Starting phenix.real_space_refine on Thu Sep 18 09:11:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k9v_62200/09_2025/9k9v_62200.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k9v_62200/09_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_62200/09_2025/9k9v_62200.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k9v_62200/09_2025/9k9v_62200.map" model { file = "/net/cci-nas-00/data/ceres_data/9k9v_62200/09_2025/9k9v_62200.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k9v_62200/09_2025/9k9v_62200.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2165 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 29 5.49 5 S 70 5.16 5 C 8806 2.51 5 N 2301 2.21 5 O 2663 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13869 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 8106 Classifications: {'peptide': 990} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 952} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1762 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 2} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 204} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 3389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3389 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 10, 'TRANS': 405} Chain breaks: 1 Chain: "P" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 345 Classifications: {'DNA': 17} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 16} Chain: "E" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 267 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Time building chain proxies: 3.56, per 1000 atoms: 0.26 Number of scatterers: 13869 At special positions: 0 Unit cell: (110.5, 124.95, 145.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 70 16.00 P 29 15.00 O 2663 8.00 N 2301 7.00 C 8806 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 752.1 milliseconds Enol-peptide restraints added in 1.2 microseconds 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3110 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 20 sheets defined 39.6% alpha, 20.2% beta 12 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 108 through 118 Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 209 through 220 removed outlier: 3.588A pdb=" N ILE A 213 " --> pdb=" O THR A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 253 Processing helix chain 'A' and resid 267 through 280 Processing helix chain 'A' and resid 331 through 339 removed outlier: 3.534A pdb=" N GLU A 339 " --> pdb=" O ILE A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 380 through 389 Processing helix chain 'A' and resid 439 through 446 removed outlier: 3.539A pdb=" N MET A 443 " --> pdb=" O ASP A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 474 removed outlier: 3.701A pdb=" N CYS A 466 " --> pdb=" O ASP A 462 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLN A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 487 Processing helix chain 'A' and resid 489 through 493 Processing helix chain 'A' and resid 502 through 514 Processing helix chain 'A' and resid 552 through 562 Processing helix chain 'A' and resid 564 through 566 No H-bonds generated for 'chain 'A' and resid 564 through 566' Processing helix chain 'A' and resid 576 through 591 Processing helix chain 'A' and resid 622 through 643 Processing helix chain 'A' and resid 646 through 665 Processing helix chain 'A' and resid 666 through 672 removed outlier: 3.590A pdb=" N GLY A 672 " --> pdb=" O TYR A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 703 Processing helix chain 'A' and resid 763 through 781 Processing helix chain 'A' and resid 837 through 854 removed outlier: 3.735A pdb=" N ASN A 841 " --> pdb=" O LYS A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 883 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.710A pdb=" N MET A 891 " --> pdb=" O GLU A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 918 removed outlier: 4.042A pdb=" N TYR A 909 " --> pdb=" O ASN A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 949 No H-bonds generated for 'chain 'A' and resid 947 through 949' Processing helix chain 'A' and resid 967 through 982 removed outlier: 4.003A pdb=" N TYR A 971 " --> pdb=" O PHE A 967 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU A 982 " --> pdb=" O GLU A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 998 Processing helix chain 'B' and resid 19 through 31 removed outlier: 4.215A pdb=" N SER B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N GLN B 25 " --> pdb=" O PRO B 21 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 26 " --> pdb=" O VAL B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 38 removed outlier: 3.540A pdb=" N LEU B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 86 through 101 Processing helix chain 'B' and resid 133 through 150 removed outlier: 5.472A pdb=" N LYS B 139 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ILE B 140 " --> pdb=" O TYR B 136 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS B 150 " --> pdb=" O GLN B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 170 removed outlier: 3.612A pdb=" N LYS B 169 " --> pdb=" O ASN B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 192 removed outlier: 3.820A pdb=" N HIS B 187 " --> pdb=" O ALA B 184 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN B 188 " --> pdb=" O ARG B 185 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N PHE B 189 " --> pdb=" O ASP B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 205 removed outlier: 3.613A pdb=" N ILE B 197 " --> pdb=" O ARG B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 214 Processing helix chain 'C' and resid 4 through 19 Processing helix chain 'C' and resid 24 through 42 Processing helix chain 'C' and resid 57 through 61 Processing helix chain 'C' and resid 107 through 121 removed outlier: 3.600A pdb=" N SER C 120 " --> pdb=" O LYS C 116 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASP C 121 " --> pdb=" O VAL C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 158 removed outlier: 4.197A pdb=" N ILE C 151 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYS C 153 " --> pdb=" O VAL C 149 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU C 154 " --> pdb=" O ASN C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 189 Processing helix chain 'C' and resid 249 through 256 Processing helix chain 'C' and resid 285 through 298 removed outlier: 3.506A pdb=" N LYS C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 324 Processing helix chain 'C' and resid 330 through 341 removed outlier: 3.541A pdb=" N SER C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 350 removed outlier: 3.604A pdb=" N ILE C 348 " --> pdb=" O VAL C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 361 Processing helix chain 'C' and resid 364 through 373 removed outlier: 3.626A pdb=" N ASN C 373 " --> pdb=" O ILE C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 396 Processing helix chain 'C' and resid 397 through 425 removed outlier: 4.325A pdb=" N ASN C 408 " --> pdb=" O TYR C 404 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N GLN C 409 " --> pdb=" O GLY C 405 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER C 412 " --> pdb=" O ASN C 408 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 134 removed outlier: 8.313A pdb=" N TYR A 140 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N PHE A 31 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N CYS A 142 " --> pdb=" O PHE A 31 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ARG A 33 " --> pdb=" O CYS A 142 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N PHE A 17 " --> pdb=" O GLU A 10 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N GLU A 10 " --> pdb=" O PHE A 17 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TYR A 19 " --> pdb=" O TRP A 8 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N TRP A 8 " --> pdb=" O TYR A 19 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LYS A 21 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N CYS A 124 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER A 126 " --> pdb=" O LYS A 151 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LYS A 151 " --> pdb=" O SER A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 43 removed outlier: 3.790A pdb=" N GLY A 61 " --> pdb=" O MET A 88 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N LEU A 90 " --> pdb=" O PRO A 59 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N GLU A 92 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ALA A 57 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N ILE A 516 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ARG A 64 " --> pdb=" O ILE A 516 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL A 518 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE A 66 " --> pdb=" O VAL A 518 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 222 through 223 removed outlier: 6.458A pdb=" N LEU A 222 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N VAL A 237 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N THR A 201 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N CYS A 239 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ILE A 203 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N SER A 184 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU A 165 " --> pdb=" O VAL A 260 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 285 through 287 Processing sheet with id=AA5, first strand: chain 'A' and resid 300 through 302 Processing sheet with id=AA6, first strand: chain 'A' and resid 355 through 362 removed outlier: 7.068A pdb=" N MET A 357 " --> pdb=" O ASP A 373 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ASP A 373 " --> pdb=" O MET A 357 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N THR A 369 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG A 407 " --> pdb=" O VAL A 418 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 732 through 734 removed outlier: 3.566A pdb=" N PHE A 743 " --> pdb=" O LEU A 707 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N SER A 747 " --> pdb=" O GLU A 758 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLU A 758 " --> pdb=" O SER A 747 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N TYR A 749 " --> pdb=" O PHE A 756 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL A 545 " --> pdb=" O VAL A 794 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL A 794 " --> pdb=" O VAL A 545 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE A 547 " --> pdb=" O GLU A 792 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LEU A 798 " --> pdb=" O THR A 807 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N THR A 807 " --> pdb=" O LEU A 798 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 568 through 574 removed outlier: 6.489A pdb=" N LEU A 568 " --> pdb=" O ASP A 616 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASP A 616 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY A 570 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLU A 611 " --> pdb=" O CYS A 601 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 892 through 895 removed outlier: 4.386A pdb=" N TYR A 929 " --> pdb=" O ILE A 954 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 892 through 895 Processing sheet with id=AB2, first strand: chain 'B' and resid 2 through 4 Processing sheet with id=AB3, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.858A pdb=" N CYS B 125 " --> pdb=" O SER B 43 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 116 through 120 removed outlier: 7.578A pdb=" N VAL B 62 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N TRP B 119 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL B 64 " --> pdb=" O TRP B 119 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N CYS B 63 " --> pdb=" O TYR B 156 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LEU B 155 " --> pdb=" O