Starting phenix.real_space_refine on Sat May 17 11:15:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k9v_62200/05_2025/9k9v_62200.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k9v_62200/05_2025/9k9v_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_62200/05_2025/9k9v_62200.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k9v_62200/05_2025/9k9v_62200.map" model { file = "/net/cci-nas-00/data/ceres_data/9k9v_62200/05_2025/9k9v_62200.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k9v_62200/05_2025/9k9v_62200.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 10.89, per 1000 atoms: 0.79 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: 3.09 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 4.70 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: 5.20 Time building geometry restraints manager: 3.64 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=" N ASN A 75 " pdb=" CA ASN A 75 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.54e-02 4.22e+03 5.83e+00 bond pdb=" N TYR A 74 " pdb=" CA TYR A 74 " ideal model delta sigma weight residual 1.455 1.484 -0.029 1.25e-02 6.40e+03 5.40e+00 bond pdb=" C TYR A 271 " pdb=" N ILE A 272 " ideal model delta sigma weight residual 1.334 1.308 0.027 1.25e-02 6.40e+03 4.51e+00 ... (remaining 14224 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 18994 1.98 - 3.97: 312 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=" N ILE A 609 " pdb=" CA ILE A 609 " pdb=" C ILE A 609 " ideal model delta sigma weight residual 113.53 109.52 4.01 9.80e-01 1.04e+00 1.67e+01 angle pdb=" CA ASN A 75 " pdb=" C ASN A 75 " pdb=" O ASN A 75 " ideal model delta sigma weight residual 121.14 117.04 4.10 1.03e+00 9.43e-01 1.58e+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: 1623 0.045 - 0.090: 394 0.090 - 0.135: 116 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: 0.000 Normalize map: mean=0, sd=1: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 37.880 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.060 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:11.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 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= 0.159 Angle : 0.606 9.914 19355 Z= 0.345 Chirality : 0.043 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.012 0.001 TRP A 8 HIS 0.005 0.001 HIS B 16 PHE 0.027 0.002 PHE C 152 TYR 0.017 0.001 TYR A 74 ARG 0.008 0.000 ARG A 287 Details of bonding type rmsd hydrogen bonds : bond 0.14477 ( 595) hydrogen bonds : angle 6.29019 ( 1672) covalent geometry : bond 0.00312 (14229) covalent geometry : angle 0.60584 (19355) *********************** 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 : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 399 GLU cc_start: 0.6690 (mm-30) cc_final: 0.6297 (mm-30) REVERT: A 837 LYS cc_start: 0.7846 (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: 0.7529 (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: 0.5974 (t0) REVERT: C 393 ASN cc_start: 0.8015 (p0) cc_final: 0.7182 (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: 1.1283 time to fit residues: 372.6571 Evaluate side-chains 269 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 127 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 ASN A 703 ASN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 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 = 0.4486 r_free = 0.4486 target = 0.193994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.152907 restraints weight = 20462.196| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 2.52 r_work: 0.3849 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 14229 Z= 0.246 Angle : 0.680 9.272 19355 Z= 0.361 Chirality : 0.047 0.301 2144 Planarity : 0.005 0.065 2357 Dihedral : 13.164 149.288 2118 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.96 % Favored : 94.91 % Rotamer: Outliers : 1.87 % Allowed : 11.47 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.21), residues: 1612 helix: 1.01 (0.22), residues: 584 sheet: 0.28 (0.31), residues: 288 loop : -1.07 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 8 HIS 0.013 0.002 HIS B 16 PHE 0.026 0.002 PHE C 152 TYR 0.023 0.002 TYR A 806 ARG 0.009 0.001 ARG C 111 Details of bonding type rmsd hydrogen bonds : bond 0.05941 ( 595) hydrogen bonds : angle 4.83364 ( 1672) covalent geometry : bond 0.00571 (14229) covalent geometry : angle 0.67986 (19355) *********************** 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 328 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 300 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 ILE cc_start: 0.8533 (tp) cc_final: 0.8280 (tt) REVERT: A 566 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7338 (pp20) REVERT: A 837 LYS cc_start: 0.8258 (tptt) cc_final: 0.8038 (tptt) REVERT: B 163 PHE cc_start: 0.7468 (m-80) cc_final: 0.7205 (m-80) REVERT: C 16 LEU cc_start: 0.8856 (mt) cc_final: 0.8629 (mt) REVERT: C 82 TYR cc_start: 0.6796 (m-10) cc_final: 0.6588 (m-10) REVERT: C 152 PHE cc_start: 0.8146 (m-80) cc_final: 0.7736 (m-80) REVERT: C 180 LEU cc_start: 0.7126 (tm) cc_final: 0.6873 (tt) REVERT: C 304 ASN cc_start: 0.7206 (m110) cc_final: 0.6900 (m110) REVERT: C 350 ASN cc_start: 0.6916 (t0) cc_final: 0.6625 (t0) REVERT: C 393 ASN cc_start: 0.8097 (p0) cc_final: 0.7510 (p0) REVERT: C 396 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.8480 (p0) REVERT: C 397 ASN cc_start: 0.8160 (t0) cc_final: 0.7922 (t0) REVERT: C 421 LYS cc_start: 0.7306 (tppp) cc_final: 0.6992 (mmtt) outliers start: 28 outliers final: 7 residues processed: 306 average time/residue: 1.1522 time to fit residues: 388.6962 Evaluate side-chains 292 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 283 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 655 SER 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 396 ASN 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 62 optimal weight: 0.7980 chunk 130 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 162 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 112 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 C 9 ASN ** C 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.195862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.155080 restraints weight = 20482.076| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 2.53 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: 0.7210 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14229 Z= 0.154 Angle : 0.606 9.911 19355 Z= 0.319 Chirality : 0.043 0.273 2144 Planarity : 0.004 0.053 2357 Dihedral : 13.207 148.834 2118 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.28 % Favored : 95.60 % Rotamer: Outliers : 1.87 % Allowed : 15.34 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.21), residues: 1612 helix: 1.08 (0.21), residues: 588 sheet: 0.28 (0.31), residues: 288 loop : -1.02 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 470 HIS 0.006 0.001 HIS B 16 PHE 0.021 0.002 PHE A 526 TYR 0.019 0.001 TYR A 162 ARG 0.009 0.001 ARG A 995 Details of bonding type rmsd hydrogen bonds : bond 0.04723 ( 595) hydrogen bonds : angle 4.58703 ( 1672) covalent geometry : bond 0.00355 (14229) covalent geometry : angle 0.60585 (19355) *********************** 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 320 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 292 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 371 ILE cc_start: 0.8528 (tp) cc_final: 0.8286 (tt) REVERT: A 809 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7561 (mtm) REVERT: A 996 MET cc_start: 0.7556 (tpp) cc_final: 0.7354 (tpp) REVERT: B 14 THR cc_start: 0.7785 (OUTLIER) cc_final: 0.7451 (p) REVERT: B 23 MET cc_start: 0.4676 (OUTLIER) cc_final: 0.4019 (tmm) REVERT: B 143 LEU cc_start: 0.7272 (tt) cc_final: 0.6999 (tp) REVERT: B 148 ILE cc_start: 0.8299 (tt) cc_final: 0.8097 (tt) REVERT: C 82 TYR cc_start: 0.6828 (m-10) cc_final: 0.6605 (m-10) REVERT: C 152 PHE cc_start: 0.8075 (m-80) cc_final: 0.7683 (m-80) REVERT: C 180 LEU cc_start: 0.7077 (tm) cc_final: 0.6849 (tt) REVERT: C 304 ASN cc_start: 0.7054 (m110) cc_final: 0.6701 (m110) REVERT: C 350 ASN cc_start: 0.6937 (t0) cc_final: 0.6644 (t0) REVERT: C 375 MET cc_start: 0.7654 (ppp) cc_final: 0.7372 (ppp) REVERT: C 377 PHE cc_start: 0.7590 (m-10) cc_final: 0.7345 (m-10) REVERT: C 387 PHE cc_start: 0.8004 (p90) cc_final: 0.7724 (p90) REVERT: C 393 ASN cc_start: 0.8213 (p0) cc_final: 0.7727 (p0) REVERT: C 396 ASN cc_start: 0.8752 (OUTLIER) cc_final: 0.8446 (p0) outliers start: 28 outliers final: 9 residues processed: 300 average time/residue: 1.0914 time to fit residues: 362.3134 Evaluate side-chains 284 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 271 time to evaluate : 1.597 ------------------------------------------------------------------------------- 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 492 MET 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 843 ILE Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 396 ASN 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 139 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 109 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 158 optimal weight: 0.0870 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 120 ASN C 9 ASN C 339 ASN ** C 