Starting phenix.real_space_refine on Sat May 17 11:09:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k9u_62199/05_2025/9k9u_62199.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k9u_62199/05_2025/9k9u_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9k9u_62199/05_2025/9k9u_62199.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k9u_62199/05_2025/9k9u_62199.map" model { file = "/net/cci-nas-00/data/ceres_data/9k9u_62199/05_2025/9k9u_62199.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k9u_62199/05_2025/9k9u_62199.cif" } resolution = 3.08 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 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 8.59, per 1000 atoms: 0.62 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: 2.99 Conformation dependent library (CDL) restraints added in 1.5 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: 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: 4.86 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: 5.55 Time building geometry restraints manager: 3.50 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=" 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=" N ILE A 78 " pdb=" CA ILE A 78 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.20e-02 6.94e+03 6.23e+00 bond pdb=" N ASN A 75 " pdb=" CA ASN A 75 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.29e-02 6.01e+03 5.07e+00 bond pdb=" N ASP A 77 " pdb=" CA ASP A 77 " ideal model delta sigma weight residual 1.462 1.483 -0.021 1.26e-02 6.30e+03 2.78e+00 ... (remaining 14223 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 18948 1.70 - 3.40: 347 3.40 - 5.10: 46 5.10 - 6.80: 8 6.80 - 8.50: 4 Bond angle restraints: 19353 Sorted by residual: 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=" C THR A 209 " pdb=" N GLU A 210 " pdb=" CA GLU A 210 " ideal model delta sigma weight residual 120.82 126.16 -5.34 1.50e+00 4.44e-01 1.27e+01 angle pdb=" C TYR A 74 " pdb=" CA TYR A 74 " pdb=" CB TYR A 74 " ideal model delta sigma weight residual 110.17 104.70 5.47 1.69e+00 3.50e-01 1.05e+01 angle pdb=" CA ASP A 77 " pdb=" C ASP A 77 " pdb=" O ASP A 77 " ideal model delta sigma weight residual 120.92 117.57 3.35 1.04e+00 9.25e-01 1.04e+01 angle pdb=" C ASP A 77 " pdb=" N ILE A 78 " pdb=" CA ILE A 78 " ideal model delta sigma weight residual 123.19 119.29 3.90 1.24e+00 6.50e-01 9.87e+00 ... (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: 1460 0.035 - 0.071: 483 0.071 - 0.106: 146 0.106 - 0.142: 48 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: 2.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 35.990 Find NCS groups from input model: 0.150 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14228 Z= 0.127 Angle : 0.556 8.501 19353 Z= 0.307 Chirality : 0.042 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 (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: 0.48 (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 TRP 0.008 0.001 TRP A 470 HIS 0.002 0.000 HIS A 839 PHE 0.022 0.001 PHE C 377 TYR 0.016 0.001 TYR A 681 ARG 0.006 0.000 ARG A 995 Details of bonding type rmsd hydrogen bonds : bond 0.14728 ( 598) hydrogen bonds : angle 5.76117 ( 1672) covalent geometry : bond 0.00248 (14228) covalent geometry : angle 0.55599 (19353) *********************** 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 : 1.386 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: 0.2928 time to fit residues: 143.4963 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 : 1.480 ------------------------------------------------------------------------------- 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 137 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 127 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 148 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN A 296 HIS ** A 839 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 HIS C 339 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.179159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.137870 restraints weight = 20854.592| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.50 r_work: 0.3606 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14228 Z= 0.219 Angle : 0.621 