Starting phenix.real_space_refine on Fri Jul 3 18:42:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k9u_62199/07_2026/9k9u_62199.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k9u_62199/07_2026/9k9u_62199.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k9u_62199/07_2026/9k9u_62199.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k9u_62199/07_2026/9k9u_62199.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k9u_62199/07_2026/9k9u_62199.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k9u_62199/07_2026/9k9u_62199.map" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2165 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 29 5.49 5 S 70 5.16 5 C 8805 2.51 5 N 2302 2.21 5 O 2662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13868 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: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 344 Classifications: {'DNA': 17} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 16} Chain: "E" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 267 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Time building chain proxies: 3.00, per 1000 atoms: 0.22 Number of scatterers: 13868 At special positions: 0 Unit cell: (109.65, 119.85, 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 2662 8.00 N 2302 7.00 C 8805 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 640.2 milliseconds 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3110 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 20 sheets defined 40.9% alpha, 20.2% beta 13 base pairs and 22 stacking pairs defined. Time for finding SS restraints: 1.60 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 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 209 through 220 removed outlier: 3.596A pdb=" N ILE A 213 " --> pdb=" O THR A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.618A pdb=" N GLU A 229 " --> pdb=" O SER A 226 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 226 through 230' 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: 3.627A 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 390 removed outlier: 3.594A pdb=" N THR A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 446 removed outlier: 3.674A pdb=" N MET A 443 " --> pdb=" O ASP A 439 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP A 446 " --> pdb=" O GLN A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 474 removed outlier: 3.667A pdb=" N CYS A 466 " --> pdb=" O ASP A 462 " (cutoff:3.500A) removed outlier: 3.888A 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 496 removed outlier: 4.822A pdb=" N PHE A 494 " --> pdb=" O SER A 491 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU A 495 " --> pdb=" O MET A 492 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N TYR A 496 " --> pdb=" O VAL A 493 " (cutoff:3.500A) 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: 3.691A 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 855 removed outlier: 4.077A pdb=" N ASN A 841 " --> pdb=" O LYS A 837 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N SER A 855 " --> pdb=" O SER A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 883 removed outlier: 3.615A pdb=" N ASP A 867 " --> pdb=" O GLN A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.944A pdb=" N MET A 891 " --> pdb=" O GLU A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 918 Processing helix chain 'A' and resid 946 through 949 removed outlier: 3.875A pdb=" N THR A 949 " --> pdb=" O ASN A 946 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 946 through 949' Processing helix chain 'A' and resid 967 through 982 removed outlier: 4.314A pdb=" N TYR A 971 " --> pdb=" O PHE A 967 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU A 982 " --> pdb=" O GLU A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 997 Processing helix chain 'B' and resid 16 through 18 No H-bonds generated for 'chain 'B' and resid 16 through 18' Processing helix chain 'B' and resid 19 through 31 removed outlier: 3.997A pdb=" N SER B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLN B 25 " --> pdb=" O PRO B 21 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU B 28 " --> pdb=" O SER B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 38 Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 51 through 55 removed outlier: 3.660A pdb=" N LYS B 54 " --> pdb=" O ILE B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 101 Processing helix chain 'B' and resid 133 through 150 removed outlier: 5.545A pdb=" N LYS B 139 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ILE B 140 " --> pdb=" O TYR B 136 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS B 150 " --> pdb=" O GLN B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 170 removed outlier: 3.821A pdb=" N LYS B 169 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU B 170 " --> pdb=" O ILE B 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 165 through 170' Processing helix chain 'B' and resid 188 through 192 Processing helix chain 'B' and resid 193 through 205 removed outlier: 3.618A pdb=" N ILE B 197 " --> pdb=" O ARG B 193 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN B 199 " --> pdb=" O PHE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 214 Processing helix chain 'C' and resid 3 through 19 removed outlier: 4.479A pdb=" N LEU C 7 " --> pdb=" O SER C 3 " (cutoff:3.500A) 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: 