Starting phenix.real_space_refine on Sat Jun 14 01:01:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k9v_62200/06_2025/9k9v_62200.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k9v_62200/06_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_62200/06_2025/9k9v_62200.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k9v_62200/06_2025/9k9v_62200.map" model { file = "/net/cci-nas-00/data/ceres_data/9k9v_62200/06_2025/9k9v_62200.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k9v_62200/06_2025/9k9v_62200.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2165 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 29 5.49 5 S 70 5.16 5 C 8806 2.51 5 N 2301 2.21 5 O 2663 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 13869 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 8106 Classifications: {'peptide': 990} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 952} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1762 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 2} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 204} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 3389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3389 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 10, 'TRANS': 405} Chain breaks: 1 Chain: "P" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 345 Classifications: {'DNA': 17} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 16} Chain: "E" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 267 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Time building chain proxies: 8.72, per 1000 atoms: 0.63 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: 2.98 Conformation dependent library (CDL) restraints added in 1.6 seconds 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3110 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 20 sheets defined 39.6% alpha, 20.2% beta 12 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 4.55 Creating SS restraints... Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 108 through 118 Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 209 through 220 removed outlier: 3.588A pdb=" N ILE A 213 " --> pdb=" O THR A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 253 Processing helix chain 'A' and resid 267 through 280 Processing helix chain 'A' and resid 331 through 339 removed outlier: 3.534A pdb=" N GLU A 339 " --> pdb=" O ILE A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 380 through 389 Processing helix chain 'A' and resid 439 through 446 removed outlier: 3.539A pdb=" N MET A 443 " --> pdb=" O ASP A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 474 removed outlier: 3.701A pdb=" N CYS A 466 " --> pdb=" O ASP A 462 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLN A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 487 Processing helix chain 'A' and resid 489 through 493 Processing helix chain 'A' and resid 502 through 514 Processing helix chain 'A' and resid 552 through 562 Processing helix chain 'A' and resid 564 through 566 No H-bonds generated for 'chain 'A' and resid 564 through 566' Processing helix chain 'A' and resid 576 through 591 Processing helix chain 'A' and resid 622 through 643 Processing helix chain 'A' and resid 646 through 665 Processing helix chain 'A' and resid 666 through 672 removed outlier: 3.590A pdb=" N GLY A 672 " --> pdb=" O TYR A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 703 Processing helix chain 'A' and resid 763 through 781 Processing helix chain 'A' and resid 837 through 854 removed outlier: 3.735A pdb=" N ASN A 841 " --> pdb=" O LYS A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 883 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.710A pdb=" N MET A 891 " --> pdb=" O GLU A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 918 removed outlier: 4.042A pdb=" N TYR A 909 " --> pdb=" O ASN A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 949 No H-bonds generated for 'chain 'A' and resid 947 through 949' Processing helix chain 'A' and resid 967 through 982 removed outlier: 4.003A pdb=" N TYR A 971 " --> pdb=" O PHE A 967 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU A 982 " --> pdb=" O GLU A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 998 Processing helix chain 'B' and resid 19 through 31 removed outlier: 4.215A pdb=" N SER B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N GLN B 25 " --> pdb=" O PRO B 21 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 26 " --> pdb=" O VAL B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 38 removed outlier: 3.540A pdb=" N LEU B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 86 through 101 Processing helix chain 'B' and resid 133 through 150 removed outlier: 5.472A pdb=" N LYS B 139 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ILE B 140 " --> pdb=" O TYR B 136 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS B 150 " --> pdb=" O GLN B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 170 removed outlier: 3.612A pdb=" N LYS B 169 " --> pdb=" O ASN B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 192 removed outlier: 3.820A pdb=" N HIS B 187 " --> pdb=" O ALA B 184 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN B 188 " --> pdb=" O ARG B 185 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N PHE B 189 " --> pdb=" O ASP B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 205 removed outlier: 3.613A pdb=" N ILE B 197 " --> pdb=" O ARG B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 214 Processing helix chain 'C' and resid 4 through 19 Processing helix chain 'C' and resid 24 through 42 Processing helix chain 'C' and resid 57 through 61 Processing helix chain 'C' and resid 107 through 121 removed outlier: 3.600A pdb=" N SER C 120 " --> pdb=" O LYS C 116 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASP C 121 " --> pdb=" O VAL