9.274 19353 Z= 0.330 Chirality : 0.046 0.176 2144 Planarity : 0.005 0.064 2357 Dihedral : 13.463 159.008 2122 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.02 % Favored : 94.85 % Rotamer: Outliers : 1.00 % Allowed : 9.94 % Favored : 89.06 % 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: 0.19 (0.21), residues: 1612 helix: 1.24 (0.22), residues: 591 sheet: 0.50 (0.29), residues: 331 loop : -1.03 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 470 HIS 0.005 0.001 HIS B 181 PHE 0.024 0.002 PHE C 387 TYR 0.020 0.001 TYR A 846 ARG 0.005 0.000 ARG A 995 Details of bonding type rmsd hydrogen bonds : bond 0.05598 ( 598) hydrogen bonds : angle 4.46214 ( 1672) covalent geometry : bond 0.00514 (14228) covalent geometry : angle 0.62066 (19353) *********************** 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 367 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 352 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 ASP cc_start: 0.7634 (t0) cc_final: 0.7227 (t0) REVERT: A 469 LEU cc_start: 0.8338 (mt) cc_final: 0.8121 (mt) REVERT: A 638 LYS cc_start: 0.8131 (mmtp) cc_final: 0.7806 (mttm) REVERT: A 859 MET cc_start: 0.6544 (mmp) cc_final: 0.6305 (mmp) REVERT: C 138 MET cc_start: 0.4297 (mmp) cc_final: 0.3976 (mmp) REVERT: C 347 LYS cc_start: 0.7513 (ttpp) cc_final: 0.7242 (ttpt) REVERT: C 375 MET cc_start: 0.7219 (ptp) cc_final: 0.6958 (ptp) REVERT: C 383 LYS cc_start: 0.7456 (mmtm) cc_final: 0.7153 (mmtm) REVERT: C 388 ASN cc_start: 0.7445 (p0) cc_final: 0.7186 (p0) outliers start: 15 outliers final: 12 residues processed: 359 average time/residue: 0.2984 time to fit residues: 146.1803 Evaluate side-chains 353 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 341 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 180 ILE 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 663 VAL Chi-restraints excluded: chain A residue 783 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 B residue 35 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 54 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 130 optimal weight: 40.0000 chunk 60 optimal weight: 0.6980 chunk 162 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 839 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 397 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.179140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.138771 restraints weight = 20756.712| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.37 r_work: 0.3615 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14228 Z= 0.176 Angle : 0.574 8.369 19353 Z= 0.307 Chirality : 0.044 0.179 2144 Planarity : 0.004 0.062 2357 Dihedral : 13.477 156.955 2118 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.71 % Favored : 95.16 % Rotamer: Outliers : 1.20 % Allowed : 13.88 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.43 (0.22), residues: 583 sheet: 0.43 (0.29), residues: 333 loop : -0.91 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 470 HIS 0.004 0.001 HIS B 181 PHE 0.024 0.002 PHE C 387 TYR 0.017 0.001 TYR A 846 ARG 0.004 0.000 ARG A 995 Details of bonding type rmsd hydrogen bonds : bond 0.04863 ( 598) hydrogen bonds : angle 4.34506 ( 1672) covalent geometry : bond 0.00412 (14228) covalent geometry : angle 0.57447 (19353) *********************** 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 371 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 353 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 SER cc_start: 0.8736 (m) cc_final: 0.8406 (m) REVERT: A 198 LEU cc_start: 0.8531 (mt) cc_final: 0.8311 (mp) REVERT: A 413 ASN cc_start: 0.8181 (t0) cc_final: 0.7899 (t0) REVERT: A 462 ASP cc_start: 0.7918 (t0) cc_final: 0.7632 (t0) REVERT: A 638 LYS cc_start: 0.8213 (mmtp) cc_final: 0.7882 (mttm) REVERT: A 784 PHE cc_start: 0.8354 (p90) cc_final: 0.8128 (p90) REVERT: A 842 MET cc_start: 0.8963 (tpp) cc_final: 0.8553 (tpp) REVERT: A 880 PHE cc_start: 0.8333 (t80) cc_final: 0.8079 (t80) REVERT: C 138 MET cc_start: 0.4411 (mmp) cc_final: 0.4065 (mmp) REVERT: C 184 MET cc_start: 0.8703 (mmp) cc_final: 0.8480 (mmp) REVERT: C 375 MET cc_start: 0.7663 (ptp) cc_final: 0.7411 (ptp) REVERT: C 383 LYS cc_start: 0.7604 (mmtm) cc_final: 0.7269 (mmtm) REVERT: C 388 ASN cc_start: 0.7725 (p0) cc_final: 0.7409 (p0) outliers start: 18 outliers final: 15 residues processed: 360 average time/residue: 0.3041 time to fit residues: 150.4440 Evaluate side-chains 355 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 340 time to evaluate : 1.442 ------------------------------------------------------------------------------- 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 459 CYS 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 671 MET 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 6 optimal weight: 0.0970 chunk 140 optimal weight: 9.9990 chunk 139 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 100 optimal weight: 4.9990 chunk 108 optimal weight: 20.0000 chunk 69 optimal weight: 3.9990 chunk 109 optimal weight: 20.0000 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 839 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 897 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 985 ASN B 133 HIS C 339 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.179216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.138337 restraints weight = 20742.020| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.50 r_work: 0.3614 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14228 Z= 0.164 Angle : 0.568 8.152 19353 Z= 0.302 Chirality : 0.044 0.180 2144 Planarity : 0.004 0.061 2357 Dihedral : 13.480 155.616 2118 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.78 % Favored : 95.10 % Rotamer: Outliers : 1.67 % Allowed : 15.41 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.46 (0.22), residues: 583 sheet: 0.42 (0.29), residues: 334 loop : -0.95 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 470 HIS 0.004 0.001 HIS A 897 PHE 0.024 0.002 PHE C 387 TYR 0.017 0.001 TYR A 162 ARG 0.005 0.000 ARG A 894 Details of bonding type rmsd hydrogen bonds : bond 0.04627 ( 598) hydrogen bonds : angle 4.28275 ( 1672) covalent geometry : bond 0.00381 (14228) covalent geometry : angle 0.56803 (19353) *********************** 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 366 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 341 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 SER cc_start: 0.8674 (m) cc_final: 0.8371 (m) REVERT: A 198 LEU cc_start: 0.8444 (mt) cc_final: 0.8211 (mp) REVERT: A 207 MET cc_start: 0.6878 (mtt) cc_final: 0.6287 (mtp) REVERT: A 413 ASN cc_start: 0.8075 (t0) cc_final: 0.7722 (t0) REVERT: A 462 ASP cc_start: 0.7622 (t0) cc_final: 0.7283 (t0) REVERT: A 859 MET cc_start: 0.6746 (mmp) cc_final: 0.6317 (mmp) REVERT: A 880 PHE cc_start: 0.8272 (t80) cc_final: 0.8026 (t80) REVERT: C 138 MET cc_start: 0.4317 (mmp) cc_final: 0.4018 (mmp) REVERT: C 318 GLN cc_start: 0.7126 (mp10) cc_final: 0.6711 (mp10) REVERT: C 375 MET cc_start: 0.7283 (ptp) cc_final: 0.7037 (ptp) REVERT: C 376 ARG cc_start: 0.7493 (mmt180) cc_final: 0.7289 (mmt180) REVERT: C 388 ASN cc_start: 0.7657 (p0) cc_final: 0.7350 (p0) REVERT: C 395 LEU cc_start: 0.8503 (mt) cc_final: 0.8301 (mm) outliers start: 25 outliers final: 20 residues processed: 352 average time/residue: 0.3225 time to fit residues: 156.7761 Evaluate side-chains 359 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 339 time to evaluate : 2.232 ------------------------------------------------------------------------------- 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 230 MET Chi-restraints excluded: chain A residue 459 CYS Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 540 MET 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 851 SER Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 901 LYS 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 238 ILE Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 337 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 131 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 109 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 149 optimal weight: 0.3980 chunk 66 optimal weight: 1.9990 chunk 117 optimal weight: 20.0000 chunk 0 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 897 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.177981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.136610 