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 397 ASN C 415 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.193289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.152321 restraints weight = 20493.324| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 2.50 r_work: 0.3856 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14229 Z= 0.195 Angle : 0.633 8.324 19355 Z= 0.335 Chirality : 0.045 0.269 2144 Planarity : 0.005 0.055 2357 Dihedral : 13.292 150.336 2118 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.84 % Favored : 95.04 % Rotamer: Outliers : 3.00 % Allowed : 16.88 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.20), residues: 1612 helix: 1.00 (0.21), residues: 588 sheet: 0.16 (0.31), residues: 283 loop : -1.09 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 470 HIS 0.010 0.002 HIS B 16 PHE 0.019 0.002 PHE C 377 TYR 0.021 0.002 TYR A 162 ARG 0.007 0.001 ARG A 744 Details of bonding type rmsd hydrogen bonds : bond 0.05114 ( 595) hydrogen bonds : angle 4.62293 ( 1672) covalent geometry : bond 0.00454 (14229) covalent geometry : angle 0.63323 (19355) *********************** 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 340 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 295 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 ILE cc_start: 0.8510 (tp) cc_final: 0.8296 (tt) REVERT: A 398 ASP cc_start: 0.7541 (t0) cc_final: 0.7331 (t0) REVERT: A 513 THR cc_start: 0.8421 (OUTLIER) cc_final: 0.8164 (t) REVERT: A 566 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7365 (pp20) REVERT: B 22 VAL cc_start: 0.6480 (OUTLIER) cc_final: 0.6199 (p) REVERT: B 23 MET cc_start: 0.4798 (OUTLIER) cc_final: 0.3951 (tmm) REVERT: B 120 ASN cc_start: 0.7631 (m110) cc_final: 0.7427 (m-40) REVERT: B 148 ILE cc_start: 0.8262 (tt) cc_final: 0.8053 (tt) REVERT: B 163 PHE cc_start: 0.7440 (m-80) cc_final: 0.7169 (m-80) REVERT: C 16 LEU cc_start: 0.8825 (mt) cc_final: 0.8595 (mt) REVERT: C 82 TYR cc_start: 0.6873 (m-10) cc_final: 0.6668 (m-10) REVERT: C 111 ARG cc_start: 0.8026 (mmm160) cc_final: 0.7766 (tpp80) REVERT: C 152 PHE cc_start: 0.8011 (m-80) cc_final: 0.7643 (m-80) REVERT: C 160 LEU cc_start: 0.8037 (tt) cc_final: 0.7817 (tm) REVERT: C 180 LEU cc_start: 0.7098 (tm) cc_final: 0.6862 (tt) REVERT: C 218 MET cc_start: 0.4100 (OUTLIER) cc_final: 0.2838 (tmt) REVERT: C 304 ASN cc_start: 0.7035 (m110) cc_final: 0.6695 (m110) REVERT: C 339 ASN cc_start: 0.8598 (m110) cc_final: 0.8232 (p0) REVERT: C 347 LYS cc_start: 0.8078 (mmpt) cc_final: 0.7620 (mmtm) REVERT: C 350 ASN cc_start: 0.7082 (t0) cc_final: 0.6765 (t0) REVERT: C 377 PHE cc_start: 0.7774 (m-10) cc_final: 0.7429 (m-10) REVERT: C 387 PHE cc_start: 0.8064 (p90) cc_final: 0.7853 (p90) REVERT: C 393 ASN cc_start: 0.8262 (p0) cc_final: 0.7912 (p0) REVERT: C 396 ASN cc_start: 0.8790 (OUTLIER) cc_final: 0.8501 (p0) outliers start: 45 outliers final: 15 residues processed: 313 average time/residue: 1.0685 time to fit residues: 371.3480 Evaluate side-chains 311 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 290 time to evaluate : 1.417 ------------------------------------------------------------------------------- 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 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 582 ILE Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 937 ASN Chi-restraints excluded: chain B residue 22 VAL 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 85 SER Chi-restraints excluded: chain C residue 165 TYR Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 396 ASN 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 72 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 117 optimal weight: 7.9990 chunk 0 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 154 optimal weight: 0.0970 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 151 HIS C 9 ASN C 351 GLN C 391 ASN C 415 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.191390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.150151 restraints weight = 20613.453| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 2.50 r_work: 0.3831 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 14229 Z= 0.244 Angle : 0.677 9.520 19355 Z= 0.356 Chirality : 0.046 0.272 2144 Planarity : 0.005 0.061 2357 Dihedral : 13.366 150.578 2118 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.21 % Favored : 94.67 % Rotamer: Outliers : 2.94 % Allowed : 18.01 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.20), residues: 1612 helix: 0.90 (0.21), residues: 580 sheet: -0.07 (0.31), residues: 282 loop : -1.15 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 8 HIS 0.012 0.002 HIS B 