) covalent geometry : angle 0.62064 / 0.33 (19355) hydrogen bonds : bond 0.04629 / 3.09 ( 595) hydrogen bonds : angle 4.56112 / 3.20 ( 1672) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 289 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 ILE cc_start: 0.8535 (tp) cc_final: 0.8334 (tt) REVERT: A 513 THR cc_start: 0.8385 (OUTLIER) cc_final: 0.8159 (t) REVERT: A 809 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.7543 (mtm) REVERT: A 837 LYS cc_start: 0.8167 (tptt) cc_final: 0.7965 (tptt) REVERT: A 873 GLU cc_start: 0.7026 (mm-30) cc_final: 0.6789 (mm-30) REVERT: A 996 MET cc_start: 0.7599 (tpp) cc_final: 0.7388 (tpp) REVERT: B 14 THR cc_start: 0.7786 (OUTLIER) cc_final: 0.7446 (p) REVERT: B 23 MET cc_start: 0.4695 (OUTLIER) cc_final: 0.4063 (tmm) REVERT: B 143 LEU cc_start: 0.7254 (tt) cc_final: 0.6958 (tp) REVERT: B 148 ILE cc_start: 0.8248 (tt) cc_final: 0.8025 (tt) REVERT: C 16 LEU cc_start: 0.8840 (mt) cc_final: 0.8610 (mt) REVERT: C 82 TYR cc_start: 0.6769 (m-10) cc_final: 0.6536 (m-10) REVERT: C 152 PHE cc_start: 0.7900 (m-80) cc_final: 0.7418 (m-10) REVERT: C 160 LEU cc_start: 0.8026 (tt) cc_final: 0.7821 (tm) REVERT: C 180 LEU cc_start: 0.7125 (tm) cc_final: 0.6882 (tt) REVERT: C 304 ASN cc_start: 0.7054 (m110) cc_final: 0.6716 (m110) REVERT: C 339 ASN cc_start: 0.8673 (OUTLIER) cc_final: 0.8280 (p0) REVERT: C 344 VAL cc_start: 0.7526 (OUTLIER) cc_final: 0.7106 (p) REVERT: C 387 PHE cc_start: 0.7970 (p90) cc_final: 0.7664 (p90) REVERT: C 393 ASN cc_start: 0.8366 (p0) cc_final: 0.8009 (p0) REVERT: C 396 ASN cc_start: 0.8728 (p0) cc_final: 0.8480 (p0) REVERT: C 397 ASN cc_start: 0.8114 (t0) cc_final: 0.7885 (t0) REVERT: C 421 LYS cc_start: 0.7417 (tppp) cc_final: 0.6907 (tmtt) outliers start: 33 outliers final: 14 residues processed: 303 average time/residue: 0.4561 time to fit residues: 153.8751 Evaluate side-chains 311 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 291 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 809 MET Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 165 TYR Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 418 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 40 optimal weight: 2.9990 chunk 146 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 120 optimal weight: 0.0980 chunk 15 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 ASN A 263 ASN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN C 415 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.194330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.153578 restraints weight = 20638.678| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 2.53 r_work: 0.3877 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14229 Z= 0.162 Angle : 0.646 14.208 19355 Z= 0.338 Chirality : 0.044 0.235 2144 Planarity : 0.004 0.057 2357 Dihedral : 13.492 151.696 2118 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.40 % Favored : 95.47 % Rotamer: Outliers : 2.40 % Allowed : 19.35 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.09 (0.21), residues: 1612 helix: 1.15 (0.22), residues: 582 sheet: -0.04 (0.30), residues: 301 loop : -1.05 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 98 TYR 0.027 0.001 TYR A 468 PHE 0.023 0.002 PHE A 526 TRP 0.016 0.002 TRP A 470 HIS 0.006 0.001 HIS B 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (14229) covalent geometry : angle 0.64615 / 0.34 (19355) hydrogen bonds : bond 0.04672 / 3.13 ( 595) hydrogen bonds : angle 4.56863 / 3.21 ( 1672) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 291 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 MET