restraints weight = 20889.205| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.46 r_work: 0.3594 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14228 Z= 0.222 Angle : 0.603 9.189 19353 Z= 0.320 Chirality : 0.045 0.180 2144 Planarity : 0.005 0.062 2357 Dihedral : 13.553 157.896 2118 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.58 % Favored : 94.29 % Rotamer: Outliers : 2.40 % Allowed : 15.81 % Favored : 81.79 % 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: 1.18 (0.22), residues: 592 sheet: 0.38 (0.29), residues: 337 loop : -1.12 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 470 HIS 0.007 0.001 HIS B 133 PHE 0.027 0.002 PHE A 784 TYR 0.019 0.001 TYR A 162 ARG 0.010 0.000 ARG A 995 Details of bonding type rmsd hydrogen bonds : bond 0.05262 ( 598) hydrogen bonds : angle 4.37348 ( 1672) covalent geometry : bond 0.00523 (14228) covalent geometry : angle 0.60266 (19353) *********************** 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 394 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 358 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 172 ASP cc_start: 0.7351 (OUTLIER) cc_final: 0.7065 (p0) REVERT: A 207 MET cc_start: 0.7049 (mtt) cc_final: 0.6656 (mtp) REVERT: A 413 ASN cc_start: 0.8088 (t0) cc_final: 0.7676 (t0) REVERT: A 416 LYS cc_start: 0.8396 (pptt) cc_final: 0.7983 (pptt) REVERT: A 462 ASP cc_start: 0.7576 (t0) cc_final: 0.7257 (t0) REVERT: A 754 SER cc_start: 0.8489 (t) cc_final: 0.7973 (m) REVERT: A 837 LYS cc_start: 0.8124 (tptt) cc_final: 0.7896 (tptp) REVERT: A 842 MET cc_start: 0.8751 (tpp) cc_final: 0.8295 (tpp) REVERT: A 859 MET cc_start: 0.6670 (mmp) cc_final: 0.6310 (mmp) REVERT: A 863 GLN cc_start: 0.7338 (tm-30) cc_final: 0.6894 (tm-30) REVERT: A 880 PHE cc_start: 0.8291 (t80) cc_final: 0.8045 (t80) REVERT: A 995 ARG cc_start: 0.7662 (ttp80) cc_final: 0.6936 (ttp80) REVERT: A 996 MET cc_start: 0.7199 (mmm) cc_final: 0.6942 (mmm) REVERT: C 138 MET cc_start: 0.4323 (mmp) cc_final: 0.4104 (mmp) REVERT: C 184 MET cc_start: 0.8679 (mmp) cc_final: 0.8458 (mmp) REVERT: C 302 TYR cc_start: 0.6855 (p90) cc_final: 0.6629 (p90) REVERT: C 304 ASN cc_start: 0.8054 (t0) cc_final: 0.7757 (t0) REVERT: C 336 ASP cc_start: 0.8112 (m-30) cc_final: 0.7784 (m-30) REVERT: C 346 ARG cc_start: 0.7824 (ptt90) cc_final: 0.7581 (ptt90) REVERT: C 388 ASN cc_start: 0.7882 (p0) cc_final: 0.7627 (p0) REVERT: C 395 LEU cc_start: 0.8510 (mt) cc_final: 0.8296 (mm) outliers start: 36 outliers final: 30 residues processed: 373 average time/residue: 0.3264 time to fit residues: 168.3817 Evaluate side-chains 392 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 361 time to evaluate : 1.391 ------------------------------------------------------------------------------- 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 285 ILE Chi-restraints excluded: chain A residue 459 CYS Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 540 MET 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 663 VAL Chi-restraints excluded: chain A residue 696 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 881 ASP Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 901 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 13 LEU Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 416 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 129 optimal weight: 0.1980 chunk 33 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 149 optimal weight: 0.0010 chunk 153 optimal weight: 0.9990 chunk 112 optimal weight: 0.5980 chunk 114 optimal weight: 4.9990 chunk 97 optimal weight: 0.1980 chunk 53 optimal weight: 0.6980 overall best weight: 0.