C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 158 removed outlier: 4.197A pdb=" N ILE C 151 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYS C 153 " --> pdb=" O VAL C 149 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU C 154 " --> pdb=" O ASN C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 189 Processing helix chain 'C' and resid 249 through 256 Processing helix chain 'C' and resid 285 through 298 removed outlier: 3.506A pdb=" N LYS C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 324 Processing helix chain 'C' and resid 330 through 341 removed outlier: 3.541A pdb=" N SER C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 350 removed outlier: 3.604A pdb=" N ILE C 348 " --> pdb=" O VAL C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 361 Processing helix chain 'C' and resid 364 through 373 removed outlier: 3.626A pdb=" N ASN C 373 " --> pdb=" O ILE C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 396 Processing helix chain 'C' and resid 397 through 425 removed outlier: 4.325A pdb=" N ASN C 408 " --> pdb=" O TYR C 404 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N GLN C 409 " --> pdb=" O GLY C 405 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER C 412 " --> pdb=" O ASN C 408 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 134 removed outlier: 8.313A pdb=" N TYR A 140 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N PHE A 31 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N CYS A 142 " --> pdb=" O PHE A 31 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ARG A 33 " --> pdb=" O CYS A 142 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N PHE A 17 " --> pdb=" O GLU A 10 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N GLU A 10 " --> pdb=" O PHE A 17 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TYR A 19 " --> pdb=" O TRP A 8 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N TRP A 8 " --> pdb=" O TYR A 19 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LYS A 21 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N CYS A 124 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER A 126 " --> pdb=" O LYS A 151 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LYS A 151 " --> pdb=" O SER A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 43 removed outlier: 3.790A pdb=" N GLY A 61 " --> pdb=" O MET A 88 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N LEU A 90 " --> pdb=" O PRO A 59 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N GLU A 92 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ALA A 57 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N ILE A 516 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ARG A 64 " --> pdb=" O ILE A 516 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL A 518 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE A 66 " --> pdb=" O VAL A 518 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 222 through 223 removed outlier: 6.458A pdb=" N LEU A 222 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N VAL A 237 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N THR A 201 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N CYS A 239 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ILE A 203 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N SER A 184 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU A 165 " --> pdb=" O VAL A 260 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 285 through 287 Processing sheet with id=AA5, first strand: chain 'A' and resid 300 through 302 Processing sheet with id=AA6, first strand: chain 'A' and resid 355 through 362 removed outlier: 7.068A pdb=" N MET A 357 " --> pdb=" O ASP A 373 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ASP A 373 " --> pdb=" O MET A 357 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N THR A 369 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG A 407 " --> pdb=" O VAL A 418 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 732 through 734 removed outlier: 3.566A pdb=" N PHE A 743 " --> pdb=" O LEU A 707 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N SER A 747 " --> pdb=" O GLU A 758 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLU A 758 " --> pdb=" O SER A 747 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N TYR A 749 " --> pdb=" O PHE A 756 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL A 545 " --> pdb=" O VAL A 794 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL A 794 " --> pdb=" O VAL A 545 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE A 547 " --> pdb=" O GLU A 792 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LEU A 798 " --> pdb=" O THR A 807 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N THR A 807 " --> pdb=" O LEU A 798 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 568 through 574 removed outlier: 6.489A pdb=" N LEU A 568 " --> pdb=" O ASP A 616 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASP A 616 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY A 570 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLU A 611 " --> pdb=" O CYS A 601 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 892 through 895 removed outlier: 4.386A pdb=" N TYR A 929 " --> pdb=" O ILE A 954 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 892 through 895 Processing sheet with id=AB2, first strand: chain 'B' and resid 2 through 4 Processing sheet with id=AB3, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.858A pdb=" N CYS B 125 " --> pdb=" O SER B 43 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 116 through 120 removed outlier: 7.578A pdb=" N VAL B 62 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N TRP B 119 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL B 64 " --> pdb=" O TRP B 119 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N CYS B 63 " --> pdb=" O TYR B 156 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LEU