3.605A pdb=" N SER C 120 " --> pdb=" O LYS C 116 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ASP C 121 " --> pdb=" O VAL C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 158 removed outlier: 3.694A pdb=" N LYS C 153 " --> pdb=" O VAL C 149 " (cutoff:3.500A) removed outlier: 4.028A 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 257 Processing helix chain 'C' and resid 285 through 298 removed outlier: 3.505A 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: 3.505A pdb=" N SER C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 351 removed outlier: 3.928A pdb=" N ILE C 348 " --> pdb=" O VAL C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 362 removed outlier: 3.547A pdb=" N LEU C 356 " --> pdb=" O SER C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 373 removed outlier: 3.616A pdb=" N PHE C 368 " --> pdb=" O PRO C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 396 Processing helix chain 'C' and resid 397 through 425 removed outlier: 4.732A pdb=" N ASN C 408 " --> pdb=" O TYR C 404 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N GLN C 409 " --> pdb=" O GLY C 405 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE C 410 " --> pdb=" O ASN C 406 " (cutoff:3.500A) removed outlier: 4.031A 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: 8.287A pdb=" N TYR A 140 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N PHE A 31 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N CYS A 142 " --> pdb=" O PHE A 31 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ARG A 33 " --> pdb=" O CYS A 142 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N PHE A 17 " --> pdb=" O GLU A 10 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N GLU A 10 " --> pdb=" O PHE A 17 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N TYR A 19 " --> pdb=" O TRP A 8 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N TRP A 8 " --> pdb=" O TYR A 19 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LYS A 21 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N CYS A 124 " --> pdb=" O ILE A 153 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 43 removed outlier: 3.634A pdb=" N GLY A 61 " --> pdb=" O MET A 88 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N LEU A 90 " --> pdb=" O PRO A 59 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N GLU A 92 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ALA A 57 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 73 removed outlier: 6.517A pdb=" N SER A 73 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU A 568 " --> pdb=" O ASP A 616 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASP A 616 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY A 570 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU A 611 " --> pdb=" O CYS A 601 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 223 removed outlier: 6.329A pdb=" N LEU A 222 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N VAL A 237 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N THR A 201 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU A 163 " --> pdb=" O VAL A 260 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 285 through 287 Processing sheet with id=AA6, first strand: chain 'A' and resid 300 through 302 Processing sheet with id=AA7, first strand: chain 'A' and resid 355 through 362 removed outlier: 6.672A pdb=" N MET A 357 " --> pdb=" O ASP A 373 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ASP A 373 " --> pdb=" O MET A 357 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N THR A 369 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG A 407 " --> pdb=" O VAL A 418 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 732 through 734 removed outlier: 3.534A pdb=" N PHE A 743 " --> pdb=" O LEU A 707 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N SER A 747 " --> pdb=" O GLU A 758 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLU A 758 " --> pdb=" O SER A 747 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N TYR A 749 " --> pdb=" O PHE A 756 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL A 545 " --> pdb=" O VAL A 794 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL A 794 " --> pdb=" O VAL A 545 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE A 547 " --> pdb=" O GLU A 792 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU A 798 " --> pdb=" O THR A 807 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N THR A 807 " --> pdb=" O LEU A 798 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 892 through 895 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 5 Processing sheet with id=AB3, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.939A 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: 7.058A pdb=" N VAL B 62 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N TRP B 119 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL B 64 " --> pdb=" O TRP B 119 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N CYS B 63 " --> pdb=" O TYR B 156 " (cutoff:3.500A) removed outlier: 6.259A 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: 3.912A 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: 3.750A 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: 6.319A pdb=" N ILE C 124 " --> pdb=" O SER C 143 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N SER C 143 " --> pdb=" O ILE C 124 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N PHE C 126 " --> pdb=" O ALA C 141 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ALA C 141 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ARG C 128 " --> pdb=" O GLU C 139 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU C 139 " --> pdb=" O ARG C 128 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 244 through 245 removed outlier: 3.895A pdb=" N ILE C 245 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL C 237 " --> pdb=" O ILE C 245 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE C 234 " --> pdb=" O ASP C 226 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS C 214 " --> pdb=" O LYS C 268 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 302 through 303 Processing sheet with id=AC2, first strand: chain 'C' and resid 375 through 380 removed outlier: 7.022A pdb=" N ARG C 376 " --> pdb=" O PHE C 387 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N PHE C 387 " --> pdb=" O ARG C 376 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LYS C 378 " --> pdb=" O VAL C 385 " (cutoff:3.500A) 573 hydrogen bonds defined for protein. 1614 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 29 hydrogen bonds 58 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 22 stacking parallelities Total time for adding SS restraints: 2.76 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4243 1.34 - 1.46: 2512 1.46 - 1.58: 7309 1.58 - 1.70: 57 1.70 - 1.82: 107 Bond restraints: 14228 Sorted by residual: bond pdb=" N TYR A 74 " pdb=" CA TYR A 74 " ideal model delta sigma weight residual 1.455 1.498 -0.042 1.33e-02 5.65e+03 1.02e+01 bond pdb=" C3' DG E 21 " pdb=" C2' DG E 21 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" N LEU A 76 " pdb=" CA LEU A 76 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.08e-02 8.57e+03 9.89e+00 bond pdb=" C3' DA P 20 " pdb=" C2' DA P 20 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.81e+00 bond pdb=" C3' DT E 25 " pdb=" C2' DT E 25 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.18e+00 ... (remaining 14223 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 18898 1.70 - 3.40: 397 3.40 - 5.10: 46 5.10 - 6.80: 8 6.80 - 8.50: 4 Bond angle restraints: 19353 Sorted by residual: angle pdb=" N3 DT E 19 " pdb=" C4 DT E 19 " pdb=" O4 DT E 19 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT E 22 " pdb=" C4 DT E 22 " pdb=" O4 DT E 22 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT P 16 " pdb=" C4 DT P 16 " pdb=" O4 DT P 16 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" O SER A 73 " pdb=" C SER A 73 " pdb=" N TYR A 74 " ideal model delta sigma weight residual 123.21 117.96 5.25 1.27e+00 6.20e-01 1.71e+01 angle pdb=" N3 DT P 12 " pdb=" C4 DT P 12 " pdb=" O4 DT P 12 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.66e+01 ... (remaining 19348 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.20: 8101 29.20 - 58.39: 399 58.39 - 87.59: 20 87.59 - 116.78: 0 116.78 - 145.98: 1 Dihedral angle restraints: 8521 sinusoidal: 3701 harmonic: 4820 Sorted by residual: dihedral pdb=" CA ASN A 905 " pdb=" C ASN A 905 " pdb=" N PRO A 906 " pdb=" CA PRO A 906 " ideal model delta harmonic sigma weight residual 180.00 -157.62 -22.38 0 5.00e+00 4.00e-02 2.00e+01 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 -158.48 -21.52 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA SER A 836 " pdb=" C SER A 836 " pdb=" N LYS A 837 " pdb=" CA LYS A 837 " ideal model delta harmonic sigma weight residual 180.00 159.40 20.60 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 8518 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1424 0.035 - 0.071: 495 0.071 - 0.106: 165 0.106 - 0.142: 53 0.142 - 0.177: 7 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 -2.45 -0.18 2.00e-01 2.50e+01 7.83e-01 chirality pdb=" CB VAL C 311 " pdb=" CA VAL C 311 " pdb=" CG1 VAL C 311 " pdb=" CG2 VAL C 311 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.24e-01 chirality pdb=" CA PRO A 906 " pdb=" N PRO A 906 " pdb=" C PRO A 906 " pdb=" CB PRO A 906 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.19e-01 ... (remaining 2141 not shown) Planarity restraints: 2357 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 73 " -0.022 2.00e-02 2.50e+03 4.23e-02 1.79e+01 pdb=" C SER A 73 " 0.073 2.00e-02 2.50e+03 pdb=" O SER A 73 " -0.027 2.00e-02 2.50e+03 pdb=" N TYR A 74 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 737 " -0.037 5.00e-02 4.00e+02 5.70e-02 5.19e+00 pdb=" N PRO A 738 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 738 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 738 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 288 " -0.037 5.00e-02 4.00e+02 5.66e-02 5.12e+00 pdb=" N PRO A 289 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 289 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 289 " -0.031 5.00e-02 4.00e+02 ... (remaining 2354 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2450 2.77 - 3.31: 12626 3.31 - 3.84: 22238 3.84 - 4.37: 24916 4.37 - 4.90: 43642 Nonbonded interactions: 105872 Sorted by model distance: nonbonded pdb=" OG SER B 97 " pdb=" O VAL B 102 " model vdw 2.242 3.040 nonbonded pdb=" OH TYR C 302 " pdb=" O GLY C 362 " model vdw 2.257 3.040 nonbonded pdb=" O LYS A 796 " pdb=" OG1 THR A 808 " model vdw 2.270 3.040 nonbonded pdb=" O ASN A 181 " pdb=" OH TYR A 271 " model vdw 2.276 3.040 nonbonded pdb=" O ASN A 551 " pdb=" ND2 ASN A 556 " model vdw 2.287 3.120 ... (remaining 105867 