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 318 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.181547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.140494 restraints weight = 21175.717| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.51 r_work: 0.3650 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14228 Z= 0.107 Angle : 0.530 9.041 19353 Z= 0.283 Chirality : 0.042 0.221 2144 Planarity : 0.004 0.060 2357 Dihedral : 13.483 151.608 2118 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.97 % Favored : 95.91 % Rotamer: Outliers : 2.00 % Allowed : 17.21 % Favored : 80.79 % 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: 0.42 (0.21), residues: 1612 helix: 1.54 (0.22), residues: 585 sheet: 0.52 (0.29), residues: 331 loop : -0.93 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 470 HIS 0.008 0.001 HIS A 897 PHE 0.027 0.001 PHE A 784 TYR 0.017 0.001 TYR A 162 ARG 0.008 0.000 ARG A 995 Details of bonding type rmsd hydrogen bonds : bond 0.03634 ( 598) hydrogen bonds : angle 4.10391 ( 1672) covalent geometry : bond 0.00236 (14228) covalent geometry : angle 0.53038 (19353) *********************** 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 378 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 348 time to evaluate : 1.341 Fit side-chains revert: symmetry clash REVERT: A 413 ASN cc_start: 0.8089 (t0) cc_final: 0.7674 (t0) REVERT: A 416 LYS cc_start: 0.8367 (pptt) cc_final: 0.7942 (pptt) REVERT: A 837 LYS cc_start: 0.8048 (tptt) cc_final: 0.7812 (tptp) REVERT: A 859 MET cc_start: 0.6531 (mmp) cc_final: 0.6175 (mmp) REVERT: A 880 PHE cc_start: 0.8279 (t80) cc_final: 0.8040 (t80) REVERT: C 220 ILE cc_start: 0.6872 (pt) cc_final: 0.5820 (mm) REVERT: C 336 ASP cc_start: 0.8086 (m-30) cc_final: 0.7868 (m-30) REVERT: C 377 PHE cc_start: 0.8444 (m-10) cc_final: 0.8144 (m-10) REVERT: C 388 ASN cc_start: 0.7727 (p0) cc_final: 0.7403 (p0) outliers start: 30 outliers final: 18 residues processed: 361 average time/residue: 0.3117 time to fit residues: 154.5430 Evaluate side-chains 359 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 341 time to evaluate : 1.456 ------------------------------------------------------------------------------- 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 230 MET Chi-restraints excluded: chain A residue 459 CYS Chi-restraints excluded: chain A residue 502 ILE 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 959 LYS Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 243 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 35 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 17 optimal weight: 0.0170 chunk 148 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 142 optimal weight: 0.8980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 841 ASN C 406 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.180601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.139361 restraints weight = 21249.403| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.51 r_work: 0.3635 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14228 Z= 0.129 Angle : 0.558 9.359 19353 Z= 0.296 Chirality : 0.042 0.182 2144 Planarity : 0.004 0.060 2357 Dihedral : 13.486 153.948 2118 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.59 % Favored : 95.29 % Rotamer: Outliers : 1.80 % Allowed : 18.08 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.21), residues: 1612 helix: 1.51 (0.22), residues: 586 sheet: 0.46 (0.29), residues: 331 loop : -0.98 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 470 HIS 0.009 0.001 HIS A 897 PHE 0.030 0.001 PHE A 784 TYR 0.016 0.001 TYR A 162 ARG 0.008 0.000 ARG A 995 Details of bonding type rmsd hydrogen bonds : bond 0.04031 ( 598) hydrogen bonds : angle 4.10597 ( 1672) covalent geometry : bond 0.00297 (14228) covalent geometry : angle 0.55834 (19353) *********************** 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 368 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 341 time to evaluate : 1.427 Fit side-chains revert: symmetry clash REVERT: A 172 ASP cc_start: 0.7314 (OUTLIER) cc_final: 0.7079 (p0) REVERT: A 207 MET cc_start: 0.6916 (mtt) cc_final: 0.6407 (mtp) REVERT: A 413 ASN cc_start: 0.8084 (t0) cc_final: 0.7640 (t0) REVERT: A 416 LYS cc_start: 0.8370 (pptt) cc_final: 0.7964 (pptt) REVERT: A 837 LYS cc_start: 0.8099 (tptt) cc_final: 0.7868 (tptp) REVERT: A 859 MET cc_start: 0.6568 (mmp) cc_final: 0.6269 (mmt) REVERT: A 880 PHE cc_start: 0.8186 (t80) cc_final: 0.7969 (t80) REVERT: C 336 ASP cc_start: 0.8191 (m-30) cc_final: 0.7902 (m-30) REVERT: C 388 ASN cc_start: 0.7447 (p0) cc_final: 0.7153 (p0) outliers start: 27 outliers final: 25 residues processed: 351 average time/residue: 0.3115 time