B 155 " --> pdb=" O ILE B 177 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 107 through 108 Processing sheet with id=AB6, first strand: chain 'C' and resid 70 through 71 removed outlier: 3.839A pdb=" N THR C 174 " --> pdb=" O ILE C 71 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 166 through 169 removed outlier: 3.867A pdb=" N GLN C 208 " --> pdb=" O TYR C 199 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 95 through 97 removed outlier: 6.477A pdb=" N ILE C 124 " --> pdb=" O SER C 143 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N SER C 143 " --> pdb=" O ILE C 124 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N PHE C 126 " --> pdb=" O ALA C 141 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ALA C 141 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ARG C 128 " --> pdb=" O GLU C 139 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU C 139 " --> pdb=" O ARG C 128 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 233 through 239 removed outlier: 3.717A pdb=" N ILE C 234 " --> pdb=" O ASP C 226 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER C 222 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 302 through 303 removed outlier: 3.823A pdb=" N TYR C 302 " --> pdb=" O SER C 309 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 375 through 380 removed outlier: 3.642A pdb=" N ASN C 386 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLU C 380 " --> pdb=" O VAL C 384 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N VAL C 384 " --> pdb=" O GLU C 380 " (cutoff:3.500A) 573 hydrogen bonds defined for protein. 1620 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 26 hydrogen bonds 52 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 5.90 Time building geometry restraints manager: 3.70 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: 9.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 37.010 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:15.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14229 Z= 0.159 Angle : 0.606 9.914 19355 Z= 0.345 Chirality : 0.043 0.225 2144 Planarity : 0.005 0.079 2357 Dihedral : 15.072 145.151 5411 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.71 % Favored : 95.16 % Rotamer: Outliers : 0.20 % Allowed : 0.47 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.21), residues: 1612 helix: 1.38 (0.22), residues: 572 sheet: 0.47 (0.31), residues: 293 loop : -0.79 (0.22), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 8 HIS 0.005 0.001 HIS B 16 PHE 0.027 0.002 PHE C 152 TYR 0.017 0.001 TYR A 74 ARG 0.008 0.000 ARG A 287 Details of bonding type rmsd hydrogen bonds : bond 0.14477 ( 595) hydrogen bonds : angle 6.29019 ( 1672) covalent geometry : bond 0.00312 (14229) covalent geometry : angle 0.60584 (19355) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 298 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 399 GLU cc_start: 0.6690 (mm-30) cc_final: 0.6297 (mm-30) REVERT: A 837 LYS cc_start: 0.7846 (tptt) cc_final: 0.7641 (tptt) REVERT: B 146 GLN cc_start: 0.7110 (mt0) cc_final: 0.6819 (mt0) REVERT: C 95 MET cc_start: -0.1021 (ppp) cc_final: -0.1355 (tpp) REVERT: C 152 PHE cc_start: 0.8083 (m-80) cc_final: 0.7529 (m-10) REVERT: C 304 ASN cc_start: 0.6921 (m110) cc_final: 0.6673 (m110) REVERT: C 391 ASN cc_start: 0.6518 (t0) cc_final: 0.5974 (t0) REVERT: C 393 ASN cc_start: 0.8015 (p0) cc_final: 0.7182 (p0) REVERT: C 421 LYS cc_start: 0.7245 (tppp) cc_final: 0.6837 (tppp) outliers start: 3 outliers final: 0 residues processed: 299 average time/residue: 1.4257 time to fit residues: 473.6210 Evaluate side-chains 269 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 127 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 ASN A 703 ASN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 ASN C 339 ASN C 397 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.193994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.152894 restraints weight = 20462.196| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 2.52 r_work: 0.3849 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 14229 Z= 0.246 Angle : 0.680 9.272 19355 Z= 0.361 Chirality : 0.047 0.301 2144 Planarity : 0.005 0.065 2357 Dihedral : 13.164 149.288 2118 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.96 % Favored : 94.91 % Rotamer: Outliers : 1.87 % Allowed : 11.47 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.21), residues: 1612 helix: 1.01 (0.22), residues: 584 sheet: 0.28 (0.31), residues: 288 loop : -1.07 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 8 HIS 0.013 0.002 HIS B 16 PHE 0.026 0.002 PHE C 152 TYR 0.023 0.002 TYR A 806 ARG 0.009 0.001 ARG C 111 Details of bonding type rmsd hydrogen bonds : bond 0.05941 ( 595) hydrogen bonds : angle 4.83364 ( 1672) covalent geometry : bond 0.00571 (14229) covalent geometry : angle 0.67986 (19355) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 300 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 ILE cc_start: 0.8536 (tp) cc_final: 0.8282 (tt) REVERT: A 566 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7343 (pp20) REVERT: A 837 LYS cc_start: 0.8254 (tptt) cc_final: 0.8035 (tptt) REVERT: B 163 PHE cc_start: 0.7467 (m-80) cc_final: 0.7201 (m-80) REVERT: C 16 LEU cc_start: 0.8850 (mt) cc_final: 0.8622 (mt) REVERT: C 82 TYR cc_start: 0.6792 (m-10) cc_final: 0.6587 (m-10) REVERT: C 152 PHE cc_start: 0.8139 (m-80) cc_final: 0.7729 (m-80) REVERT: C 177 ASP cc_start: 0.6807 (t0) cc_final: 0.6606 (t0) REVERT: C 180 LEU cc_start: 0.7124 (tm) cc_final: 0.6871 (tt) REVERT: C 304 ASN cc_start: 0.7207 (m110) cc_final: 0.6899 (m110) REVERT: C 350 ASN cc_start: 0.6915 (t0) cc_final: 0.6624 (t0) REVERT: C 393 ASN cc_start: 0.8096 (p0) cc_final: 0.7512 (p0) REVERT: C 396 ASN cc_start: 0.8728 (OUTLIER) cc_final: 0.8482 (p0) REVERT: C 397 ASN cc_start: 0.8164 (t0) cc_final: 0.7925 (t0) REVERT: C 421 LYS