ILE B 177 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 107 through 108 Processing sheet with id=AB6, first strand: chain 'C' and resid 70 through 71 removed outlier: 3.839A pdb=" N THR C 174 " --> pdb=" O ILE C 71 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 166 through 169 removed outlier: 3.867A pdb=" N GLN C 208 " --> pdb=" O TYR C 199 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 95 through 97 removed outlier: 6.477A pdb=" N ILE C 124 " --> pdb=" O SER C 143 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N SER C 143 " --> pdb=" O ILE C 124 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N PHE C 126 " --> pdb=" O ALA C 141 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ALA C 141 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ARG C 128 " --> pdb=" O GLU C 139 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU C 139 " --> pdb=" O ARG C 128 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 233 through 239 removed outlier: 3.717A pdb=" N ILE C 234 " --> pdb=" O ASP C 226 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER C 222 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 302 through 303 removed outlier: 3.823A pdb=" N TYR C 302 " --> pdb=" O SER C 309 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 375 through 380 removed outlier: 3.642A pdb=" N ASN C 386 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLU C 380 " --> pdb=" O VAL C 384 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N VAL C 384 " --> pdb=" O GLU C 380 " (cutoff:3.500A) 573 hydrogen bonds defined for protein. 1620 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 26 hydrogen bonds 52 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 2.87 Time building geometry restraints manager: 1.56 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: 3.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.290 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.100 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.21), residues: 1612 helix: 1.38 (0.22), residues: 572 sheet: 0.47 (0.31), residues: 293 loop : -0.79 (0.22), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 287 TYR 0.017 0.001 TYR A 74 PHE 0.027 0.002 PHE C 152 TRP 0.012 0.001 TRP A 8 HIS 0.005 0.001 HIS B 16 Details of bonding type rmsd covalent geometry : bond 0.00312 (14229) covalent geometry : angle 0.60584 (19355) hydrogen bonds : bond 0.14477 ( 595) hydrogen bonds : angle 6.29019 ( 1672) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 298 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 399 GLU cc_start: 0.6690 (mm-30) cc_final: 0.6298 (mm-30) REVERT: A 837 LYS cc_start: 0.7846 (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: 0.5998 (t0) REVERT: C 393 ASN cc_start: 0.8015 (p0) cc_final: 0.7150 (p0) REVERT: C 421 LYS cc_start: 0.7245 (tppp) cc_final: 0.6837 (tppp) outliers start: 3 outliers final: 0 residues processed: 299 average time/residue: 0.5561 time to fit residues: 183.0392 Evaluate side-chains 268 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 397 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.190767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.149586 restraints weight = 20533.129| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 2.52 r_work: 0.3821 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 14229 Z= 0.326 Angle : 0.741 9.720 19355 Z= 0.394 Chirality : 0.050 0.318 2144 Planarity : 0.006 0.071 2357 Dihedral : 13.285 150.722 2118 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.21 % Favored : 94.60 % Rotamer: Outliers : 1.87 % Allowed : 11.87 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.20), residues: 1612 helix: 0.79 (0.21), residues: 583 sheet: 0.21 (0.31), residues: 297 loop : -1.18 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 111 TYR 0.027 0.002 TYR A 806 PHE 0.027 0.003 PHE C 354 TRP 0.025 0.003 TRP A 8 HIS 0.018 0.002 HIS B 16 Details of bonding type rmsd covalent geometry : bond 0.00758 (14229) covalent geometry : angle 0.74070 (19355) hydrogen bonds : bond 0.06672 ( 595) hydrogen bonds : angle 5.00974 ( 1672) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 305 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 LYS cc_start: 0.8266 (mtmt) cc_final: 0.7387 (mtmt) REVERT: A 371 ILE cc_start: 0.8538 (tp) cc_final: 0.8281 (tt) REVERT: A 492 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7893 (mtp) REVERT: A 566 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7377 (pp20) REVERT: A 837 LYS cc_start: 0.8272 (tptt) cc_final: 0.8064 (tptt) REVERT: C 16 LEU cc_start: 0.8861 (mt) cc_final: 0.8641 (mt) REVERT: C 152 PHE cc_start: 0.8211 (m-80) cc_final: 0.7805 (m-80) REVERT: C 177 ASP cc_start: 0.6878 (t0) cc_final: 0.6675 (t0) REVERT: C 304 ASN cc_start: 0.7249 (m110) cc_final: 0.6921 (m110) REVERT: C 347 LYS cc_start: 0.8067 (mppt) cc_final: 0.7866 (mmtm) REVERT: C 350 ASN cc_start: 0.7023 (t0) cc_final: 0.6718 (t0) REVERT: C 375 MET cc_start: 0.7663 (ppp) cc_final: 0.7330 (ppp) REVERT: C 396 ASN cc_start: 0.8779 (OUTLIER) cc_final: 0.8517 (p0) REVERT: C 421 LYS cc_start: 0.7382 (tppp) cc_final: 0.7071 (mmtt) outliers start: 28 outliers final: 9 residues processed: 311 average time/residue: 0.5832 time to fit residues: 199.1251 Evaluate side-chains 302 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 290 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 MET 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 A residue 937 ASN Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 150 LYS 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 95 optimal weight: 0.8980 chunk 133 optimal weight: 8.9990 chunk 58 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 113 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 156 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN A 263 ASN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 9 ASN C 339 ASN C 391 