16 PHE 0.025 0.002 PHE A 526 TYR 0.023 0.002 TYR A 162 ARG 0.010 0.001 ARG B 98 Details of bonding type rmsd hydrogen bonds : bond 0.05530 ( 595) hydrogen bonds : angle 4.74904 ( 1672) covalent geometry : bond 0.00569 (14229) covalent geometry : angle 0.67715 (19355) *********************** 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 345 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 301 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 ASP cc_start: 0.7635 (t0) cc_final: 0.7354 (t0) REVERT: A 513 THR cc_start: 0.8429 (OUTLIER) cc_final: 0.8191 (t) REVERT: A 566 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7368 (pp20) REVERT: A 639 LYS cc_start: 0.7996 (ttpp) cc_final: 0.7650 (tttp) REVERT: A 837 LYS cc_start: 0.8148 (tptt) cc_final: 0.7874 (tptp) REVERT: A 859 MET cc_start: 0.4395 (mpp) cc_final: 0.3121 (mpp) REVERT: A 873 GLU cc_start: 0.6868 (mm-30) cc_final: 0.6551 (tp30) REVERT: B 22 VAL cc_start: 0.6743 (OUTLIER) cc_final: 0.6481 (t) REVERT: B 148 ILE cc_start: 0.8365 (tt) cc_final: 0.8129 (tt) REVERT: B 160 LYS cc_start: 0.6761 (mmtt) cc_final: 0.6419 (mmtt) REVERT: C 16 LEU cc_start: 0.8847 (mt) cc_final: 0.8627 (mt) REVERT: C 87 PHE cc_start: 0.7345 (OUTLIER) cc_final: 0.6301 (t80) REVERT: C 97 GLU cc_start: 0.6769 (pp20) cc_final: 0.6202 (mp0) REVERT: C 111 ARG cc_start: 0.8072 (mmm160) cc_final: 0.7351 (mmm160) REVERT: C 160 LEU cc_start: 0.8097 (tt) cc_final: 0.7893 (tm) REVERT: C 218 MET cc_start: 0.4148 (OUTLIER) cc_final: 0.2733 (tmm) REVERT: C 304 ASN cc_start: 0.7057 (m110) cc_final: 0.6657 (m110) REVERT: C 322 LYS cc_start: 0.8597 (tppp) cc_final: 0.8374 (tppp) REVERT: C 347 LYS cc_start: 0.8106 (mmpt) cc_final: 0.7714 (mmtm) REVERT: C 350 ASN cc_start: 0.7199 (t0) cc_final: 0.6866 (t0) REVERT: C 359 GLU cc_start: 0.6934 (tt0) cc_final: 0.6721 (tm-30) REVERT: C 375 MET cc_start: 0.7758 (ppp) cc_final: 0.7410 (ppp) REVERT: C 387 PHE cc_start: 0.8081 (p90) cc_final: 0.7812 (p90) REVERT: C 396 ASN cc_start: 0.8844 (OUTLIER) cc_final: 0.8532 (p0) outliers start: 44 outliers final: 24 residues processed: 316 average time/residue: 1.0936 time to fit residues: 383.4204 Evaluate side-chains 320 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 290 time to evaluate : 1.439 ------------------------------------------------------------------------------- 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 513 THR Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 937 ASN Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 150 LYS Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 7 LEU 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 218 MET Chi-restraints excluded: chain C residue 252 HIS Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 396 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 149 optimal weight: 5.9990 chunk 153 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 139 optimal weight: 9.9990 chunk 92 optimal weight: 0.0770 chunk 17 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 ASN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.195389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.154474 restraints weight = 20719.114| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 2.51 r_work: 0.3877 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.2501 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= 0.135 Angle : 0.619 10.792 19355 Z= 0.322 Chirality : 0.043 0.250 2144 Planarity : 0.004 0.053 2357 Dihedral : 13.228 147.569 2118 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.22 % Favored : 95.66 % Rotamer: Outliers : 2.00 % Allowed : 21.21 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.21), residues: 1612 helix: 1.16 (0.22), residues: 582 sheet: 0.01 (0.31), residues: 284 loop : -1.04 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 470 HIS 0.004 0.001 HIS A 170 PHE 0.023 0.001 PHE A 930 TYR 0.021 0.001 TYR A 162 ARG 0.011 0.001 ARG B 98 Details of bonding type rmsd hydrogen bonds : bond 0.04257 ( 595) hydrogen bonds : angle 4.51554 ( 1672) covalent geometry : bond 0.00309 (14229) covalent geometry : angle 0.61902 (19355) *********************** 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 328 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 298 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 ASP cc_start: 0.7536 (t0) cc_final: 0.7254 (t0) REVERT: A 513 THR cc_start: 0.8421 (OUTLIER) cc_final: 0.8209 (t) REVERT: A 566 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7323 (pp20) REVERT: A 639 LYS cc_start: 0.7913 (ttpp) cc_final: 0.7583 (ttpp) REVERT: A 679 TYR cc_start: 0.8478 (t80) cc_final: 0.8197 (t80) REVERT: A 859 MET cc_start: 0.4335 (mpp) cc_final: 0.3066 (mpp) REVERT: B 22 VAL cc_start: 0.6624 (OUTLIER) cc_final: 0.6345 (t) REVERT: B 148 ILE cc_start: 0.8302 (tt) cc_final: 0.8076 (tt) REVERT: B 160 LYS cc_start: 0.6695 (mmtt) cc_final: 0.6342 (mmtt) REVERT: C 16 LEU cc_start: 0.8837 (mt) cc_final: 0.8613 (mt) REVERT: C 95 MET cc_start: 0.1966 (pmm) cc_final: 0.0179 (ppp) REVERT: C 152 PHE cc_start: 0.7717 (m-10) cc_final: 0.7111 (m-80) REVERT: C 218 MET cc_start: 0.4013 (OUTLIER) cc_final: 0.2685 (tmm) REVERT: C 244 LYS cc_start: 0.8350 (tppt) cc_final: 0.8000 (tppt) REVERT: C 304 ASN cc_start: 0.6994 (m110) cc_final: 0.6610 (m110) REVERT: C 322 LYS cc_start: 0.8509 (tppp) cc_final: 0.8049 (tppp) REVERT: C 350 ASN cc_start: 0.7145 (t0) cc_final: 0.6804 (t0) REVERT: C 359 GLU cc_start: 0.6837 (tt0) cc_final: 0.6559 (tm-30) REVERT: C 387 PHE cc_start: 0.8029 (p90) cc_final: 0.7691 (p90) REVERT: C 391 ASN cc_start: 0.7280 (t0) cc_final: 0.7008 (t0) REVERT: C 393 ASN cc_start: 0.8607 (p0) cc_final: 0.8131 (p0) REVERT: C 396 ASN cc_start: 0.8755 (OUTLIER) cc_final: 0.8464 (p0) outliers start: 30 outliers final: 17 residues processed: 309 average time/residue: 1.0995 time to fit residues: 376.2367 Evaluate side-chains 308 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 286 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 471 GLU 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 638 LYS Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 837 LYS Chi-restraints excluded: chain B residue 22 VAL 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 7 LEU Chi-restraints excluded: chain C residue 165 TYR Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 252 HIS Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 396 ASN 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 52 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 71 optimal weight: 0.1980 chunk 4 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 ASN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.192280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.151194 restraints weight = 20555.034| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 2.50 r_work: 0.3847 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14229 Z= 0.192 Angle : 0.660 10.931 19355 Z= 0.344 Chirality : 0.045 0.216 2144 Planarity : 0.005 0.056 2357 Dihedral : 13.283 149.305 2118 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.96 % Favored : 94.91 % Rotamer: Outliers : 2.20 % Allowed : 21.21 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.21), residues: 1612 helix: 0.99 (0.22), residues: 582 sheet: -0.05 (0.31), residues: 283 loop : -1.06 (0.21), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 470 HIS 0.008 0.001 HIS B 16 PHE 0.028 0.002 PHE A 930 TYR 0.023 0.002 TYR A 162 ARG 0.014 0.001 ARG B 98 Details of bonding type rmsd hydrogen bonds : bond 0.05030 ( 595) hydrogen bonds : angle 4.61544 ( 1672) covalent geometry : bond 0.00448 (14229) covalent geometry : angle 0.65973 (19355) *********************** 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 340 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 307 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ASP cc_start: 0.7926 (t70) cc_final: 0.7714 (t0) REVERT: A 398 ASP cc_start: 0.7640 (t0) cc_final: 0.7316 (t0) REVERT: A 513 THR cc_start: 0.8445 (OUTLIER) cc_final: 0.8200 (t) REVERT: A 566 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7361 (pp20) REVERT: A 639 LYS cc_start: 0.7959 (ttpp) cc_final: 0.7633 (ttpp) REVERT: A 837 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7826 (tptp) REVERT: A 859 MET cc_start: 0.4358 (mpp) cc_final: 0.3113 (mpp) REVERT: A 873 GLU cc_start: 0.6849 (tp30) cc_final: 0.6521 (mm-30) REVERT: A 908 MET cc_start: 0.6644 (tmm) cc_final: 0.6386 (tmm) REVERT: A 952 THR cc_start: 0.7943 (p) cc_final: 0.7436 (t) REVERT: B 22 VAL cc_start: 0.6839 (OUTLIER) cc_final: 0.6544 (t) REVERT: B 148 ILE cc_start: 0.8302 (tt) cc_final: 0.8084 (tt) REVERT: B 160 LYS cc_start: 0.6752 (mmtt) cc_final: 0.6376 (mmtt) REVERT: B 163 PHE cc_start: 0.7442 (m-80) cc_final: 0.7219 (m-80) REVERT: C 16 LEU cc_start: 0.8855 (mt) cc_final: 0.8637 (mt) REVERT: C 95 MET cc_start: 0.2249 (pmm) cc_final: 0.0729 (ppp) REVERT: C 111 ARG cc_start: 0.8062 (mmm160) cc_final: 0.7785 (tpp80) REVERT: C 218 MET cc_start: 0.4055 (OUTLIER) cc_final: 0.2656 (tmm) REVERT: C 244 LYS cc_start: 0.8431 (tppt) cc_final: 0.8125 (tppt) REVERT: C 304 ASN cc_start: 0.7060 (m110) cc_final: 0.6681 (m110) REVERT: C 339 ASN cc_start: 0.8689 (m110) cc_final: 0.8267 (p0) REVERT: C 347 LYS cc_start: 0.7920 (mmpt) cc_final: 0.7166 (mptt) REVERT: C 350 ASN cc_start: 0.7249 (t0) cc_final: 0.6884 (t0) REVERT: C 387 PHE cc_start: 0.8042 (p90) cc_final: 0.7756 (p90) REVERT: C 391 ASN cc_start: 0.7265 (t0) cc_final: 0.6996 (t0) REVERT: C 393 ASN cc_start: 0.8444 (p0) cc_final: 0.8047 (p0) REVERT: C 396 ASN cc_start: 0.8809 (OUTLIER) cc_final: 0.8503 (p0) outliers start: 33 outliers final: 21 residues processed: 320 average time/residue: 1.0385 time to fit residues: 367.8031 Evaluate side-chains 317 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 290 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 421 CYS 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 576 ASN Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 837 LYS Chi-restraints excluded: chain A residue 937 ASN Chi-restraints excluded: chain B residue 22 VAL 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 7 LEU Chi-restraints excluded: chain C residue 165 TYR Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 252 HIS Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 396 ASN Chi-restraints excluded: chain C residue 402 THR 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 96 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 13 optimal weight: 0.0870 chunk 39 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.193669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.153072 restraints weight = 20502.991| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 2.50 r_work: 0.3866 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14229 Z= 0.148 Angle : 0.652 10.902 19355 Z= 0.338 Chirality : 0.043 0.222 2144 Planarity : 0.005 0.053 2357 Dihedral : 13.233 147.527 2118 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.34 % Favored : 95.53 % Rotamer: Outliers : 2.54 % Allowed : 21.75 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.21), residues: 1612 helix: 1.04 (0.22), residues: 582 sheet: -0.01 (0.30), residues: 296 loop : -0.97 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 470 HIS 0.005 0.001 HIS A 170 PHE 0.029 0.002 PHE A 930 TYR 0.022 0.001 TYR A 162 ARG 0.016 0.001 ARG B 98 Details of bonding type rmsd hydrogen bonds : bond 0.04478 ( 595) hydrogen bonds : angle 4.51936 ( 1672) covalent geometry : bond 0.00342 (14229) covalent geometry : angle 0.65182 (19355) *********************** 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 326 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 288 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ASP cc_start: 0.7864 (t70) cc_final: 0.7636 (t0) REVERT: A 398 ASP cc_start: 0.7601 (t0) cc_final: 0.7300 (t0) REVERT: A 513 THR cc_start: 0.8428 (OUTLIER) cc_final: 0.8207 (t) REVERT: A 566 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7318 (pp20) REVERT: A 639 LYS cc_start: 0.7894 (ttpp) cc_final: 0.7570 (ttpp) REVERT: A 859 MET cc_start: 0.4339 (mpp) cc_final: 0.3097 (mpp) REVERT: A 908 MET cc_start: 0.6564 (tmm) cc_final: 0.6301 (tmm) REVERT: A 926 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7501 (tm-30) REVERT: A 930 PHE cc_start: 0.8679 (p90) cc_final: 0.8469 (p90) REVERT: B 22 VAL cc_start: 0.6750 (OUTLIER) cc_final: 0.6428 (t) REVERT: B 148 ILE cc_start: 0.8290 (tt) cc_final: 0.8080 (tt) REVERT: C 16 LEU cc_start: 0.8841 (mt) cc_final: 0.8622 (mt) REVERT: C 95 MET cc_start: 0.2290 (pmm) cc_final: 0.0616 (ppp) REVERT: C 152 PHE cc_start: 0.7836 (m-80) cc_final: 0.7366 (m-80) REVERT: C 244 LYS cc_start: 0.8451 (tppt) cc_final: 0.8180 (tppt) REVERT: C 304 ASN cc_start: 0.7059 (m110) cc_final: 0.6694 (m110) REVERT: C 339 ASN cc_start: 0.8684 (m110) cc_final: 0.8245 (p0) REVERT: C 347 LYS cc_start: 0.7962 (mmpt) cc_final: 0.7374 (mmtm) REVERT: C 350 ASN cc_start: 0.7254 (t0) cc_final: 0.6895 (t0) REVERT: C 375 MET cc_start: 0.7780 (ppp) cc_final: 0.7234 (ppp) REVERT: C 387 PHE cc_start: 0.8054 (p90) cc_final: 0.7752 (p90) REVERT: C 391 ASN cc_start: 0.7256 (t0) cc_final: 0.6986 (t0) REVERT: C 393 ASN cc_start: 0.8387 (p0) cc_final: 0.7964 (p0) REVERT: C 396 ASN cc_start: 0.8769 (OUTLIER) cc_final: 0.8454 (p0) outliers start: 38 outliers final: 22 residues processed: 303 average time/residue: 1.0647 time to fit residues: 357.6652 Evaluate side-chains 307 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 281 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 471 GLU 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 578 LEU Chi-restraints excluded: chain A residue 638 LYS Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 837 LYS Chi-restraints excluded: chain B residue 22 VAL 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 7 LEU Chi-restraints excluded: chain C residue 252 