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: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.300 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 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 0.042 14228 Z= 0.199 Angle : 0.575 8.501 19353 Z= 0.356 Chirality : 0.043 0.177 2144 Planarity : 0.004 0.057 2357 Dihedral : 15.650 145.979 5411 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.09 % Favored : 95.78 % Rotamer: Outliers : 0.20 % Allowed : 0.07 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.21), residues: 1612 helix: 1.56 (0.23), residues: 579 sheet: 0.55 (0.29), residues: 342 loop : -0.86 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 995 TYR 0.016 0.001 TYR A 681 PHE 0.022 0.001 PHE C 377 TRP 0.008 0.001 TRP A 470 HIS 0.002 0.000 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.20 (14228) covalent geometry : angle 0.57504 / 0.36 (19353) hydrogen bonds : bond 0.14728 / 9.80 ( 598) hydrogen bonds : angle 5.76117 / 4.03 ( 1672) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 353 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 ASN cc_start: 0.7618 (OUTLIER) cc_final: 0.6291 (p0) REVERT: A 469 LEU cc_start: 0.8374 (mt) cc_final: 0.8143 (mt) REVERT: B 123 LEU cc_start: 0.8312 (mp) cc_final: 0.8103 (mt) REVERT: C 138 MET cc_start: 0.3780 (mmp) cc_final: 0.3445 (mmp) REVERT: C 321 ASN cc_start: 0.7743 (t0) cc_final: 0.7475 (t0) outliers start: 3 outliers final: 1 residues processed: 354 average time/residue: 0.1365 time to fit residues: 67.6677 Evaluate side-chains 335 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 333 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 78 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 40.0000 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 30.0000 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.0030 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 ASN ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 HIS A 720 ASN ** A 839 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 HIS ** 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 = 0.4270 r_free = 0.4270 target = 0.180798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.139852 restraints weight = 20912.503| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.48 r_work: 0.3628 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14228 Z= 0.199 Angle : 0.623 13.098 19353 Z= 0.335 Chirality : 0.046 0.180 2144 Planarity : 0.005 0.059 2357 Dihedral : 13.345 156.994 2122 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.02 % Favored : 94.85 % Rotamer: Outliers : 1.20 % Allowed : 8.94 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.21), residues: 1612 helix: 1.35 (0.22), residues: 597 sheet: 0.40 (0.29), residues: 349 loop : -0.97 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 995 TYR 0.014 0.001 TYR A 846 PHE 0.022 0.002 PHE C 387 TRP 0.017 0.002 TRP A 470 HIS 0.004 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.20 (14228) covalent geometry : angle 0.62316 / 0.34 (19353) hydrogen bonds : bond 0.05585 / 3.66 ( 598) hydrogen bonds : angle 4.47115 / 3.13 ( 1672) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 345 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 363 ARG cc_start: 0.8123 (mtt180) cc_final: 0.7911 (mtt180) REVERT: A 859 MET cc_start: 0.6547 (mmp) cc_final: 0.6315 (mmp) REVERT: C 138 MET cc_start: 0.4110 (mmp) cc_final: 0.3864 (mmp) REVERT: C 288 GLU cc_start: 0.7478 (pm20) cc_final: 0.7251 (pm20) REVERT: C 321 ASN cc_start: 0.8149 (t0) cc_final: 0.7883 (t0) REVERT: C 337 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7479 (mt-10) outliers start: 18 outliers final: 13 residues processed: 353 average time/residue: 0.1384 time to fit residues: 68.1276 Evaluate side-chains 344 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 331 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 851 SER Chi-restraints excluded: chain A residue 901 LYS Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain C residue 13 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 95 optimal weight: 1.9990 chunk 133 optimal weight: 8.9990 chunk 58 optimal weight: 0.0070 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 chunk 113 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 120 optimal weight: 9.9990 chunk 131 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 156 optimal weight: 0.7980 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 720 ASN ** A 839 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 985 ASN C 252 HIS C 406 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.181098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.140488 restraints weight = 21085.006| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.43 r_work: 0.3643 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14228 Z= 0.145 Angle : 0.564 7.479 19353 Z= 0.304 Chirality : 0.044 0.194 2144 Planarity : 0.004 0.059 2357 Dihedral : 13.533 156.564 2118 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.22 % Favored : 95.66 % Rotamer: Outliers : 1.20 % Allowed : 12.47 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.21), residues: 1612 helix: 1.46 (0.22), residues: 583 sheet: 0.44 (0.29), residues: 337 loop : -0.90 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 995 TYR 0.014 0.001 TYR A 846 PHE 0.027 0.001 PHE A 784 TRP 0.015 0.001 TRP A 470 HIS 0.003 0.001 HIS C 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (14228) covalent