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.195339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.154251 restraints weight = 20776.284| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 2.55 r_work: 0.3864 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.1946 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= 0.153 Angle : 0.614 9.722 19355 Z= 0.323 Chirality : 0.044 0.275 2144 Planarity : 0.004 0.056 2357 Dihedral : 13.252 148.369 2118 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.16 % Favored : 95.72 % Rotamer: Outliers : 1.80 % Allowed : 16.08 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.20), residues: 1612 helix: 0.98 (0.21), residues: 587 sheet: 0.19 (0.31), residues: 283 loop : -1.08 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 995 TYR 0.021 0.001 TYR A 162 PHE 0.021 0.002 PHE A 526 TRP 0.017 0.002 TRP A 470 HIS 0.005 0.001 HIS B 16 Details of bonding type rmsd covalent geometry : bond 0.00352 (14229) covalent geometry : angle 0.61441 (19355) hydrogen bonds : bond 0.04792 ( 595) hydrogen bonds : angle 4.66622 ( 1672) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 298 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ASP cc_start: 0.7858 (t70) cc_final: 0.7626 (t0) REVERT: A 371 ILE cc_start: 0.8534 (tp) cc_final: 0.8303 (tt) REVERT: A 455 MET cc_start: 0.7758 (ttm) cc_final: 0.7462 (mtt) REVERT: A 837 LYS cc_start: 0.8127 (tptt) cc_final: 0.7902 (tptt) REVERT: B 23 MET cc_start: 0.4680 (OUTLIER) cc_final: 0.4005 (tmm) REVERT: B 148 ILE cc_start: 0.8306 (tt) cc_final: 0.8105 (tt) REVERT: C 152 PHE cc_start: 0.8088 (m-80) cc_final: 0.7725 (m-80) REVERT: C 304 ASN cc_start: 0.7083 (m110) cc_final: 0.6709 (m110) REVERT: C 322 LYS cc_start: 0.8576 (tppp) cc_final: 0.8353 (tppp) REVERT: C 339 ASN cc_start: 0.8678 (m110) cc_final: 0.8289 (p0) REVERT: C 350 ASN cc_start: 0.6967 (t0) cc_final: 0.6663 (t0) REVERT: C 375 MET cc_start: 0.7621 (ppp) cc_final: 0.7365 (ppp) REVERT: C 377 PHE cc_start: 0.7569 (m-10) cc_final: 0.7341 (m-10) REVERT: C 387 PHE cc_start: 0.8019 (p90) cc_final: 0.7750 (p90) REVERT: C 393 ASN cc_start: 0.8222 (p0) cc_final: 0.7713 (p0) REVERT: C 396 ASN cc_start: 0.8765 (OUTLIER) cc_final: 0.8445 (p0) REVERT: C 397 ASN cc_start: 0.8044 (t0) cc_final: 0.7839 (t0) REVERT: C 421 LYS cc_start: 0.7369 (tppp) cc_final: 0.7048 (mmtt) outliers start: 27 outliers final: 11 residues processed: 307 average time/residue: 0.5880 time to fit residues: 198.7527 Evaluate side-chains 297 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 284 time to evaluate : 0.587 ------------------------------------------------------------------------------- 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 576 ASN Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 165 TYR 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 18 optimal weight: 2.9990 chunk 123 optimal weight: 8.9990 chunk 92 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 128 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 101 optimal weight: 0.0980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN A 263 ASN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN C 9 ASN C 391 ASN C 415 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.193073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.152021 restraints weight = 20734.113| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 2.50 r_work: 0.3854 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14229 Z= 0.189 Angle : 0.633 9.502 19355 Z= 0.334 Chirality : 0.045 0.268 2144 Planarity : 0.005 0.057 2357 Dihedral : 13.316 149.908 2118 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.96 % Favored : 94.91 % Rotamer: Outliers : 2.60 % Allowed : 17.21 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.20), residues: 1612 helix: 0.99 (0.21), residues: 589 sheet: 0.05 (0.31), residues: 283 loop : -1.12 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 346 TYR 0.027 0.002 TYR C 165 PHE 0.019 0.002 PHE C 377 TRP 0.018 0.002 TRP A 470 HIS 0.009 0.001 HIS B 16 Details of bonding type rmsd covalent geometry : bond 0.00441 (14229) covalent geometry : angle 0.63316 (19355) hydrogen bonds : bond 0.05013 ( 595) hydrogen bonds : angle 4.67024 ( 1672) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 306 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 ILE cc_start: 0.8516 (tp) cc_final: 0.8305 (tt) REVERT: A 398 ASP cc_start: 0.7547 (t0) cc_final: 0.7347 (t0) REVERT: A 513 THR cc_start: 0.8402 (OUTLIER) cc_final: 0.8159 (t) REVERT: A 566 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7370 (pp20) REVERT: A 837 LYS cc_start: 0.8168 (tptt) cc_final: 0.7863 (tptp) REVERT: B 22 VAL cc_start: 0.6387 (OUTLIER) cc_final: 0.6125 (p) REVERT: B 23 MET cc_start: 0.4796 (OUTLIER) cc_final: 0.3952 (tmm) REVERT: B 148 ILE cc_start: 0.8282 (tt) cc_final: 0.8075 (tt) REVERT: C 16 LEU cc_start: 0.8837 (mt) cc_final: 0.8610 (mt) REVERT: C 42 TYR cc_start: 0.6882 (m-80) cc_final: 0.6663 (m-80) REVERT: C 160 LEU cc_start: 0.8034 (tt) cc_final: 0.7818 (tm) REVERT: C 304 ASN cc_start: 0.7018 (m110) cc_final: 0.6663 (m110) REVERT: C 344 VAL cc_start: 0.7482 (OUTLIER) cc_final: 0.7140 (p) REVERT: C 347 LYS cc_start: 0.7969 (mppt) cc_final: 0.7753 (mppt) REVERT: C 350 ASN cc_start: 0.7130 (t0) cc_final: 0.6809 (t0) REVERT: C 377 PHE cc_start: 0.7729 (m-10) cc_final: 0.7435 (m-10) REVERT: C 387 PHE cc_start: 0.8055 (p90) cc_final: 0.7688 (p90) REVERT: C 393 ASN cc_start: 0.8168 (p0) cc_final: 0.7770 (p0) REVERT: C 396 ASN cc_start: 0.8790 (OUTLIER) cc_final: 0.8479 (p0) REVERT: C 397 ASN cc_start: 0.8057 (t0) cc_final: 0.7828 (t0) REVERT: C 421 LYS cc_start: 0.7440 (tppp) cc_final: 0.7087 (mmmt) outliers start: 39 outliers final: 13 residues processed: 321 average time/residue: 0.5699 time to fit residues: 201.6138 Evaluate side-chains 308 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 289 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 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 576 ASN Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 711 MET 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 150 LYS Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 165 TYR Chi-restraints excluded: chain C residue 344 VAL 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 53 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 41 optimal weight: 0.0040 chunk 47 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 65 optimal weight: 0.4980 chunk 6 optimal weight: 0.5980 chunk 19 optimal weight: 0.1980 chunk 1 optimal weight: 0.1980 overall best weight: 0.