to fit residues: 149.8738 Evaluate side-chains 361 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 335 time to evaluate : 1.528 ------------------------------------------------------------------------------- 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 459 CYS Chi-restraints excluded: chain A residue 502 ILE 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 853 MET 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 148 ILE Chi-restraints excluded: chain C residue 185 GLU Chi-restraints excluded: chain C residue 243 LYS Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 340 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 52 optimal weight: 0.9990 chunk 138 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 102 optimal weight: 0.0770 chunk 93 optimal weight: 0.0060 chunk 151 optimal weight: 0.2980 chunk 63 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 154 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 107 optimal weight: 10.0000 overall best weight: 0.3754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 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 = 0.4298 r_free = 0.4298 target = 0.182681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.141727 restraints weight = 20878.723| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 2.48 r_work: 0.3660 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14228 Z= 0.110 Angle : 0.546 9.852 19353 Z= 0.289 Chirality : 0.042 0.183 2144 Planarity : 0.004 0.059 2357 Dihedral : 13.429 151.070 2118 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.85 % Favored : 96.03 % Rotamer: Outliers : 2.13 % Allowed : 17.95 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.49 (0.21), residues: 1612 helix: 1.61 (0.22), residues: 583 sheet: 0.48 (0.29), residues: 337 loop : -0.85 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 470 HIS 0.008 0.001 HIS A 897 PHE 0.030 0.001 PHE C 387 TYR 0.015 0.001 TYR A 681 ARG 0.007 0.000 ARG A 894 Details of bonding type rmsd hydrogen bonds : bond 0.03592 ( 598) hydrogen bonds : angle 4.02453 ( 1672) covalent geometry : bond 0.00243 (14228) covalent geometry : angle 0.54587 (19353) *********************** 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 374 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 342 time to evaluate : 1.579 Fit side-chains revert: symmetry clash REVERT: A 172 ASP cc_start: 0.7272 (OUTLIER) cc_final: 0.7054 (p0) REVERT: A 286 PHE cc_start: 0.8217 (m-10) cc_final: 0.7988 (m-10) REVERT: A 413 ASN cc_start: 0.8076 (t0) cc_final: 0.7628 (t0) REVERT: A 416 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.7964 (pptt) REVERT: A 837 LYS cc_start: 0.8118 (tptt) cc_final: 0.7879 (tptp) REVERT: A 842 MET cc_start: 0.8558 (tpp) cc_final: 0.8234 (tpp) REVERT: A 880 PHE cc_start: 0.8146 (t80) cc_final: 0.7882 (t80) REVERT: B 201 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7862 (mp) REVERT: C 336 ASP cc_start: 0.8236 (m-30) cc_final: 0.7901 (m-30) REVERT: C 377 PHE cc_start: 0.8280 (m-10) cc_final: 0.8030 (m-10) REVERT: C 388 ASN cc_start: 0.7385 (p0) cc_final: 0.7104 (p0) outliers start: 32 outliers final: 21 residues processed: 353 average time/residue: 0.3082 time to fit residues: 150.0134 Evaluate side-chains 360 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 336 time to evaluate : 1.371 ------------------------------------------------------------------------------- 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 172 ASP Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 459 CYS Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 618 SER 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 148 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 185 GLU Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 340 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 108 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 126 optimal weight: 0.0870 chunk 79 optimal weight: 3.9990 chunk 103 optimal weight: 0.0050 chunk 52 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 92 optimal weight: 6.9990 chunk 11 optimal weight: 0.0570 overall best weight: 0.3690 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 