geometry : angle 0.56421 / 0.30 (19353) hydrogen bonds : bond 0.04886 / 3.19 ( 598) hydrogen bonds : angle 4.32580 / 3.03 ( 1672) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 337 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 462 ASP cc_start: 0.7558 (t0) cc_final: 0.7251 (t0) REVERT: A 808 THR cc_start: 0.8691 (t) cc_final: 0.8383 (m) REVERT: A 859 MET cc_start: 0.6585 (mmp) cc_final: 0.6332 (mmp) REVERT: A 894 ARG cc_start: 0.7979 (mtm110) cc_final: 0.7574 (mtm110) REVERT: A 995 ARG cc_start: 0.7744 (ttp80) cc_final: 0.7533 (ttp80) REVERT: C 138 MET cc_start: 0.4106 (mmp) cc_final: 0.3872 (mmp) REVERT: C 337 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7540 (mt-10) outliers start: 18 outliers final: 16 residues processed: 343 average time/residue: 0.1401 time to fit residues: 67.0181 Evaluate side-chains 345 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 329 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 851 SER Chi-restraints excluded: chain A residue 901 LYS Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 959 LYS Chi-restraints excluded: chain A residue 985 ASN Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain C residue 407 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 92 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 128 optimal weight: 10.0000 chunk 120 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 119 optimal weight: 0.1980 chunk 34 optimal weight: 2.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 839 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 841 ASN A 862 ASN A 897 HIS A 985 ASN C 304 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.178321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.137076 restraints weight = 20908.196| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.54 r_work: 0.3587 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 14228 Z= 0.253 Angle : 0.624 9.301 19353 Z= 0.333 Chirality : 0.047 0.191 2144 Planarity : 0.005 0.062 2357 Dihedral : 13.678 161.248 2118 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.46 % Favored : 94.42 % Rotamer: Outliers : 1.93 % Allowed : 14.61 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.21), residues: 1612 helix: 1.19 (0.22), residues: 589 sheet: 0.38 (0.29), residues: 331 loop : -1.09 (0.22), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 995 TYR 0.019 0.002 TYR A 846 PHE 0.029 0.002 PHE A 784 TRP 0.016 0.002 TRP A 470 HIS 0.006 0.001 HIS B 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00592 / 0.25 (14228) covalent geometry : angle 0.62436 / 0.33 (19353) hydrogen bonds : bond 0.05644 / 3.67 ( 598) hydrogen bonds : angle 4.45641 / 3.12 ( 1672) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 354 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 SER cc_start: 0.8728 (m) cc_final: 0.8427 (m) REVERT: A 413 ASN cc_start: 0.8090 (t0) cc_final: 0.7725 (t0) REVERT: A 462 ASP cc_start: 0.7617 (t0) cc_final: 0.7368 (t0) REVERT: A 540 MET cc_start: 0.8582 (mtm) cc_final: 0.8246 (mtm) REVERT: A 638 LYS cc_start: 0.8060 (mmtp) cc_final: 0.7720 (mttm) REVERT: A 863 GLN cc_start: 0.7472 (tm-30) cc_final: 0.7234 (tm-30) REVERT: C 138 MET cc_start: 0.4283 (mmp) cc_final: 0.3933 (mmp) REVERT: C 288 GLU cc_start: 0.7527 (pm20) cc_final: 0.7254 (pm20) REVERT: C 318 GLN cc_start: 0.7237 (mp10) cc_final: 0.6774 (mp10) REVERT: C 336 ASP cc_start: 0.8141 (m-30) cc_final: 0.7870 (m-30) outliers start: 29 outliers final: 23 residues processed: 363 average time/residue: 0.1288 time to fit residues: 64.7380 Evaluate side-chains 366 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 343 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 459 CYS Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 671 MET Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 851 SER Chi-restraints excluded: chain A residue 901 LYS Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 407 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 87 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 839 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 ASN ** C 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.180105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.139033 restraints weight = 20950.353| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.54 r_work: 0.3618 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14228 Z= 0.137 Angle : 0.574 8.712 19353 Z= 0.308 Chirality : 0.044 0.208 2144 Planarity : 0.004 0.059 2357 Dihedral : 13.682 158.965 2118 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.53 % Favored : 95.35 % Rotamer: Outliers : 1.60 % Allowed : 16.01 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.21), residues: 1612 helix: 1.43 (0.22), residues: 584 sheet: 0.40 (0.29), residues: 329 loop : -0.94 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 995 TYR 0.016 0.001 TYR A 162 PHE 0.031 0.001 PHE A 784 TRP 0.016 0.001 TRP A 470 HIS 0.003 0.001 HIS B 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (14228) covalent geometry : angle 0.57389 / 0.31 (19353) hydrogen bonds : bond 0.04673 / 3.06 ( 598) hydrogen bonds : angle 4.32824 / 3.03 ( 1672) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 349 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: A 194 SER cc_start: 0.8699 (m) cc_final: 0.8411 (m) REVERT: A 297 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7965 (tt) REVERT: A 413 ASN cc_start: 0.8101 (t0) cc_final: 0.7700 (t0) REVERT: A 462 ASP cc_start: 0.7591 (t0) cc_final: 0.7340 (t0) REVERT: A 808 THR cc_start: 0.8701 (t) cc_final: 0.8394 (m) REVERT: A 842 MET cc_start: 0.8766 (tpp) cc_final: 0.8339 (tpp) REVERT: A 859 MET cc_start: 0.6669 (mmp) cc_final: 0.6224 (mmp) REVERT: A 880 PHE cc_start: 0.8263 (t80) cc_final: 0.7986 (t80) REVERT: A 995 ARG cc_start: 0.7657 (ttp80) cc_final: 0.6979 (ttp80) REVERT: A 996 MET cc_start: 0.7292 (mmm) cc_final: 0.7045 (mmm) REVERT: C 138 MET cc_start: 0.4234 (mmp) cc_final: 0.3890 (mmp) REVERT: C 288 GLU cc_start: 0.7518 (pm20) cc_final: 0.7064 (pm20) REVERT: C 318 GLN cc_start: 0.7140 (mp10) cc_final: 0.6538 (mp10) REVERT: C 383 LYS cc_start: 0.7469 (mmtm) cc_final: 0.7076 (mttm) outliers start: 24 outliers final: 18 residues processed: 358 average time/residue: 0.1248 time to fit residues: 62.0587 Evaluate side-chains 362 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 343 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 459 CYS Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 851 SER Chi-restraints excluded: chain A residue 901 LYS Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 959 LYS Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 407 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 159 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 108 optimal weight: 20.0000 chunk 73 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 339 ASN ** C 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.178470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.137290 restraints weight = 20899.936| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.48 r_work: 0.3598 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14228 Z= 0.213 Angle : 0.610 9.254 19353 Z= 0.325 Chirality : 0.045 0.213 2144 Planarity : 0.004 0.061 2357 Dihedral : 13.734 161.441 2118 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.33 % Favored : 94.54 % Rotamer: Outliers : 2.20 % Allowed : 15.68 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.21), residues: 1612 helix: 1.34 (0.22), residues: 583 sheet: 0.33 (0.29), residues: 331 loop : -1.00 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 995 TYR 0.020 0.001 TYR A 681 PHE 0.032 0.002 PHE A 784 TRP 0.016 0.002 TRP A 470 HIS 0.005 0.001 HIS B 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.21 (14228) covalent geometry : angle 0.60992 / 0.32 (19353) hydrogen bonds : bond 0.05200 / 3.38 ( 598) hydrogen bonds : angle 4.40262 / 3.09 ( 1672) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 349 time to evaluate : 0.529 Fit side-chains revert: symmetry clash REVERT: A 194 SER cc_start: 0.8707 (m) cc_final: 0.8461 (m) REVERT: A 413 ASN cc_start: 0.8094 (t0) cc_final: 0.7643 (t0) REVERT: A 462 ASP cc_start: 0.7616 (t0) cc_final: 0.7389 (t0) REVERT: A 754 SER cc_start: 0.8447 (t) cc_final: 0.7895 (m) REVERT: A 832 ARG cc_start: 0.8108 (ttm-80) cc_final: 0.7859 (ttt180) REVERT: A 859 MET cc_start: 0.6759 (mmp) cc_final: 0.6372 (mmp) REVERT: A 863 GLN cc_start: 0.7448 (tm-30) cc_final: 0.7032 (tm-30) REVERT: A 880 PHE cc_start: 0.8263 (t80) cc_final: 0.7996 (t80) REVERT: A 995 ARG cc_start: 0.7664 (ttp80) cc_final: 0.6935 (ttp80) REVERT: A 996 MET cc_start: 0.7223 (mmm) cc_final: 0.6610 (mmm) REVERT: C 138 MET cc_start: 0.4310 (mmp) cc_final: 0.4023 (mmp) REVERT: C 318 GLN cc_start: 0.7322 (mp10) cc_final: 0.6760 (mp10) REVERT: C 336 ASP cc_start: 0.8150 (m-30) cc_final: 0.7856 (m-30) outliers start: 33 outliers final: 23 residues processed: 361 average time/residue: 0.1343 time to fit residues: 67.3348 Evaluate side-chains 369 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 346 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 459 CYS Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 851 SER Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 901 LYS Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 959 LYS Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 407 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 15 optimal weight: 1.9990 chunk 117 optimal weight: 9.9990 chunk 151 optimal weight: 0.0870 chunk 25 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 146 optimal weight: 7.9990 chunk 61 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 130 optimal weight: 40.0000 chunk 24 optimal weight: 0.9990 overall best weight: 0.6962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.179931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.138904 restraints weight = 20750.695| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.52 r_work: 0.3611 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14228 Z= 0.138 Angle : 0.577 9.909 19353 Z= 0.311 Chirality : 0.044 0.218 2144 Planarity : 0.004 0.060 2357 Dihedral : 13.716 159.075 2118 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.59 % Favored : 95.29 % Rotamer: Outliers : 1.93 % Allowed : 16.74 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.21), residues: 1612 helix: 1.43 (0.22), residues: 584 sheet: 0.33 (0.29), residues: 331 loop : -0.95 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 894 TYR 0.020 0.001 TYR A 681 PHE 0.033 0.001 PHE A 784 TRP 0.017 0.001 TRP A 470 HIS 0.003 0.001 HIS B 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (14228) covalent geometry : angle 0.57746 / 0.31 (19353) hydrogen bonds : bond 0.04522 / 2.96 ( 598) hydrogen bonds : angle 4.32989 / 3.03 ( 1672) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 