cc_start: 0.7303 (tppp) cc_final: 0.6991 (mmtt) outliers start: 28 outliers final: 7 residues processed: 306 average time/residue: 1.2114 time to fit residues: 406.9236 Evaluate side-chains 292 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 283 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 396 ASN Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 418 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 62 optimal weight: 0.7980 chunk 130 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 162 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN A 181 ASN A 263 ASN A 576 ASN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 GLN C 9 ASN ** C 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.195867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.155047 restraints weight = 20481.150| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 2.52 r_work: 0.3877 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14229 Z= 0.155 Angle : 0.604 9.340 19355 Z= 0.318 Chirality : 0.043 0.255 2144 Planarity : 0.004 0.053 2357 Dihedral : 13.218 148.865 2118 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.22 % Favored : 95.66 % Rotamer: Outliers : 1.93 % Allowed : 15.48 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.21), residues: 1612 helix: 1.07 (0.21), residues: 588 sheet: 0.28 (0.31), residues: 288 loop : -1.02 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 470 HIS 0.006 0.001 HIS B 16 PHE 0.022 0.002 PHE A 526 TYR 0.020 0.001 TYR A 162 ARG 0.010 0.001 ARG B 98 Details of bonding type rmsd hydrogen bonds : bond 0.04682 ( 595) hydrogen bonds : angle 4.57719 ( 1672) covalent geometry : bond 0.00355 (14229) covalent geometry : angle 0.60365 (19355) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 295 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 371 ILE cc_start: 0.8523 (tp) cc_final: 0.8289 (tt) REVERT: A 442 GLN cc_start: 0.7507 (mm-40) cc_final: 0.7293 (tp-100) REVERT: A 809 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.7566 (mtm) REVERT: A 837 LYS cc_start: 0.8119 (tptt) cc_final: 0.7918 (tptt) REVERT: B 14 THR cc_start: 0.7785 (OUTLIER) cc_final: 0.7450 (p) REVERT: B 23 MET cc_start: 0.4654 (OUTLIER) cc_final: 0.3988 (tmm) REVERT: B 143 LEU cc_start: 0.7282 (tt) cc_final: 0.7006 (tp) REVERT: C 82 TYR cc_start: 0.6883 (m-10) cc_final: 0.6657 (m-10) REVERT: C 152 PHE cc_start: 0.8089 (m-80) cc_final: 0.7698 (m-80) REVERT: C 180 LEU cc_start: 0.7117 (tm) cc_final: 0.6855 (tt) REVERT: C 304 ASN cc_start: 0.7038 (m110) cc_final: 0.6691 (m110) REVERT: C 347 LYS cc_start: 0.7987 (mmtm) cc_final: 0.7600 (mppt) REVERT: C 350 ASN cc_start: 0.6935 (t0) cc_final: 0.6635 (t0) REVERT: C 375 MET cc_start: 0.7640 (ppp) cc_final: 0.7382 (ppp) REVERT: C 377 PHE cc_start: 0.7576 (m-10) cc_final: 0.7336 (m-10) REVERT: C 387 PHE cc_start: 0.7990 (p90) cc_final: 0.7715 (p90) REVERT: C 393 ASN cc_start: 0.8252 (p0) cc_final: 0.7746 (p0) REVERT: C 396 ASN cc_start: 0.8753 (OUTLIER) cc_final: 0.8439 (p0) outliers start: 29 outliers final: 12 residues processed: 303 average time/residue: 1.0952 time to fit residues: 367.3796 Evaluate side-chains 290 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 274 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 809 MET Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 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 396 ASN Chi-restraints excluded: chain C residue 418 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 139 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 109 optimal weight: 9.9990 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 158 optimal weight: 0.9980 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN A 181 ASN A 263 ASN A 576 ASN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN C 9 ASN C 339 ASN ** C 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 397 ASN C 415 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.192601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.151841 restraints weight = 20520.699| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 2.46 r_work: 0.3848 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14229 Z= 0.219 Angle : 0.647 8.448 19355 Z= 0.342 Chirality : 0.045 0.278 2144 Planarity : 0.005 0.058 2357 Dihedral : 13.341 150.844 2118 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.09 % Favored : 94.79 % Rotamer: Outliers : 3.07 % Allowed : 16.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.20), residues: 1612 helix: 0.95 (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 TRP 0.019 0.002 TRP A 470 HIS 0.011 0.002 HIS B 16 PHE 0.020 0.002 PHE C 377 TYR 0.021 0.002 TYR A 162 ARG 0.007 0.001 ARG A 744 Details of bonding type rmsd hydrogen bonds : bond 0.05386 ( 595) hydrogen bonds : angle 4.68648 ( 1672) covalent geometry : bond 0.00512 (14229) covalent geometry : angle 0.64747 (19355) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 295 time to evaluate : 2.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 ILE cc_start: 0.8513 (tp) cc_final: 0.8295 (tt) REVERT: A 398 ASP cc_start: 0.7553 (t0) cc_final: 0.7332 (t0) REVERT: A 513 THR cc_start: 0.8386 (OUTLIER) cc_final: 0.8135 (t) REVERT: A 566 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7362 (pp20) REVERT: A 837 LYS cc_start: 0.8187 (tptt) cc_final: 0.7876 (tptp) REVERT: A 873 GLU cc_start: 0.6960 (mm-30) cc_final: 0.6680 (tp30) REVERT: A 996 MET cc_start: 0.7530 (tpp) cc_final: 0.7240 (tpp) REVERT: B 22 VAL cc_start: 0.6574 (OUTLIER) cc_final: 0.6315 (p) REVERT: B 23 MET cc_start: 0.4844 (OUTLIER) cc_final: 0.3983 (tmm) REVERT: B 160 LYS cc_start: 0.6726 (mmtt) cc_final: 0.6403 (mmtt) REVERT: B 163 PHE cc_start: 0.7485 (m-80) cc_final: 0.7258 (m-80) REVERT: C 16 LEU cc_start: 0.8847 (mt) cc_final: 0.8623 (mt) REVERT: C 82 TYR cc_start: 0.6995 (m-10) cc_final: 0.6791 (m-10) REVERT: C 111 ARG cc_start: 0.8065 (mmm160) cc_final: 