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 HIS A 147 ASN A 263 ASN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 964 GLN ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN C 9 ASN C 351 GLN C 391 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.196751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.156308 restraints weight = 20735.041| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 2.51 r_work: 0.3906 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.2283 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= 0.115 Angle : 0.597 9.922 19355 Z= 0.313 Chirality : 0.042 0.220 2144 Planarity : 0.004 0.054 2357 Dihedral : 13.172 147.171 2118 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.60 % Favored : 96.28 % Rotamer: Outliers : 1.93 % Allowed : 19.01 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.21), residues: 1612 helix: 1.22 (0.22), residues: 589 sheet: 0.17 (0.31), residues: 287 loop : -1.04 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 98 TYR 0.022 0.001 TYR A 468 PHE 0.021 0.001 PHE A 526 TRP 0.015 0.001 TRP A 470 HIS 0.002 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00256 (14229) covalent geometry : angle 0.59692 (19355) hydrogen bonds : bond 0.03767 ( 595) hydrogen bonds : angle 4.44539 ( 1672) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 299 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 ASP cc_start: 0.7385 (t0) cc_final: 0.6861 (t0) REVERT: A 455 MET cc_start: 0.7632 (ttm) cc_final: 0.7384 (mtt) REVERT: A 590 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.8011 (ttmm) REVERT: A 674 ARG cc_start: 0.7218 (mtm-85) cc_final: 0.6969 (mtm-85) REVERT: A 837 LYS cc_start: 0.8028 (tptt) cc_final: 0.7735 (tptp) REVERT: A 859 MET cc_start: 0.4286 (mpp) cc_final: 0.3006 (mpp) REVERT: B 22 VAL cc_start: 0.6159 (OUTLIER) cc_final: 0.5870 (p) REVERT: B 148 ILE cc_start: 0.8283 (tt) cc_final: 0.8079 (tt) REVERT: B 166 ILE cc_start: 0.8018 (OUTLIER) cc_final: 0.7687 (mt) REVERT: C 16 LEU cc_start: 0.8827 (mt) cc_final: 0.8588 (mt) REVERT: C 111 ARG cc_start: 0.8079 (tpp80) cc_final: 0.7813 (tpp80) REVERT: C 152 PHE cc_start: 0.7797 (m-10) cc_final: 0.7300 (m-80) REVERT: C 160 LEU cc_start: 0.8057 (tt) cc_final: 0.7852 (tm) REVERT: C 304 ASN cc_start: 0.7026 (m110) cc_final: 0.6643 (m110) REVERT: C 339 ASN cc_start: 0.8616 (m110) cc_final: 0.8213 (p0) REVERT: C 344 VAL cc_start: 0.7508 (OUTLIER) cc_final: 0.7199 (p) REVERT: C 350 ASN cc_start: 0.7061 (t0) cc_final: 0.6789 (t0) REVERT: C 387 PHE cc_start: 0.7994 (p90) cc_final: 0.7616 (p90) REVERT: C 393 ASN cc_start: 0.8228 (p0) cc_final: 0.7908 (p0) REVERT: C 396 ASN cc_start: 0.8714 (OUTLIER) cc_final: 0.8423 (p0) REVERT: C 421 LYS cc_start: 0.7436 (tppp) cc_final: 0.6917 (tmtt) outliers start: 29 outliers final: 9 residues processed: 310 average time/residue: 0.5807 time to fit residues: 198.6029 Evaluate side-chains 293 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 279 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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 590 LYS Chi-restraints excluded: chain A residue 711 MET 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 153 SER Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain C residue 165 TYR Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 396 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 108 optimal weight: 7.9990 chunk 73 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 121 optimal weight: 9.9990 chunk 162 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 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 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** A 964 GLN ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 HIS C 9 ASN C 415 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.192230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.151197 restraints weight = 20536.134| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 2.51 r_work: 0.3845 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.2534 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 : 0.663 13.562 19355 Z= 0.347 Chirality : 0.046 0.219 2144 Planarity : 0.005 0.054 2357 Dihedral : 13.263 150.154 2118 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.78 % Favored : 95.10 % Rotamer: Outliers : 2.13 % Allowed : 20.08 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.21), residues: 1612 helix: 1.01 (0.22), residues: 589 sheet: -0.02 (0.30), residues: 294 loop : -1.13 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 98 TYR 0.019 0.002 TYR A 697 PHE 0.025 0.002 PHE A 930 TRP 0.016 0.002 TRP A 8 HIS 0.011 0.002 HIS B 16 Details of bonding type rmsd covalent geometry : bond 0.00497 (14229) covalent geometry : angle 0.66337 (19355) hydrogen bonds : bond 0.05155 ( 595) hydrogen bonds : angle 4.62679 ( 1672) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 305 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 ASP cc_start: 0.7666 (t0) cc_final: 0.7387 (t0) REVERT: A 638 LYS cc_start: 0.7758 (tptm) cc_final: 0.7533 (mptm) REVERT: A 639 LYS cc_start: 0.7925 (ttpp) cc_final: 0.7589 (ttpp) REVERT: A 837 LYS cc_start: 0.8206 (tptt) cc_final: 0.7902 (tptp) REVERT: A 859 MET cc_start: 0.4357 (mpp) cc_final: 0.3092 (mpp) REVERT: A 873 GLU cc_start: 0.6985 (tp30) cc_final: 0.6470 (tp30) REVERT: B 22 VAL cc_start: 0.6305 (OUTLIER) cc_final: 