348 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: A 194 SER cc_start: 0.8698 (m) cc_final: 0.8434 (m) REVERT: A 413 ASN cc_start: 0.8109 (t0) cc_final: 0.7642 (t0) REVERT: A 462 ASP cc_start: 0.7585 (t0) cc_final: 0.7376 (t0) REVERT: A 842 MET cc_start: 0.8742 (tpp) cc_final: 0.8395 (tpp) REVERT: A 859 MET cc_start: 0.6756 (mmp) cc_final: 0.6349 (mmp) REVERT: A 880 PHE cc_start: 0.8232 (t80) cc_final: 0.7987 (t80) REVERT: A 996 MET cc_start: 0.7255 (mmm) cc_final: 0.7012 (mmm) REVERT: C 138 MET cc_start: 0.4295 (mmp) cc_final: 0.4015 (mmp) REVERT: C 318 GLN cc_start: 0.7277 (mp10) cc_final: 0.6641 (mp10) REVERT: C 336 ASP cc_start: 0.8119 (m-30) cc_final: 0.7768 (m-30) outliers start: 29 outliers final: 23 residues processed: 359 average time/residue: 0.1459 time to fit residues: 72.7964 Evaluate side-chains 365 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 342 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 459 CYS Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 851 SER Chi-restraints excluded: chain A residue 901 LYS Chi-restraints excluded: chain A residue 959 LYS Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 416 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 14 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 153 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 133 HIS ** C 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.178427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.137281 restraints weight = 20747.840| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.51 r_work: 0.3594 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14228 Z= 0.210 Angle : 0.624 10.415 19353 Z= 0.330 Chirality : 0.045 0.238 2144 Planarity : 0.004 0.061 2357 Dihedral : 13.768 161.143 2118 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.21 % Favored : 94.67 % Rotamer: Outliers : 2.07 % Allowed : 17.08 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.21), residues: 1612 helix: 1.27 (0.22), residues: 589 sheet: 0.29 (0.29), residues: 331 loop : -1.08 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 995 TYR 0.019 0.001 TYR A 162 PHE 0.037 0.002 PHE A 784 TRP 0.016 0.002 TRP A 470 HIS 0.005 0.001 HIS B 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.21 (14228) covalent geometry : angle 0.62394 / 0.33 (19353) hydrogen bonds : bond 0.05102 / 3.32 ( 598) hydrogen bonds : angle 4.41270 / 3.10 ( 1672) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 346 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: A 413 ASN cc_start: 0.8112 (t0) cc_final: 0.7622 (t0) REVERT: A 416 LYS cc_start: 0.8402 (pptt) cc_final: 0.7974 (pptt) REVERT: A 462 ASP cc_start: 0.7616 (t0) cc_final: 0.7401 (t0) REVERT: A 754 SER cc_start: 0.8443 (t) cc_final: 0.7883 (m) REVERT: A 842 MET cc_start: 0.8748 (tpp) cc_final: 0.8357 (tpp) REVERT: A 859 MET cc_start: 0.6681 (mmp) cc_final: 0.6281 (mmp) REVERT: A 880 PHE cc_start: 0.8224 (t80) cc_final: 0.7913 (t80) REVERT: C 131 LEU cc_start: 0.6491 (tp) cc_final: 0.6274 (mm) REVERT: C 138 MET cc_start: 0.4345 (mmp) cc_final: 0.4056 (mmp) REVERT: C 318 GLN cc_start: 0.7484 (mp10) cc_final: 0.6785 (mp10) REVERT: C 336 ASP cc_start: 0.8176 (m-30) cc_final: 0.7802 (m-30) REVERT: C 395 LEU cc_start: 0.8677 (mm) cc_final: 0.8332 (mm) outliers start: 31 outliers final: 29 residues processed: 357 average time/residue: 0.1480 time to fit residues: 73.1172 Evaluate side-chains 370 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 341 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 459 CYS Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 758 GLU Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 851 SER Chi-restraints excluded: chain A residue 901 LYS Chi-restraints excluded: chain A residue 959 LYS Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 340 LYS Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 416 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 57 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 chunk 82 optimal weight: 0.4980 chunk 12 optimal weight: 0.8980 chunk 69 optimal weight: 0.2980 chunk 89 optimal weight: 0.7980 chunk 106 optimal weight: 0.4980 chunk 136 optimal weight: 20.0000 chunk 139 optimal weight: 0.7980 chunk 130 optimal weight: 20.0000 chunk 101 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 386 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.180085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.138952 restraints weight = 20977.030| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.54 r_work: 0.3618 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14228 Z= 0.130 Angle : 0.586 10.481 19353 Z= 0.314 Chirality : 0.043 0.189 2144 Planarity : 0.004 0.059 2357 Dihedral : 13.734 158.206 2118 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.65 % Favored : 95.22 % Rotamer: Outliers : 1.93 % Allowed : 17.61 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.21), residues: 1612 helix: 1.43 (0.22), residues: 587 sheet: 0.34 (0.29), residues: 331 loop : -0.97 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 894 TYR 0.018 0.001 TYR A 162 PHE 0.034 0.001 PHE A 784 TRP 0.017 0.001 TRP A 470 HIS 0.004 0.001 HIS B 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (14228) covalent geometry : angle 0.58566 / 0.31 (19353) hydrogen bonds : bond 0.04362 / 2.84 ( 598) hydrogen bonds : angle 4.31729 / 3.03 ( 1672) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 