cc_start: 0.7456 (OUTLIER) cc_final: 0.5347 (tpt) REVERT: A 398 ASP cc_start: 0.7512 (t0) cc_final: 0.7074 (t0) REVERT: A 513 THR cc_start: 0.8412 (OUTLIER) cc_final: 0.8167 (t) REVERT: A 566 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7332 (pp20) REVERT: A 585 GLN cc_start: 0.7983 (tp40) cc_final: 0.7533 (tm-30) REVERT: A 770 ILE cc_start: 0.7592 (mp) cc_final: 0.7364 (mt) REVERT: A 809 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7561 (mtm) REVERT: A 828 THR cc_start: 0.7143 (OUTLIER) cc_final: 0.6794 (p) REVERT: A 837 LYS cc_start: 0.8190 (tptt) cc_final: 0.7974 (tptt) REVERT: A 859 MET cc_start: 0.4415 (mpp) cc_final: 0.3116 (mpp) REVERT: A 873 GLU cc_start: 0.7006 (mm-30) cc_final: 0.6795 (mm-30) REVERT: A 996 MET cc_start: 0.7573 (tpp) cc_final: 0.7336 (tpp) REVERT: B 23 MET cc_start: 0.4729 (OUTLIER) cc_final: 0.4087 (tmm) REVERT: B 143 LEU cc_start: 0.7248 (tt) cc_final: 0.6964 (tp) REVERT: B 148 ILE cc_start: 0.8271 (tt) cc_final: 0.8044 (tt) REVERT: C 16 LEU cc_start: 0.8844 (mt) cc_final: 0.8615 (mt) REVERT: C 95 MET cc_start: -0.0254 (ppp) cc_final: -0.1964 (tpp) REVERT: C 152 PHE cc_start: 0.7879 (m-80) cc_final: 0.7435 (m-10) REVERT: C 180 LEU cc_start: 0.7115 (tm) cc_final: 0.6868 (tt) REVERT: C 304 ASN cc_start: 0.7063 (m110) cc_final: 0.6747 (m110) REVERT: C 339 ASN cc_start: 0.8667 (m110) cc_final: 0.8289 (p0) REVERT: C 344 VAL cc_start: 0.7434 (OUTLIER) cc_final: 0.7214 (p) REVERT: C 347 LYS cc_start: 0.7996 (mmpt) cc_final: 0.7531 (mmtm) REVERT: C 350 ASN cc_start: 0.6921 (t0) cc_final: 0.6618 (t0) REVERT: C 387 PHE cc_start: 0.8015 (p90) cc_final: 0.7650 (p90) REVERT: C 393 ASN cc_start: 0.8358 (p0) cc_final: 0.7936 (p0) REVERT: C 396 ASN cc_start: 0.8748 (p0) cc_final: 0.8483 (p0) REVERT: C 397 ASN cc_start: 0.8126 (t0) cc_final: 0.7858 (t0) REVERT: C 421 LYS cc_start: 0.7508 (tppp) cc_final: 0.6933 (tmtt) outliers start: 36 outliers final: 17 residues processed: 309 average time/residue: 0.4804 time to fit residues: 164.3540 Evaluate side-chains 311 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 287 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 809 MET Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 165 TYR Chi-restraints excluded: chain C residue 252 HIS Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 418 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 95 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 93 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 ASN A 263 ASN A 336 GLN A 538 GLN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN C 391 ASN C 415 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.194138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.153312 restraints weight = 20654.190| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 2.52 r_work: 0.3876 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14229 Z= 0.154 Angle : 0.644 12.439 19355 Z= 0.337 Chirality : 0.044 0.246 2144 Planarity : 0.005 0.056 2357 Dihedral : 13.485 151.959 2118 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.59 % Favored : 95.29 % Rotamer: Outliers : 2.27 % Allowed : 20.41 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.10 (0.21), residues: 1612 helix: 1.18 (0.22), residues: 576 sheet: 0.01 (0.31), residues: 288 loop : -1.09 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 98 TYR 0.030 0.001 TYR A 468 PHE 0.028 0.002 PHE A 930 TRP 0.017 0.002 TRP A 470 HIS 0.005 0.001 HIS B 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (14229) covalent geometry : angle 0.64386 / 0.34 (19355) hydrogen bonds : bond 0.04573 / 3.05 ( 595) hydrogen