0.7778 (tpp80) REVERT: C 160 LEU cc_start: 0.8038 (tt) cc_final: 0.7824 (tm) REVERT: C 218 MET cc_start: 0.4051 (OUTLIER) cc_final: 0.2763 (tmt) REVERT: C 304 ASN cc_start: 0.7009 (m110) cc_final: 0.6654 (m110) REVERT: C 344 VAL cc_start: 0.7467 (OUTLIER) cc_final: 0.7109 (p) REVERT: C 350 ASN cc_start: 0.7169 (t0) cc_final: 0.6838 (t0) REVERT: C 377 PHE cc_start: 0.7768 (m-10) cc_final: 0.7412 (m-10) REVERT: C 387 PHE cc_start: 0.8065 (p90) cc_final: 0.7690 (p90) REVERT: C 396 ASN cc_start: 0.8794 (OUTLIER) cc_final: 0.8516 (p0) outliers start: 46 outliers final: 14 residues processed: 313 average time/residue: 1.5381 time to fit residues: 535.3582 Evaluate side-chains 313 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 292 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 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 45 ILE Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 165 TYR Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 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 72 optimal weight: 0.4980 chunk 26 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 149 optimal weight: 0.7980 chunk 66 optimal weight: 0.2980 chunk 117 optimal weight: 7.9990 chunk 0 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 chunk 154 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN A 181 ASN A 263 ASN A 576 ASN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 9 ASN C 351 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.194524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.153788 restraints weight = 20615.862| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 2.52 r_work: 0.3879 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14229 Z= 0.133 Angle : 0.622 11.776 19355 Z= 0.324 Chirality : 0.043 0.249 2144 Planarity : 0.004 0.053 2357 Dihedral : 13.223 148.175 2118 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.16 % Favored : 95.72 % Rotamer: Outliers : 1.87 % Allowed : 19.35 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.21), residues: 1612 helix: 1.14 (0.22), residues: 588 sheet: 0.05 (0.31), residues: 283 loop : -1.05 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 470 HIS 0.004 0.001 HIS B 16 PHE 0.021 0.001 PHE A 526 TYR 0.020 0.001 TYR A 162 ARG 0.010 0.001 ARG B 98 Details of bonding type rmsd hydrogen bonds : bond 0.04356 ( 595) hydrogen bonds : angle 4.51382 ( 1672) covalent geometry : bond 0.00305 (14229) covalent geometry : angle 0.62215 (19355) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 292 time to evaluate : 1.396 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: 0.7485 (t0) cc_final: 0.7269 (t0) REVERT: A 513 THR cc_start: 0.8399 (OUTLIER) cc_final: 0.8186 (t) REVERT: A 566 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7334 (pp20) REVERT: A 639 LYS cc_start: 0.7946 (ttpp) cc_final: 0.7606 (ttpp) REVERT: A 837 LYS cc_start: 0.8092 (tptt) cc_final: 0.7791 (tptp) REVERT: A 859 MET cc_start: 0.4239 (mpp) cc_final: 0.2919 (mpp) REVERT: B 22 VAL cc_start: 0.6432 (OUTLIER) cc_final: 0.6178 (t) REVERT: C 16 LEU cc_start: 0.8834 (mt) cc_final: 0.8607 (mt) REVERT: C 95 MET cc_start: 0.1542 (pmm) cc_final: 0.0668 (ppp) REVERT: C 152 PHE cc_start: 0.7788 (m-10) cc_final: 0.7166 (m-80) REVERT: C 160 LEU cc_start: 0.8040 (tt) cc_final: 0.7838 (tm) REVERT: C 218 MET cc_start: 0.3890 (OUTLIER) cc_final: 0.2723 (tmt) REVERT: C 244 LYS cc_start: 0.8070 (tppt) cc_final: 0.7811 (tppt) REVERT: C 304 ASN cc_start: 0.7056 (m110) cc_final: 0.6654 (m110) REVERT: C 344 VAL cc_start: 0.7559 (OUTLIER) cc_final: 0.7226 (p) REVERT: C 347 LYS cc_start: 0.7990 (mmpt) cc_final: 0.7543 (mmtm) REVERT: C 350 ASN cc_start: 0.7072 (t0) cc_final: 0.6760 (t0) REVERT: C 387 PHE cc_start: 0.8009 (p90) cc_final: 0.7645 (p90) REVERT: C 396 ASN cc_start: 0.8755 (OUTLIER) cc_final: 0.8477 (p0) outliers start: 28 outliers final: 14 residues processed: 304 average time/residue: 1.4463 time to fit residues: 487.6372 Evaluate side-chains 300 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 280 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 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 63 CYS Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 165 TYR Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 396 ASN Chi-restraints excluded: chain C residue 418 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 149 optimal weight: 4.9990 chunk 153 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 139 optimal weight: 10.0000 chunk 92 optimal weight: 0.0270 chunk 17 optimal weight: 0.3980 chunk 61 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.6040 ------------------------------------------------------------------------------- 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 576 ASN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.194826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.154119 restraints weight = 20708.546| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 2.52 r_work: 0.3883 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14229 Z= 0.132 Angle : 0.610 10.705 19355 Z= 0.318 Chirality : 0.043 0.217 2144 Planarity : 0.004 0.054 2357 Dihedral : 13.159 148.079 2118 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.40 % Favored : 95.47 % Rotamer: Outliers : 1.93 % Allowed : 20.68 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.21), residues: 1612 helix: 1.23 (0.22), residues: 582 sheet: 0.10 (0.31), residues: 287 loop : -1.01 (0.22), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 470 HIS 0.004 0.001 HIS A 170 PHE 0.023 0.001 PHE A 930 TYR 0.020 0.001 TYR A 162 ARG 0.012 0.001 ARG B 98 Details of bonding type rmsd hydrogen bonds : bond 0.04165 ( 595) hydrogen bonds : angle 4.43889 ( 1672) covalent geometry : bond 0.00302 (14229) covalent geometry : angle 0.61014 (19355) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 293 time to evaluate : 2.