HIS Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 396 ASN Chi-restraints excluded: chain C residue 402 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 97 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 144 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 chunk 147 optimal weight: 50.0000 chunk 105 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 ASN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.192911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.151863 restraints weight = 20344.153| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 2.49 r_work: 0.3837 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14229 Z= 0.214 Angle : 0.699 12.685 19355 Z= 0.363 Chirality : 0.046 0.239 2144 Planarity : 0.005 0.063 2357 Dihedral : 13.332 149.165 2118 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.15 % Favored : 94.73 % Rotamer: Outliers : 2.33 % Allowed : 22.28 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.21), residues: 1612 helix: 0.91 (0.22), residues: 580 sheet: -0.10 (0.30), residues: 295 loop : -1.03 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 470 HIS 0.009 0.002 HIS A 170 PHE 0.027 0.002 PHE A 930 TYR 0.025 0.002 TYR A 162 ARG 0.018 0.001 ARG B 98 Details of bonding type rmsd hydrogen bonds : bond 0.05285 ( 595) hydrogen bonds : angle 4.66299 ( 1672) covalent geometry : bond 0.00501 (14229) covalent geometry : angle 0.69908 (19355) *********************** 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 329 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 294 time to evaluate : 1.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 ASP cc_start: 0.7722 (t0) cc_final: 0.7434 (t0) REVERT: A 513 THR cc_start: 0.8445 (OUTLIER) cc_final: 0.8189 (t) REVERT: A 566 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7363 (pp20) REVERT: A 639 LYS cc_start: 0.7956 (ttpp) cc_final: 0.7623 (ttpp) REVERT: A 828 THR cc_start: 0.7048 (OUTLIER) cc_final: 0.6694 (p) REVERT: A 837 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7867 (tptp) REVERT: A 859 MET cc_start: 0.4473 (mpp) cc_final: 0.3277 (mpp) REVERT: A 873 GLU cc_start: 0.6930 (mm-30) cc_final: 0.6381 (tp30) REVERT: A 996 MET cc_start: 0.7562 (tpp) cc_final: 0.7345 (tpp) REVERT: B 22 VAL cc_start: 0.6886 (OUTLIER) cc_final: 0.6562 (t) REVERT: B 160 LYS cc_start: 0.6617 (mmtt) cc_final: 0.6272 (mmtt) REVERT: C 16 LEU cc_start: 0.8836 (mt) cc_final: 0.8626 (mt) REVERT: C 95 MET cc_start: 0.2596 (pmm) cc_final: 0.0830 (ppp) REVERT: C 97 GLU cc_start: 0.6571 (pp20) cc_final: 0.6184 (pp20) REVERT: C 249 ASP cc_start: 0.6366 (p0) cc_final: 0.5389 (p0) REVERT: C 304 ASN cc_start: 0.7081 (m110) cc_final: 0.6724 (m110) REVERT: C 339 ASN cc_start: 0.8691 (m110) cc_final: 0.8245 (p0) REVERT: C 347 LYS cc_start: 0.7969 (mmpt) cc_final: 0.7406 (mmtm) REVERT: C 350 ASN cc_start: 0.7386 (t0) cc_final: 0.6998 (t0) REVERT: C 375 MET cc_start: 0.7756 (ppp) cc_final: 0.7324 (ppp) REVERT: C 387 PHE cc_start: 0.8106 (p90) cc_final: 0.7745 (p90) REVERT: C 396 ASN cc_start: 0.8835 (OUTLIER) cc_final: 0.8516 (p0) outliers start: 35 outliers final: 22 residues processed: 308 average time/residue: 1.1042 time to fit residues: 377.7060 Evaluate side-chains 313 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 285 time to evaluate : 1.394 ------------------------------------------------------------------------------- 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 399 GLU Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 471 GLU 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 707 LEU Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 837 LYS Chi-restraints excluded: chain A residue 937 ASN Chi-restraints excluded: chain B residue 22 VAL 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 252 HIS Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 396 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 69 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 133 optimal weight: 30.0000 chunk 120 optimal weight: 2.9990 chunk 143 optimal weight: 0.0020 chunk 15 optimal weight: 0.6980 chunk 154 optimal weight: 3.9990 chunk 81 optimal weight: 0.0030 chunk 94 optimal weight: 0.0980 chunk 68 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 overall best weight: 0.2798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.196481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.155711 restraints weight = 20549.599| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 2.52 r_work: 0.3891 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14229 Z= 0.129 Angle : 0.669 11.860 19355 Z= 0.346 Chirality : 0.043 0.248 2144 Planarity : 0.004 0.056 2357 