0.6102 (t) REVERT: B 148 ILE cc_start: 0.8366 (tt) cc_final: 0.8150 (tt) REVERT: B 160 LYS cc_start: 0.6710 (mmtt) cc_final: 0.6353 (mmtt) REVERT: B 166 ILE cc_start: 0.8301 (OUTLIER) cc_final: 0.8011 (tp) REVERT: C 16 LEU cc_start: 0.8854 (mt) cc_final: 0.8632 (mt) REVERT: C 95 MET cc_start: 0.1395 (pmm) cc_final: -0.0417 (ptm) REVERT: C 160 LEU cc_start: 0.8131 (tt) cc_final: 0.7921 (tm) REVERT: C 304 ASN cc_start: 0.7034 (m110) cc_final: 0.6687 (m110) REVERT: C 339 ASN cc_start: 0.8693 (m110) cc_final: 0.8258 (p0) REVERT: C 344 VAL cc_start: 0.7550 (OUTLIER) cc_final: 0.7103 (p) REVERT: C 347 LYS cc_start: 0.7922 (mmtm) cc_final: 0.7706 (mppt) REVERT: C 350 ASN cc_start: 0.7216 (t0) cc_final: 0.6875 (t0) REVERT: C 387 PHE cc_start: 0.8024 (p90) cc_final: 0.7776 (p90) REVERT: C 393 ASN cc_start: 0.8318 (p0) cc_final: 0.7986 (p0) REVERT: C 396 ASN cc_start: 0.8794 (OUTLIER) cc_final: 0.8492 (p0) REVERT: C 421 LYS cc_start: 0.7489 (tppp) cc_final: 0.7030 (mmtt) outliers start: 32 outliers final: 15 residues processed: 316 average time/residue: 0.5826 time to fit residues: 203.0739 Evaluate side-chains 310 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 291 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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 576 ASN 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 887 LEU 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 153 SER Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain C residue 165 TYR Chi-restraints excluded: chain C residue 252 HIS Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 396 ASN Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 418 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 40 optimal weight: 3.9990 chunk 146 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 130 optimal weight: 10.0000 chunk 24 optimal weight: 0.7980 chunk 120 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN A 263 ASN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN C 391 ASN C 415 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.193405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.152332 restraints weight = 20591.579| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 2.48 r_work: 0.3865 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14229 Z= 0.159 Angle : 0.642 11.195 19355 Z= 0.335 Chirality : 0.044 0.219 2144 Planarity : 0.004 0.052 2357 Dihedral : 13.220 147.913 2118 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.53 % Favored : 95.35 % Rotamer: Outliers : 2.13 % Allowed : 20.75 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.21), residues: 1612 helix: 1.04 (0.21), residues: 589 sheet: -0.04 (0.30), residues: 296 loop : -1.04 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 98 TYR 0.023 0.001 TYR A 162 PHE 0.027 0.002 PHE A 930 TRP 0.016 0.002 TRP A 470 HIS 0.006 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00367 (14229) covalent geometry : angle 0.64210 (19355) hydrogen bonds : bond 0.04533 ( 595) hydrogen bonds : angle 4.52136 ( 1672) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 300 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ASN cc_start: 0.7629 (m-40) cc_final: 0.7423 (m-40) REVERT: A 398 ASP cc_start: 0.7684 (t0) cc_final: 0.7373 (t0) REVERT: A 638 LYS cc_start: 0.7760 (tptm) cc_final: 0.7555 (mptm) REVERT: A 639 LYS cc_start: 0.7891 (ttpp) cc_final: 0.7558 (ttpp) REVERT: A 837 LYS cc_start: 0.8112 (tptt) cc_final: 0.7801 (tptp) REVERT: A 859 MET cc_start: 0.4293 (mpp) cc_final: 0.3040 (mpp) REVERT: B 22 VAL cc_start: 0.6512 (OUTLIER) cc_final: 0.6280 (t) REVERT: B 148 ILE cc_start: 0.8313 (tt) cc_final: 0.8103 (tt) REVERT: B 160 LYS cc_start: 0.6684 (mmtt) cc_final: 0.6304 (mmtt) REVERT: C 16 LEU cc_start: 0.8847 (mt) cc_final: 0.8623 (mt) REVERT: C 80 PRO cc_start: 0.8167 (Cg_endo) cc_final: 0.7925 (Cg_exo) REVERT: C 97 GLU cc_start: 0.6534 (pp20) cc_final: 0.6270 (pp20) REVERT: C 111 ARG cc_start: 0.8185 (tpp80) cc_final: 0.7823 (tpp-160) REVERT: C 152 PHE cc_start: 0.7877 (m-10) cc_final: 0.7387 (m-80) REVERT: C 267 LYS cc_start: 0.7185 (ttmm) cc_final: 0.6941 (ttmt) REVERT: C 304 ASN cc_start: 0.7019 (m110) cc_final: 0.6669 (m110) REVERT: C 339 ASN cc_start: 0.8670 (OUTLIER) cc_final: 0.8231 (p0) REVERT: C 344 VAL cc_start: 0.7482 (OUTLIER) cc_final: 0.7163 (p) REVERT: C 347 LYS cc_start: 0.7965 (mmtm) cc_final: 0.7665 (mptt) REVERT: C 350 ASN cc_start: 0.7255 (t0) cc_final: 0.6898 (t0) REVERT: C 359 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6768 (tm-30) REVERT: C 387 PHE cc_start: 0.8017 (p90) cc_final: 0.7678 (p90) REVERT: C 396 ASN cc_start: 0.8770 (OUTLIER) cc_final: 0.8480 (p0) REVERT: C 421 LYS cc_start: 0.7489 (tppp) cc_final: 0.7071 (mmmt) REVERT: C 422 LYS cc_start: 0.8655 (tttt) cc_final: 0.8425 (tttt) outliers start: 32 outliers final: 18 residues processed: 313 average time/residue: 0.5674 time to fit residues: 195.8566 Evaluate side-chains 316 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 293 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 421 CYS Chi-restraints excluded: chain A residue 492 MET 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 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 339 ASN Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 359 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 95 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 93 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 108 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 109 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** A 964 GLN ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 ASN ** 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 = 0.4484 r_free = 0.4484 target = 0.193415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.152419 restraints weight = 20571.898| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 2.47 r_work: 0.3867 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14229 Z= 0.154 