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 ASP cc_start: 0.7485 (t0) cc_final: 0.7243 (t0) REVERT: A 513 THR cc_start: 0.8434 (OUTLIER) cc_final: 0.8207 (t) REVERT: A 566 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7327 (pp20) REVERT: A 639 LYS cc_start: 0.7894 (ttpp) cc_final: 0.7573 (ttpp) REVERT: A 679 TYR cc_start: 0.8473 (t80) cc_final: 0.8188 (t80) REVERT: A 837 LYS cc_start: 0.8104 (tptt) cc_final: 0.7798 (tptp) REVERT: A 859 MET cc_start: 0.4334 (mpp) cc_final: 0.3046 (mpp) REVERT: A 873 GLU cc_start: 0.6982 (tp30) cc_final: 0.6605 (tp30) REVERT: A 952 THR cc_start: 0.7920 (p) cc_final: 0.7439 (t) REVERT: A 996 MET cc_start: 0.7585 (tpp) cc_final: 0.7363 (tpp) REVERT: B 22 VAL cc_start: 0.6465 (OUTLIER) cc_final: 0.6248 (t) REVERT: B 160 LYS cc_start: 0.6671 (mmtt) cc_final: 0.6304 (mmtt) REVERT: C 16 LEU cc_start: 0.8841 (mt) cc_final: 0.8615 (mt) REVERT: C 95 MET cc_start: 0.1863 (pmm) cc_final: 0.0889 (ppp) REVERT: C 160 LEU cc_start: 0.8083 (tt) cc_final: 0.7883 (tm) REVERT: C 244 LYS cc_start: 0.8288 (tppt) cc_final: 0.7887 (tppt) REVERT: C 304 ASN cc_start: 0.6997 (m110) cc_final: 0.6642 (m110) REVERT: C 322 LYS cc_start: 0.8552 (tppp) cc_final: 0.8303 (tppp) REVERT: C 344 VAL cc_start: 0.7517 (OUTLIER) cc_final: 0.7162 (p) REVERT: C 347 LYS cc_start: 0.8022 (mmpt) cc_final: 0.7593 (mmtm) REVERT: C 350 ASN cc_start: 0.7003 (t0) cc_final: 0.6656 (t0) REVERT: C 387 PHE cc_start: 0.7957 (p90) cc_final: 0.7562 (p90) REVERT: C 396 ASN cc_start: 0.8749 (OUTLIER) cc_final: 0.8461 (p0) outliers start: 29 outliers final: 16 residues processed: 305 average time/residue: 1.1866 time to fit residues: 399.0498 Evaluate side-chains 303 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 282 time to evaluate : 2.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 937 ASN Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 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 418 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 52 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 111 optimal weight: 0.0010 chunk 94 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 ASN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 9 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.195853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.155062 restraints weight = 20528.001| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 2.51 r_work: 0.3879 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.2536 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= 0.141 Angle : 0.616 10.883 19355 Z= 0.321 Chirality : 0.043 0.219 2144 Planarity : 0.005 0.052 2357 Dihedral : 13.147 147.871 2118 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.28 % Favored : 95.60 % Rotamer: Outliers : 1.67 % Allowed : 21.61 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.21), residues: 1612 helix: 1.20 (0.22), residues: 588 sheet: 0.10 (0.31), residues: 286 loop : -0.97 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 470 HIS 0.005 0.001 HIS A 170 PHE 0.029 0.002 PHE A 930 TYR 0.021 0.001 TYR A 668 ARG 0.014 0.001 ARG B 98 Details of bonding type rmsd hydrogen bonds : bond 0.04267 ( 595) hydrogen bonds : angle 4.40999 ( 1672) covalent geometry : bond 0.00324 (14229) covalent geometry : angle 0.61566 (19355) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 296 time to evaluate : 1.616 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: 0.7590 (t0) cc_final: 0.7296 (t0) REVERT: A 513 THR cc_start: 0.8435 (OUTLIER) cc_final: 0.8192 (t) REVERT: A 566 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7324 (pp20) REVERT: A 639 LYS cc_start: 0.7885 (ttpp) cc_final: 0.7560 (ttpp) REVERT: A 837 LYS cc_start: 0.8118 (tptt) cc_final: 0.7824 (tptp) REVERT: A 859 MET cc_start: 0.4315 (mpp) cc_final: 0.3080 (mpp) REVERT: A 873 GLU cc_start: 0.6965 (tp30) cc_final: 0.6302 (tp30) REVERT: A 908 MET cc_start: 0.6568 (tmm) cc_final: 0.6298 (tmm) REVERT: A 996 MET cc_start: 0.7464 (tpp) cc_final: 0.7052 (tpp) REVERT: B 22 VAL cc_start: 0.6553 (OUTLIER) cc_final: 0.6299 (t) REVERT: B 160 LYS cc_start: 0.6679 (mmtt) cc_final: 0.6299 (mmtt) REVERT: C 16 LEU cc_start: 0.8847 (mt) cc_final: 0.8629 (mt) REVERT: C 95 MET cc_start: 0.2118 (pmm) cc_final: 0.1636 (ppp) REVERT: C 111 ARG cc_start: 0.8066 (mmm160) cc_final: 0.7775 (tpp80) REVERT: C 152 PHE cc_start: 0.7762 (m-10) cc_final: 0.7285 (m-80) REVERT: C 244 LYS cc_start: 0.8397 (tppt) cc_final: 0.8195 (tppt) REVERT: C 304 ASN cc_start: 0.7024 (m110) cc_final: 0.6660 (m110) REVERT: C 344 VAL cc_start: 0.7550 (OUTLIER) cc_final: 0.7160 (p) REVERT: C 347 LYS cc_start: 0.7993 (mmpt) cc_final: 0.7638 (mmtm) REVERT: C 350 ASN cc_start: 0.7054 (t0) cc_final: 0.6712 (t0) REVERT: C 387 PHE cc_start: 0.7932 (p90) cc_final: 0.7559 (p90) REVERT: C 393 ASN cc_start: 0.8652 (p0) cc_final: 0.8228 (p0) REVERT: C 396 ASN cc_start: 0.8750 (OUTLIER) cc_final: 0.8475 (p0) outliers start: 25 outliers final: 15 residues processed: 306 average time/residue: 1.2989 time to fit residues: 438.3015 Evaluate side-chains 300 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 280 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 937 ASN Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 211 ASN 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 418 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 96 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 149 optimal weight: 0.0060 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 ASN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 9 ASN C 339 ASN C 415 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.194397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.153603 restraints weight = 20554.611| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 2.51 r_work: 0.3877 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14229 Z= 0.139 Angle : 0.636 12.575 19355 Z= 0.330 Chirality : 0.043 0.221 2144 Planarity : 0.004 0.053 2357 Dihedral : 13.135 147.404 2118 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.53 % Favored : 95.35 % Rotamer: Outliers : 1.53 % Allowed : 22.35 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.21), residues: 1612 helix: 1.20 (0.22), residues: 588 sheet: 0.02 (0.29), residues: 313 loop : -0.98 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 470 HIS 0.004 0.001 HIS A 170 PHE 0.017 0.001 PHE C 152 TYR 0.022 0.001 TYR A 668 ARG 0.015 0.001 ARG B 98 Details of bonding type rmsd hydrogen bonds : bond 0.04166 ( 595) hydrogen bonds : angle 4.37918 ( 1672) covalent geometry : bond 0.00319 (14229) covalent geometry : angle 0.63645 (19355) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 288 time to evaluate : 1.