Dihedral : 13.219 146.045 2118 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.09 % Favored : 95.78 % Rotamer: Outliers : 1.60 % Allowed : 23.75 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.21), residues: 1612 helix: 1.15 (0.22), residues: 581 sheet: -0.05 (0.30), residues: 305 loop : -1.00 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 470 HIS 0.003 0.001 HIS A 185 PHE 0.045 0.001 PHE C 152 TYR 0.021 0.001 TYR A 162 ARG 0.020 0.000 ARG B 98 Details of bonding type rmsd hydrogen bonds : bond 0.03991 ( 595) hydrogen bonds : angle 4.48545 ( 1672) covalent geometry : bond 0.00293 (14229) covalent geometry : angle 0.66904 (19355) ********************** 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 318 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 294 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.8232 (t80) cc_final: 0.8019 (t80) REVERT: A 357 MET cc_start: 0.7299 (mpp) cc_final: 0.6720 (mpp) REVERT: A 398 ASP cc_start: 0.7657 (t0) cc_final: 0.7162 (t0) REVERT: A 513 THR cc_start: 0.8431 (OUTLIER) cc_final: 0.8207 (t) REVERT: A 639 LYS cc_start: 0.7915 (ttpp) cc_final: 0.7602 (ttpp) REVERT: A 828 THR cc_start: 0.7232 (OUTLIER) cc_final: 0.6904 (p) REVERT: A 859 MET cc_start: 0.4309 (mpp) cc_final: 0.3103 (mpp) REVERT: A 873 GLU cc_start: 0.6777 (mm-30) cc_final: 0.5993 (tp30) REVERT: A 926 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7506 (tm-30) REVERT: A 930 PHE cc_start: 0.8687 (p90) cc_final: 0.8454 (p90) REVERT: A 995 ARG cc_start: 0.8456 (ttp80) cc_final: 0.8245 (mtm110) REVERT: A 996 MET cc_start: 0.7680 (tpp) cc_final: 0.7142 (tpp) REVERT: B 22 VAL cc_start: 0.6668 (OUTLIER) cc_final: 0.6363 (t) REVERT: B 160 LYS cc_start: 0.6693 (mmtt) cc_final: 0.6334 (mmtt) REVERT: C 16 LEU cc_start: 0.8828 (mt) cc_final: 0.8610 (mt) REVERT: C 95 MET cc_start: 0.2450 (pmm) cc_final: 0.0840 (ppp) REVERT: C 97 GLU cc_start: 0.6542 (pp20) cc_final: 0.6205 (pp20) REVERT: C 111 ARG cc_start: 0.8096 (mmm160) cc_final: 0.7440 (mmm-85) REVERT: C 244 LYS cc_start: 0.8302 (tppt) cc_final: 0.7800 (tppt) REVERT: C 249 ASP cc_start: 0.6360 (p0) cc_final: 0.5410 (p0) REVERT: C 304 ASN cc_start: 0.7086 (m110) cc_final: 0.6672 (m110) REVERT: C 339 ASN cc_start: 0.8625 (m110) cc_final: 0.8099 (p0) REVERT: C 347 LYS cc_start: 0.7909 (mmpt) cc_final: 0.7466 (mmtm) REVERT: C 350 ASN cc_start: 0.7290 (t0) cc_final: 0.6913 (t0) REVERT: C 375 MET cc_start: 0.7759 (ppp) cc_final: 0.7436 (ppp) REVERT: C 387 PHE cc_start: 0.8076 (p90) cc_final: 0.7752 (p90) REVERT: C 393 ASN cc_start: 0.8552 (p0) cc_final: 0.8171 (p0) REVERT: C 396 ASN cc_start: 0.8734 (OUTLIER) cc_final: 0.8415 (p0) outliers start: 24 outliers final: 19 residues processed: 303 average time/residue: 1.0373 time to fit residues: 348.9933 Evaluate side-chains 309 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 286 time to evaluate : 1.516 ------------------------------------------------------------------------------- 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 492 MET Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 837 LYS Chi-restraints excluded: chain B residue 22 VAL 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 155 LEU Chi-restraints excluded: chain C residue 252 HIS Chi-restraints excluded: chain C residue 396 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 62 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 139 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 ASN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.191163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.150125 restraints weight = 20535.092| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 2.49 r_work: 0.3835 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 14229 Z= 0.217 Angle : 0.723 12.892 19355 Z= 0.378 Chirality : 0.046 0.251 2144 Planarity : 0.005 0.065 2357 Dihedral : 13.329 148.878 2118 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.78 % Favored : 95.10 % Rotamer: Outliers : 1.67 % Allowed : 23.75 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.21), residues: 1612 helix: 0.97 (0.22), residues: 580 sheet: -0.18 (0.29), residues: 306 loop : -1.10 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 470 HIS 0.008 0.002 HIS B 16 PHE 0.047 0.002 PHE C 152 TYR 0.026 0.002 TYR A 668 ARG 0.020 0.001 ARG B 98 Details of bonding type rmsd hydrogen bonds : bond 0.05245 ( 595) hydrogen bonds : angle 4.64534 ( 1672) covalent geometry : bond 0.00508 (14229) covalent geometry : angle 0.72283 (19355) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10275.26 seconds wall clock time: 177 minutes 25.26 seconds (10645.26 seconds total)