bonds : angle 4.53537 / 3.18 ( 1672) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 287 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 MET cc_start: 0.7462 (OUTLIER) cc_final: 0.5359 (tpt) REVERT: A 357 MET cc_start: 0.7373 (mpp) cc_final: 0.6728 (mpp) REVERT: A 513 THR cc_start: 0.8423 (OUTLIER) cc_final: 0.8162 (t) REVERT: A 566 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7339 (pp20) REVERT: A 828 THR cc_start: 0.7121 (OUTLIER) cc_final: 0.6781 (p) REVERT: A 837 LYS cc_start: 0.8181 (tptt) cc_final: 0.7974 (tptt) REVERT: A 859 MET cc_start: 0.4360 (mpp) cc_final: 0.3038 (mpp) REVERT: A 873 GLU cc_start: 0.6919 (mm-30) cc_final: 0.6705 (mm-30) REVERT: A 996 MET cc_start: 0.7560 (tpp) cc_final: 0.7325 (tpp) REVERT: B 23 MET cc_start: 0.4795 (OUTLIER) cc_final: 0.3961 (tmm) REVERT: B 148 ILE cc_start: 0.8277 (tt) cc_final: 0.8051 (tt) REVERT: C 152 PHE cc_start: 0.7900 (m-80) cc_final: 0.7472 (m-10) REVERT: C 180 LEU cc_start: 0.7104 (tm) cc_final: 0.6860 (tt) REVERT: C 304 ASN cc_start: 0.7050 (m110) cc_final: 0.6727 (m110) REVERT: C 339 ASN cc_start: 0.8689 (OUTLIER) cc_final: 0.8316 (p0) REVERT: C 344 VAL cc_start: 0.7455 (OUTLIER) cc_final: 0.7050 (p) REVERT: C 350 ASN cc_start: 0.6965 (t0) cc_final: 0.6645 (t0) REVERT: C 387 PHE cc_start: 0.8004 (p90) cc_final: 0.7592 (p90) REVERT: C 393 ASN cc_start: 0.8304 (p0) cc_final: 0.7906 (p0) REVERT: C 396 ASN cc_start: 0.8759 (p0) cc_final: 0.8454 (p0) REVERT: C 397 ASN cc_start: 0.8121 (t0) cc_final: 0.7840 (t0) REVERT: C 421 LYS cc_start: 0.7513 (tppp) cc_final: 0.6955 (tmtt) outliers start: 34 outliers final: 18 residues processed: 299 average time/residue: 0.5025 time to fit residues: 166.6759 Evaluate side-chains 316 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 291 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 165 TYR Chi-restraints excluded: chain C residue 207 ARG Chi-restraints excluded: chain C residue 252 HIS Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 418 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 130 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 139 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 ASN A 263 ASN A 336 GLN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 386 ASN C 391 ASN C 415 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.193575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.152793 restraints weight = 20653.527| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 2.50 r_work: 0.3867 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14229 Z= 0.173 Angle : 0.664 11.868 19355 Z= 0.347 Chirality : 0.044 0.231 2144 Planarity : 0.005 0.058 2357 Dihedral : 13.507 152.665 2118 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.53 % Favored : 95.35 % Rotamer: Outliers : 2.27 % Allowed : 20.81 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.11 (0.21), residues: 1612 helix: 1.13 (0.22), residues: 582 sheet: -0.07 (0.30), residues: 301 loop : -1.05 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 98 TYR 0.031 0.002 TYR A 468 PHE 0.026 0.002 PHE A 526 TRP 0.016 0.002 TRP A 470 HIS 0.007 0.001 HIS B 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (14229) covalent geometry : angle 0.66394 / 0.35 (19355) hydrogen bonds : bond 0.04726 / 3.17 ( 595) hydrogen bonds : angle 4.57968 / 3.21 ( 1672) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 292 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ASN cc_start: 0.7663 (m-40) cc_final: 0.7462 (m-40) REVERT: A 513 THR cc_start: 0.8425 (OUTLIER) cc_final: 0.8165 (t) REVERT: A 566 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7370 (pp20) REVERT: A 585 GLN cc_start: 0.7991 (tp40) cc_final: 0.7595 (tm-30) REVERT: A 679 TYR cc_start: 0.8492 (t80) cc_final: 0.8193 (t80) REVERT: A 828 THR cc_start: 0.7135 (OUTLIER) cc_final: 0.6815 (p) REVERT: A 837 LYS cc_start: 0.8188 (tptt) cc_final: 0.7908 (tptp) REVERT: A 859 MET cc_start: 0.4325 (mpp) cc_final: 0.3038 (mpp) REVERT: A 873 GLU cc_start: 0.6877 (mm-30) cc_final: 0.6216 (tp30) REVERT: A 926 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7540 (tm-30) REVERT: A 996 MET cc_start: 0.7526 (tpp) cc_final: 0.7064 (tpp) REVERT: B 148 ILE cc_start: 0.8288 (tt) cc_final: 0.8056 (tt) REVERT: C 7 LEU cc_start: 0.7876 (pp) cc_final: 0.7659 (pp) REVERT: C 11 LYS cc_start: 0.8158 (mptt) cc_final: 0.7957 (mppt) REVERT: C 80 PRO cc_start: 0.8002 (Cg_endo) cc_final: 0.7780 (Cg_exo) REVERT: C 97 GLU cc_start: 0.6956 (tm-30) cc_final: 0.6637 (pp20) REVERT: C 152 PHE cc_start: 0.7925 (m-80) cc_final: 0.7498 (m-10) REVERT: C 180 LEU cc_start: 0.7091 (tm) cc_final: 0.6839 (tt) REVERT: C 304 ASN cc_start: 0.7045 (m110) cc_final: 0.6714 (m110) REVERT: C 339 ASN cc_start: 0.8721 (OUTLIER) cc_final: 0.8345 (p0) REVERT: C 347 LYS cc_start: 0.7919 (mmpt) cc_final: 0.7213 (mptt) REVERT: C 350 ASN cc_start: 0.7010 (t0) cc_final: 0.6685 (t0) REVERT: C 387 PHE cc_start: 0.7968 (p90) cc_final: 0.7571 (p90) REVERT: C 391 ASN cc_start: 0.7010 (t0) cc_final: 0.6809 (t160) REVERT: C 393 ASN cc_start: 0.8323 (p0) cc_final: 0.7917 (p0) REVERT: C 396 ASN cc_start: 0.8771 (p0) cc_final: 0.8444 (p0) REVERT: C 397 ASN cc_start: 0.8136 (t0) cc_final: 0.7851 (t0) REVERT: C 421 LYS cc_start: 0.7538 (tppp) cc_final: 0.7220 (tppp) outliers start: 34 outliers final: 18 residues processed: 306 average time/residue: 0.5008 time to fit residues: 169.4143 Evaluate side-chains 312 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 290 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 252 HIS Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 418 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 109 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 115 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 263 ASN A 336 GLN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 386 ASN C 415 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.195586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.154704 restraints weight = 20562.756| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 2.52 r_work: 0.3868 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14229 Z= 0.160 Angle : 0.673 12.013 19355 Z= 0.351 Chirality : 0.044 0.232 2144 Planarity : 0.005 0.058 2357 Dihedral : 13.504 152.557 2118 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.40 % Favored : 95.47 % Rotamer: Outliers : 1.60 % Allowed : 21.75 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.10 (0.21), residues: 1612 helix: 1.13 (0.22), residues: 582 sheet: -0.05 (0.30), residues: 301 loop : -1.03 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B 98 TYR 0.033 0.001 TYR A 468 PHE 0.025 0.002 PHE A 930 TRP 0.017 0.002 TRP A 470 HIS 0.006 0.001 HIS B 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (14229) covalent geometry : angle 0.67325 / 0.35 (19355) hydrogen bonds : bond 0.04618 / 3.07 ( 595) hydrogen bonds : angle 4.56087 / 3.20 ( 1672) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 284 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ASN cc_start: 0.7668 (m-40) cc_final: 0.7466 (m-40) REVERT: A 513 THR cc_start: 0.8427 (OUTLIER) cc_final: 0.8167 (t) REVERT: A 566 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7377 (pp20) REVERT: A 639 LYS cc_start: 0.7902 (ttpp) cc_final: 0.7550 (ttpp) REVERT: A 828 THR cc_start: 0.7140 (OUTLIER) cc_final: 0.6815 (p) REVERT: A 837 LYS cc_start: 0.8182 (tptt) cc_final: 0.7894 (tptp) REVERT: A 859 MET cc_start: 0.4358 (mpp) cc_final: 0.3081 (mpp) REVERT: A 873 GLU cc_start: 0.6859 (mm-30) cc_final: 0.6196 (tp30) REVERT: A 926 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7583 (tm-30) REVERT: A 996 MET cc_start: 0.7539 (tpp) cc_final: 0.7075 (tpp) REVERT: B 23 MET cc_start: 0.4579 (tmm) cc_final: 0.4271 (ttt) REVERT: B 148 ILE cc_start: 0.8278 (tt) cc_final: 0.8049 (tt) REVERT: C 80 PRO cc_start: 0.8035 (Cg_endo) cc_final: 0.7734 (Cg_exo) REVERT: C 97 GLU cc_start: 0.6980 (tm-30) cc_final: 0.6709 (pp20) REVERT: C 152 PHE cc_start: 0.7848 (m-80) cc_final: 0.7445 (m-10) REVERT: C 180 LEU cc_start: 0.7066 (tm) cc_final: 0.6842 (tt) REVERT: C 304 ASN cc_start: 0.7089 (m110) cc_final: 0.6755 (m110) REVERT: C 339 ASN cc_start: 0.8661 (OUTLIER) cc_final: 0.8257 (p0) REVERT: C 347 LYS cc_start: 0.7957 (mmpt) cc_final: 0.7450 (mmtm) REVERT: C 350 ASN cc_start: 0.7001 (t0) cc_final: 0.6683 (t0) REVERT: C 359 GLU cc_start: 0.6687 (mt-10) cc_final: 0.6414 (tt0) REVERT: C 387 PHE cc_start: 0.7978 (p90) cc_final: 0.7529 (p90) REVERT: C 391 ASN cc_start: 0.6995 (t0) cc_final: 0.6712 (t0) REVERT: C 393 ASN cc_start: 0.8346 (p0) cc_final: 0.7728 (p0) REVERT: C 396 ASN cc_start: 0.8773 (p0) cc_final: 0.8437 (p0) REVERT: C 397 ASN cc_start: 0.8143 (t0) cc_final: 0.7839 (t0) REVERT: C 421 LYS cc_start: 0.7535 (tppp) cc_final: 0.6991 (tmtt) outliers start: 24 outliers final: 19 residues processed: 292 average time/residue: 0.5085 time to fit residues: 164.2997 Evaluate side-chains 310 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 287 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 207 ARG Chi-restraints excluded: chain C residue 252 HIS Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 418 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 20 optimal weight: 0.6980 chunk 136 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 52 optimal weight: 0.3980 chunk 153 optimal weight: 0.9980 chunk 36 optimal weight: 0.0370 chunk 19 optimal weight: 0.4980 chunk 2 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 263 ASN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 964 GLN ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 386 ASN C 415 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.196706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.156211 restraints weight = 20541.667| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 2.50 r_work: 0.3888 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14229 Z= 0.133 Angle : 0.664 12.823 19355 Z= 0.344 Chirality : 0.044 0.293 2144 Planarity : 0.005 0.058 2357 Dihedral : 13.486 152.010 2118 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.28 % Favored : 95.60 % Rotamer: Outliers : 1.60 % Allowed : 22.15 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.02 (0.21), residues: 1612 helix: 1.16 (0.22), residues: 582 sheet: 0.00 (0.30), residues: 301 loop : -0.96 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 98 TYR 0.034 0.001 TYR A 468 PHE 0.029 0.001 PHE A 930 TRP 0.018 0.002 TRP A 470 HIS 0.004 0.001 HIS A 897 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (14229) covalent geometry : angle 0.66370 / 0.34 (19355) hydrogen bonds : bond 0.04278 / 2.80 ( 595) hydrogen bonds : angle 4.48419 / 3.14 ( 1672) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4767.52 seconds wall clock time: 82 minutes 1.73 seconds (4921.73 seconds total)