Angle : 0.650 11.921 19355 Z= 0.335 Chirality : 0.043 0.219 2144 Planarity : 0.005 0.052 2357 Dihedral : 13.202 147.981 2118 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.84 % Favored : 95.04 % Rotamer: Outliers : 1.93 % Allowed : 21.81 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.21), residues: 1612 helix: 1.04 (0.22), residues: 589 sheet: -0.02 (0.31), residues: 283 loop : -1.08 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 995 TYR 0.022 0.001 TYR A 162 PHE 0.018 0.002 PHE C 377 TRP 0.015 0.002 TRP A 470 HIS 0.005 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00358 (14229) covalent geometry : angle 0.64971 (19355) hydrogen bonds : bond 0.04435 ( 595) hydrogen bonds : angle 4.48910 ( 1672) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 295 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ASN cc_start: 0.7623 (m-40) cc_final: 0.7416 (m-40) REVERT: A 398 ASP cc_start: 0.7714 (t0) cc_final: 0.7370 (t0) REVERT: A 638 LYS cc_start: 0.7745 (tptm) cc_final: 0.7515 (mptm) REVERT: A 639 LYS cc_start: 0.7924 (ttpp) cc_final: 0.7598 (ttpp) REVERT: A 828 THR cc_start: 0.7099 (OUTLIER) cc_final: 0.6779 (p) REVERT: A 837 LYS cc_start: 0.8113 (tptt) cc_final: 0.7821 (tptp) REVERT: A 859 MET cc_start: 0.4338 (mpp) cc_final: 0.3107 (mpp) REVERT: A 926 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7544 (tm-30) REVERT: B 22 VAL cc_start: 0.6584 (OUTLIER) cc_final: 0.6366 (t) REVERT: B 160 LYS cc_start: 0.6673 (mmtt) cc_final: 0.6285 (mmtt) REVERT: B 166 ILE cc_start: 0.8263 (OUTLIER) cc_final: 0.7973 (tp) REVERT: C 16 LEU cc_start: 0.8844 (mt) cc_final: 0.8624 (mt) REVERT: C 111 ARG cc_start: 0.8156 (tpp80) cc_final: 0.7747 (tpp-160) REVERT: C 244 LYS cc_start: 0.8228 (tppt) cc_final: 0.7817 (tppt) REVERT: C 249 ASP cc_start: 0.6270 (p0) cc_final: 0.5244 (p0) REVERT: C 267 LYS cc_start: 0.7186 (ttmm) cc_final: 0.6884 (ttmt) REVERT: C 304 ASN cc_start: 0.6998 (m110) cc_final: 0.6671 (m110) REVERT: C 339 ASN cc_start: 0.8644 (OUTLIER) cc_final: 0.8209 (p0) REVERT: C 344 VAL cc_start: 0.7508 (OUTLIER) cc_final: 0.7205 (p) REVERT: C 347 LYS cc_start: 0.7982 (mmtm) cc_final: 0.7742 (mptt) REVERT: C 350 ASN cc_start: 0.7308 (t0) cc_final: 0.6932 (t0) REVERT: C 359 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6748 (tm-30) REVERT: C 375 MET cc_start: 0.7797 (ppp) cc_final: 0.7274 (ppp) REVERT: C 387 PHE cc_start: 0.8017 (p90) cc_final: 0.7659 (p90) REVERT: C 396 ASN cc_start: 0.8734 (OUTLIER) cc_final: 0.8449 (p0) REVERT: C 421 LYS cc_start: 0.7449 (tppp) cc_final: 0.6940 (tmtt) REVERT: C 422 LYS cc_start: 0.8650 (tttt) cc_final: 0.8436 (tttt) outliers start: 29 outliers final: 15 residues processed: 310 average time/residue: 0.5748 time to fit residues: 196.6260 Evaluate side-chains 309 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 287 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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 421 CYS Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain B residue 22 VAL 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 166 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 252 HIS Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 359 GLU 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 130 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 119 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 114 optimal weight: 0.0670 chunk 139 optimal weight: 8.9990 chunk 76 optimal weight: 0.0570 chunk 25 optimal weight: 1.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- 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 25 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 = 0.4487 r_free = 0.4487 target = 0.193698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.152776 restraints weight = 20547.147| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 2.50 r_work: 0.3868 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14229 Z= 0.150 Angle : 0.656 11.548 19355 Z= 0.341 Chirality : 0.044 0.233 2144 Planarity : 0.005 0.055 2357 Dihedral : 13.197 147.481 2118 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.65 % Favored : 95.22 % Rotamer: Outliers : 1.60 % Allowed : 22.82 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.21), residues: 1612 helix: 1.08 (0.22), residues: 594 sheet: -0.02 (0.30), residues: 295 loop : -1.01 (0.22), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 98 TYR 0.021 0.001 TYR A 162 PHE 0.041 0.002 PHE C 152 TRP 0.015 0.002 TRP A 470 HIS 0.005 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00344 (14229) covalent geometry : angle 0.65596 (19355) hydrogen bonds : bond 0.04365 ( 595) hydrogen bonds : angle 4.46068 ( 1672) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 294 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ASN cc_start: 0.7615 (m-40) cc_final: 0.7410 (m-40) REVERT: A 398 ASP cc_start: 0.7732 (t0) cc_final: 0.7435 (t0) REVERT: A 639 LYS cc_start: 0.7933 (ttpp) cc_final: 0.7616 (ttpp) REVERT: A 828 THR cc_start: 0.7087 (OUTLIER) cc_final: 0.6755 (p) REVERT: A 837 LYS cc_start: 0.8100 (tptt) cc_final: 0.7807 (tptp) REVERT: A 859 MET cc_start: 0.4394 (mpp) cc_final: 0.3181 (mpp) REVERT: B 22 VAL cc_start: 0.6574 (OUTLIER) cc_final: 0.6358 (t) REVERT: B 160 LYS cc_start: 0.6680 (mmtt) cc_final: 0.6287 (mmtt) REVERT: B 166 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.7964 (tp) REVERT: C 16 LEU cc_start: 0.8843 (mt) cc_final: 0.8626 (mt) REVERT: C 111 ARG cc_start: 0.8146 (tpp80) cc_final: 0.7734 (tpp-160) REVERT: C 152 PHE cc_start: 0.7998 (m-80) cc_final: 0.7564 (m-80) REVERT: C 244 LYS cc_start: 0.8265 (tppt) cc_final: 0.7782 (tppt) REVERT: C 249 ASP cc_start: 0.6300 (p0) cc_final: 0.5295 (p0) REVERT: C 304 ASN cc_start: 0.7021 (m110) cc_final: 0.6677 (m110) REVERT: C 339 ASN cc_start: 0.8649 (OUTLIER) cc_final: 0.8200 (p0) REVERT: C 344 VAL cc_start: 0.7478 (OUTLIER) cc_final: 0.7043 (p) REVERT: C 350 ASN cc_start: 0.7337 (t0) cc_final: 0.6959 (t0) REVERT: C 359 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6692 (tm-30) REVERT: C 375 MET cc_start: 0.7795 (ppp) cc_final: 0.7343 (ppp) REVERT: C 387 PHE cc_start: 0.8026 (p90) cc_final: 0.7646 (p90) REVERT: C 396 ASN cc_start: 0.8727 (OUTLIER) cc_final: 0.8436 (p0) outliers start: 24 outliers final: 16 residues processed: 306 average time/residue: 0.5521 time to fit residues: 186.4969 Evaluate side-chains 317 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 294 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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 421 CYS Chi-restraints excluded: chain A residue 492 MET 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 B residue 22 VAL 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 166 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 252 HIS Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 359 GLU 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 109 optimal weight: 9.9990 chunk 55 optimal weight: 0.3980 chunk 79 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- 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** A 964 GLN B 25 GLN ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 9 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.193333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.152399 restraints weight = 20573.507| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 2.50 r_work: 0.3863 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14229 Z= 0.160 Angle : 0.684 12.459 19355 Z= 0.353 Chirality : 0.044 0.234 2144 Planarity : 0.005 0.055 2357 Dihedral : 13.210 147.641 2118 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.78 % Favored : 95.10 % Rotamer: Outliers : 1.87 % Allowed : 22.48 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.21), residues: 1612 helix: 1.03 (0.22), residues: 594 sheet: -0.03 (0.31), residues: 294 loop : -1.04 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 98 TYR 0.023 0.001 TYR A 668 PHE 0.042 0.002 PHE C 152 TRP 0.015 0.002 TRP A 470 HIS 0.006 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00373 (14229) covalent geometry : angle 0.68354 (19355) hydrogen bonds : bond 0.04527 ( 595) hydrogen bonds : angle 4.45225 ( 1672) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 297 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 ASP cc_start: 0.7726 (t0) cc_final: 0.7422 (t0) REVERT: A 828 THR cc_start: 0.7087 (OUTLIER) cc_final: 0.6734 (p) REVERT: A 837 LYS cc_start: 0.8104 (tptt) cc_final: 0.7813 (tptp) REVERT: A 859 MET cc_start: 0.4354 (mpp) cc_final: 0.3132 (mpp) REVERT: A 926 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7521 (tm-30) REVERT: B 22 VAL cc_start: 0.6584 (OUTLIER) cc_final: 0.6373 (t) REVERT: B 160 LYS cc_start: 0.6837 (mmtt) cc_final: 0.6479 (mmtt) REVERT: B 166 ILE cc_start: 0.8271 (OUTLIER) cc_final: 0.7995 (tp) REVERT: C 16 LEU cc_start: 0.8843 (mt) cc_final: 0.8630 (mt) REVERT: C 111 ARG cc_start: 0.8140 (tpp80) cc_final: 0.7722 (tpp-160) REVERT: C 244 LYS cc_start: 0.8277 (tppt) cc_final: 0.7895 (tppt) REVERT: C 249 ASP cc_start: 0.6432 (p0) cc_final: 0.5470 (p0) REVERT: C 304 ASN cc_start: 0.6995 (m110) cc_final: 0.6693 (m110) REVERT: C 339 ASN cc_start: 0.8624 (OUTLIER) cc_final: 0.8182 (p0) REVERT: C 344 VAL cc_start: 0.7388 (OUTLIER) cc_final: 0.6947 (p) REVERT: C 345 LYS cc_start: 0.7808 (mmmm) cc_final: 0.7597 (mmmm) REVERT: C 347 LYS cc_start: 0.7954 (mppt) cc_final: 0.7645 (mmtm) REVERT: C 350 ASN cc_start: 0.7359 (t0) cc_final: 0.6994 (t0) REVERT: C 375 MET cc_start: 0.7791 (ppp) cc_final: 0.7428 (ppp) REVERT: C 387 PHE cc_start: 0.8020 (p90) cc_final: 0.7691 (p90) REVERT: C 393 ASN cc_start: 0.8675 (p0) cc_final: 0.8346 (p0) REVERT: C 396 ASN cc_start: 0.8714 (OUTLIER) cc_final: 0.8444 (p0) REVERT: C 421 LYS cc_start: 0.7455 (tppp) cc_final: 0.7001 (tppp) outliers start: 28 outliers final: 19 residues processed: 307 average time/residue: 0.5385 time to fit residues: 182.7509 Evaluate side-chains 316 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 291 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 421 CYS Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 492 MET 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 807 THR Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain B residue 22 VAL 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 166 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 252 HIS Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 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 20 optimal weight: 0.5980 chunk 136 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 52 optimal weight: 0.2980 chunk 153 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 2 optimal weight: 0.0770 chunk 129 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 HIS 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.194802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.154192 restraints weight = 20436.424| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 2.46 r_work: 0.3890 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14229 Z= 0.132 Angle : 0.678 15.638 19355 Z= 0.350 Chirality : 0.043 0.246 2144 Planarity : 0.005 0.057 2357 Dihedral : 13.175 146.539 2118 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.47 % Favored : 95.41 % Rotamer: Outliers : 1.40 % Allowed : 23.48 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.21), residues: 1612 helix: 1.12 (0.22), residues: 588 sheet: 0.01 (0.30), residues: 299 loop : -1.01 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG B 98 TYR 0.023 0.001 TYR A 668 PHE 0.063 0.002 PHE C 152 TRP 0.016 0.001 TRP A 470 HIS 0.003 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00302 (14229) covalent geometry : angle 0.67764 (19355) hydrogen bonds : bond 0.04113 ( 595) hydrogen bonds : angle 4.43240 ( 1672) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5634.63 seconds wall clock time: 96 minutes 46.74 seconds (5806.74 seconds total)