350 time to evaluate : 0.575 Fit side-chains revert: symmetry clash REVERT: A 172 ASP cc_start: 0.7375 (OUTLIER) cc_final: 0.7064 (p0) REVERT: A 413 ASN cc_start: 0.8108 (t0) cc_final: 0.7628 (t0) REVERT: A 416 LYS cc_start: 0.8393 (pptt) cc_final: 0.7956 (pptt) REVERT: A 754 SER cc_start: 0.8415 (t) cc_final: 0.7850 (m) REVERT: A 842 MET cc_start: 0.8736 (tpp) cc_final: 0.8379 (tpp) REVERT: A 859 MET cc_start: 0.6686 (mmp) cc_final: 0.6291 (mmp) REVERT: A 880 PHE cc_start: 0.8207 (t80) cc_final: 0.7954 (t80) REVERT: C 318 GLN cc_start: 0.7353 (mp10) cc_final: 0.6757 (mp10) REVERT: C 336 ASP cc_start: 0.8151 (m-30) cc_final: 0.7768 (m-30) REVERT: C 395 LEU cc_start: 0.8682 (mm) cc_final: 0.8320 (mm) outliers start: 29 outliers final: 26 residues processed: 359 average time/residue: 0.1447 time to fit residues: 72.1241 Evaluate side-chains 373 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 346 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 459 CYS Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 851 SER Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 901 LYS Chi-restraints excluded: chain A residue 943 LYS Chi-restraints excluded: chain A residue 959 LYS Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 340 LYS Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 416 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 86 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 130 optimal weight: 40.0000 chunk 19 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 141 optimal weight: 6.9990 chunk 109 optimal weight: 0.0870 chunk 55 optimal weight: 0.4980 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.179300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.138000 restraints weight = 20984.502| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.48 r_work: 0.3609 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14228 Z= 0.185 Angle : 0.628 10.326 19353 Z= 0.332 Chirality : 0.045 0.358 2144 Planarity : 0.004 0.061 2357 Dihedral : 13.778 159.799 2118 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.21 % Favored : 94.67 % Rotamer: Outliers : 2.00 % Allowed : 17.55 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.21), residues: 1612 helix: 1.33 (0.22), residues: 586 sheet: 0.32 (0.29), residues: 331 loop : -1.01 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 894 TYR 0.020 0.001 TYR A 162 PHE 0.037 0.002 PHE A 784 TRP 0.016 0.002 TRP A 470 HIS 0.006 0.001 HIS B 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (14228) covalent geometry : angle 0.62761 / 0.33 (19353) hydrogen bonds : bond 0.04826 / 3.15 ( 598) hydrogen bonds : angle 4.38325 / 3.08 ( 1672) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 347 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 172 ASP cc_start: 0.7350 (OUTLIER) cc_final: 0.7079 (p0) REVERT: A 413 ASN cc_start: 0.8097 (t0) cc_final: 0.7633 (t0) REVERT: A 416 LYS cc_start: 0.8385 (pptt) cc_final: 0.7996 (pptt) REVERT: A 754 SER cc_start: 0.8466 (t) cc_final: 0.7932 (m) REVERT: A 842 MET cc_start: 0.8670 (tpp) cc_final: 0.8309 (tpp) REVERT: A 859 MET cc_start: 0.6645 (mmp) cc_final: 0.6240 (mmp) REVERT: A 880 PHE cc_start: 0.8208 (t80) cc_final: 0.7944 (t80) REVERT: C 318 GLN cc_start: 0.7415 (mp10) cc_final: 0.6852 (mp10) REVERT: C 336 ASP cc_start: 0.8080 (m-30) cc_final: 0.7656 (m-30) REVERT: C 395 LEU cc_start: 0.8677 (mm) cc_final: 0.8321 (mm) outliers start: 30 outliers final: 28 residues processed: 356 average time/residue: 0.1459 time to fit residues: 72.0514 Evaluate side-chains 372 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 343 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 459 CYS Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 851 SER Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 901 LYS Chi-restraints excluded: chain A residue 959 LYS Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 340 LYS Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 416 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 96 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 82 optimal weight: 0.3980 chunk 137 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 136 optimal weight: 20.0000 chunk 77 optimal weight: 0.9980 chunk 52 optimal weight: 0.0970 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.179895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.138746 restraints weight = 20994.513| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.47 r_work: 0.3623 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14228 Z= 0.155 Angle : 0.614 10.548 19353 Z= 0.326 Chirality : 0.044 0.285 2144 Planarity : 0.004 0.060 2357 Dihedral : 13.772 158.407 2118 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.78 % Favored : 95.10 % Rotamer: Outliers : 2.13 % Allowed : 18.01 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.21), residues: 1612 helix: 1.35 (0.22), residues: 587 sheet: 0.33 (0.30), residues: 331 loop : -1.00 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 894 TYR 0.019 0.001 TYR A 162 PHE 0.035 0.002 PHE A 784 TRP 0.017 0.002 TRP C 136 HIS 0.005 0.001 HIS B 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (14228) covalent geometry : angle 0.61375 / 0.33 (19353) hydrogen bonds : bond 0.04551 / 2.98 ( 598) hydrogen bonds : angle 4.35401 / 3.06 ( 1672) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3817.15 seconds wall clock time: 66 minutes 11.64 seconds (3971.64 seconds total)