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 MET cc_start: 0.7195 (tpt) cc_final: 0.5035 (tpt) REVERT: A 398 ASP cc_start: 0.7667 (t0) cc_final: 0.7354 (t0) REVERT: A 513 THR cc_start: 0.8427 (OUTLIER) cc_final: 0.8195 (t) REVERT: A 566 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7300 (pp20) REVERT: A 639 LYS cc_start: 0.7932 (ttpp) cc_final: 0.7618 (ttpp) REVERT: A 837 LYS cc_start: 0.8123 (tptt) cc_final: 0.7830 (tptp) REVERT: A 859 MET cc_start: 0.4311 (mpp) cc_final: 0.3074 (mpp) REVERT: A 908 MET cc_start: 0.6549 (tmm) cc_final: 0.6286 (tmm) REVERT: A 926 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7522 (tm-30) REVERT: B 22 VAL cc_start: 0.6545 (OUTLIER) cc_final: 0.6265 (t) REVERT: B 160 LYS cc_start: 0.6664 (mmtt) cc_final: 0.6270 (mmtt) REVERT: C 16 LEU cc_start: 0.8850 (mt) cc_final: 0.8629 (mt) REVERT: C 80 PRO cc_start: 0.8168 (Cg_endo) cc_final: 0.7947 (Cg_exo) REVERT: C 95 MET cc_start: 0.2179 (pmm) cc_final: 0.1632 (ppp) REVERT: C 111 ARG cc_start: 0.8076 (mmm160) cc_final: 0.7777 (tpp80) REVERT: C 304 ASN cc_start: 0.7040 (m110) cc_final: 0.6670 (m110) REVERT: C 339 ASN cc_start: 0.8671 (OUTLIER) cc_final: 0.8225 (p0) REVERT: C 344 VAL cc_start: 0.7578 (OUTLIER) cc_final: 0.7066 (p) REVERT: C 350 ASN cc_start: 0.7042 (t0) cc_final: 0.6710 (t0) REVERT: C 375 MET cc_start: 0.7805 (ppp) cc_final: 0.7194 (ppp) REVERT: C 387 PHE cc_start: 0.7931 (p90) cc_final: 0.7535 (p90) REVERT: C 393 ASN cc_start: 0.8604 (p0) cc_final: 0.8201 (p0) REVERT: C 396 ASN cc_start: 0.8727 (OUTLIER) cc_final: 0.8424 (p0) outliers start: 23 outliers final: 13 residues processed: 299 average time/residue: 1.2416 time to fit residues: 412.2120 Evaluate side-chains 298 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 279 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 590 LYS 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 63 CYS Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 211 ASN 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 418 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 97 optimal weight: 0.5980 chunk 92 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 70 optimal weight: 0.2980 chunk 144 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 147 optimal weight: 40.0000 chunk 105 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 ASN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 ASN C 415 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.194506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.153514 restraints weight = 20505.960| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 2.50 r_work: 0.3878 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14229 Z= 0.145 Angle : 0.661 13.373 19355 Z= 0.340 Chirality : 0.043 0.220 2144 Planarity : 0.005 0.053 2357 Dihedral : 13.140 147.390 2118 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.40 % Favored : 95.47 % Rotamer: Outliers : 1.80 % Allowed : 22.21 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.21), residues: 1612 helix: 1.17 (0.22), residues: 588 sheet: -0.01 (0.29), residues: 313 loop : -0.99 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 470 HIS 0.004 0.001 HIS A 170 PHE 0.038 0.002 PHE C 152 TYR 0.023 0.001 TYR A 668 ARG 0.018 0.001 ARG B 98 Details of bonding type rmsd hydrogen bonds : bond 0.04258 ( 595) hydrogen bonds : angle 4.38128 ( 1672) covalent geometry : bond 0.00334 (14229) covalent geometry : angle 0.66106 (19355) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 289 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 ASP cc_start: 0.7692 (t0) cc_final: 0.7360 (t0) REVERT: A 513 THR cc_start: 0.8430 (OUTLIER) cc_final: 0.8198 (t) REVERT: A 566 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7281 (pp20) REVERT: A 639 LYS cc_start: 0.8001 (ttpp) cc_final: 0.7690 (ttpp) REVERT: A 837 LYS cc_start: 0.8132 (tptt) cc_final: 0.7876 (tptp) REVERT: A 859 MET cc_start: 0.4306 (mpp) cc_final: 0.3069 (mpp) REVERT: A 873 GLU cc_start: 0.7005 (tp30) cc_final: 0.6688 (tp30) REVERT: A 908 MET cc_start: 0.6545 (tmm) cc_final: 0.6281 (tmm) REVERT: B 22 VAL cc_start: 0.6597 (OUTLIER) cc_final: 0.6326 (t) REVERT: B 160 LYS cc_start: 0.6641 (mmtt) cc_final: 0.6256 (mmtt) REVERT: C 16 LEU cc_start: 0.8844 (mt) cc_final: 0.8626 (mt) REVERT: C 95 MET cc_start: 0.2344 (pmm) cc_final: 0.1403 (ppp) REVERT: C 152 PHE cc_start: 0.7906 (m-80) cc_final: 0.7431 (m-80) REVERT: C 244 LYS cc_start: 0.8377 (tppt) cc_final: 0.7876 (tppt) REVERT: C 304 ASN cc_start: 0.7036 (m110) cc_final: 0.6680 (m110) REVERT: C 339 ASN cc_start: 0.8694 (m110) cc_final: 0.8219 (p0) REVERT: C 344 VAL cc_start: 0.7558 (OUTLIER) cc_final: 0.7324 (p) REVERT: C 347 LYS cc_start: 0.7908 (mmpt) cc_final: 0.7127 (mptt) REVERT: C 350 ASN cc_start: 0.7065 (t0) cc_final: 0.6735 (t0) REVERT: C 375 MET cc_start: 0.7776 (ppp) cc_final: 0.7267 (ppp) REVERT: C 387 PHE cc_start: 0.7935 (p90) cc_final: 0.7484 (p90) REVERT: C 393 ASN cc_start: 0.8630 (p0) cc_final: 0.8231 (p0) REVERT: C 396 ASN cc_start: 0.8707 (OUTLIER) cc_final: 0.8422 (p0) REVERT: C 422 LYS cc_start: 0.8646 (tttt) cc_final: 0.8445 (tttp) outliers start: 27 outliers final: 16 residues processed: 303 average time/residue: 1.1366 time to fit residues: 380.1695 Evaluate side-chains 303 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 282 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 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 590 LYS 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 63 CYS Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 211 ASN 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 402 THR Chi-restraints excluded: chain C residue 418 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 69 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 133 optimal weight: 20.0000 chunk 120 optimal weight: 9.9990 chunk 143 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 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 181 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** ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 HIS C 396 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 = 0.4436 r_free = 0.4436 target = 0.189005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.147868 restraints weight = 20401.829| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 2.48 r_work: 0.3806 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 14229 Z= 0.326 Angle : 0.792 13.598 19355 Z= 0.414 Chirality : 0.051 0.216 2144 Planarity : 0.006 0.063 2357 Dihedral : 13.500 151.582 2118 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.15 % Favored : 94.73 % Rotamer: Outliers : 2.07 % Allowed : 22.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.20), residues: 1612 helix: 0.69 (0.22), residues: 580 sheet: -0.14 (0.31), residues: 279 loop : -1.24 (0.21), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 8 HIS 0.013 0.002 HIS B 16 PHE 0.040 0.003 PHE C 152 TYR 0.028 0.002 TYR A 668 ARG 0.020 0.001 ARG B 98 Details of bonding type rmsd hydrogen bonds : bond 0.06392 ( 595) hydrogen bonds : angle 4.88034 ( 1672) covalent geometry : bond 0.00764 (14229) covalent geometry : angle 0.79171 (19355) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 301 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 LYS cc_start: 0.8533 (ptpp) cc_final: 0.8266 (ptpp) REVERT: A 513 THR cc_start: 0.8430 (OUTLIER) cc_final: 0.8166 (t) REVERT: A 639 LYS cc_start: 0.7942 (ttpp) cc_final: 0.7644 (tttm) REVERT: A 828 THR cc_start: 0.7051 (OUTLIER) cc_final: 0.6713 (p) REVERT: A 837 LYS cc_start: 0.8276 (tptt) cc_final: 0.7959 (tptp) REVERT: A 859 MET cc_start: 0.4430 (mpp) cc_final: 0.3253 (mpp) REVERT: A 908 MET cc_start: 0.6613 (tmm) cc_final: 0.6376 (tmm) REVERT: A 926 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7568 (tm-30) REVERT: A 976 THR cc_start: 0.7899 (t) cc_final: 0.7497 (m) REVERT: B 22 VAL cc_start: 0.7070 (OUTLIER) cc_final: 0.6724 (t) REVERT: B 160 LYS cc_start: 0.6722 (mmtt) cc_final: 0.6367 (mmtt) REVERT: B 166 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.8127 (tp) REVERT: C 16 LEU cc_start: 0.8853 (mt) cc_final: 0.8644 (mt) REVERT: C 95 MET cc_start: 0.2951 (pmm) cc_final: 0.1925 (ppp) REVERT: C 111 ARG cc_start: 0.8113 (mmm160) cc_final: 0.7910 (tpt170) REVERT: C 249 ASP cc_start: 0.6482 (p0) cc_final: 0.5513 (p0) REVERT: C 304 ASN cc_start: 0.7042 (m110) cc_final: 0.6678 (m110) REVERT: C 339 ASN cc_start: 0.8717 (OUTLIER) cc_final: 0.8210 (p0) REVERT: C 344 VAL cc_start: 0.7501 (OUTLIER) cc_final: 0.7149 (p) REVERT: C 347 LYS cc_start: 0.8039 (mmpt) cc_final: 0.7395 (mmtm) REVERT: C 350 ASN cc_start: 0.7310 (t0) cc_final: 0.6952 (t0) REVERT: C 375 MET cc_start: 0.7801 (ppp) cc_final: 0.7423 (ppp) REVERT: C 387 PHE cc_start: 0.8095 (p90) cc_final: 0.7709 (p90) REVERT: C 393 ASN cc_start: 0.8610 (p0) cc_final: 0.8350 (p0) REVERT: C 395 LEU cc_start: 0.8700 (mt) cc_final: 0.8459 (mt) REVERT: C 396 ASN cc_start: 0.8872 (p0) cc_final: 0.8568 (p0) REVERT: C 422 LYS cc_start: 0.8702 (tttt) cc_final: 0.8481 (tttt) outliers start: 31 outliers final: 18 residues processed: 314 average time/residue: 1.6394 time to fit residues: 570.5007 Evaluate side-chains 323 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 299 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 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 A residue 937 ASN Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 148 ILE 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 402 THR Chi-restraints excluded: chain C residue 418 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 62 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 139 optimal weight: 6.9990 chunk 92 optimal weight: 0.0870 chunk 78 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 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 120 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.192584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.151510 restraints weight = 20528.123| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 2.51 r_work: 0.3858 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14229 Z= 0.162 Angle : 0.704 12.903 19355 Z= 0.365 Chirality : 0.045 0.223 2144 Planarity : 0.005 0.054 2357 Dihedral : 13.336 146.709 2118 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.22 % Favored : 95.66 % Rotamer: Outliers : 1.80 % Allowed : 23.35 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.21), residues: 1612 helix: 0.92 (0.22), residues: 581 sheet: -0.20 (0.29), residues: 306 loop : -1.14 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 470 HIS 0.004 0.001 HIS A 185 PHE 0.062 0.002 PHE C 152 TYR 0.024 0.001 TYR A 668 ARG 0.020 0.001 ARG B 98 Details of bonding type rmsd hydrogen bonds : bond 0.04613 ( 595) hydrogen bonds : angle 4.57948 ( 1672) covalent geometry : bond 0.00377 (14229) covalent geometry : angle 0.70420 (19355) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12087.00 seconds wall clock time: 216 minutes 47.62 seconds (13007.62 seconds total)