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 = 0.4302 r_free = 0.4302 target = 0.183057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.141835 restraints weight = 20953.426| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.49 r_work: 0.3661 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14228 Z= 0.110 Angle : 0.552 9.634 19353 Z= 0.291 Chirality : 0.042 0.185 2144 Planarity : 0.004 0.059 2357 Dihedral : 13.408 151.170 2118 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.09 % Favored : 95.78 % Rotamer: Outliers : 1.80 % Allowed : 19.21 % Favored : 78.99 % 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: 0.51 (0.21), residues: 1612 helix: 1.65 (0.22), residues: 582 sheet: 0.45 (0.29), residues: 339 loop : -0.84 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 470 HIS 0.008 0.001 HIS A 897 PHE 0.030 0.001 PHE A 784 TYR 0.014 0.001 TYR A 162 ARG 0.008 0.000 ARG A 894 Details of bonding type rmsd hydrogen bonds : bond 0.03554 ( 598) hydrogen bonds : angle 3.99346 ( 1672) covalent geometry : bond 0.00244 (14228) covalent geometry : angle 0.55163 (19353) *********************** 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 364 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 337 time to evaluate : 1.412 Fit side-chains revert: symmetry clash REVERT: A 172 ASP cc_start: 0.7266 (OUTLIER) cc_final: 0.7055 (p0) REVERT: A 413 ASN cc_start: 0.8062 (t0) cc_final: 0.7633 (t0) REVERT: A 416 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.7937 (pptt) REVERT: A 837 LYS cc_start: 0.8075 (tptt) cc_final: 0.7848 (tptp) REVERT: A 842 MET cc_start: 0.8542 (tpp) cc_final: 0.8290 (tpp) REVERT: A 859 MET cc_start: 0.6648 (mmp) cc_final: 0.6179 (mmp) REVERT: A 880 PHE cc_start: 0.8164 (t80) cc_final: 0.7899 (t80) REVERT: B 201 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7850 (mp) REVERT: C 336 ASP cc_start: 0.8244 (m-30) cc_final: 0.7891 (m-30) REVERT: C 375 MET cc_start: 0.7199 (ppp) cc_final: 0.6922 (ppp) REVERT: C 388 ASN cc_start: 0.7390 (p0) cc_final: 0.6996 (p0) outliers start: 27 outliers final: 21 residues processed: 349 average time/residue: 0.3099 time to fit residues: 148.9585 Evaluate side-chains 355 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 331 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASN Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 459 CYS Chi-restraints excluded: chain A residue 576 ASN 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 24 SER Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 243 LYS Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 340 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 77 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 141 optimal weight: 0.4980 chunk 76 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 339 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.180558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.139146 restraints weight = 21032.716| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 2.47 r_work: 0.3626 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14228 Z= 0.154 Angle : 0.593 9.474 19353 Z= 0.313 Chirality : 0.043 0.203 2144 Planarity : 0.004 0.060 2357 Dihedral : 13.442 153.828 2118 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.53 % Favored : 95.35 % Rotamer: Outliers : 2.00 % Allowed : 19.28 % Favored : 78.72 % 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: 0.32 (0.21), residues: 1612 helix: 1.44 (0.22), residues: 586 sheet: 0.46 (0.30), residues: 331 loop : -0.97 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 470 HIS 0.009 0.001 HIS A 897 PHE 0.034 0.002 PHE A 784 TYR 0.020 0.001 TYR A 591 ARG 0.008 0.000 ARG A 894 Details of bonding type rmsd hydrogen bonds : bond 0.04329 ( 598) hydrogen bonds : angle 4.12567 ( 1672) covalent geometry : bond 0.00359 (14228) covalent geometry : angle 0.59328 (19353) ********************** 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 366 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 336 time to evaluate : 1.577 Fit side-chains revert: symmetry clash REVERT: A 172 ASP cc_start: 0.7305 (OUTLIER) cc_final: 0.7077 (p0) REVERT: A 207 MET cc_start: 0.6975 (mtt) cc_final: 0.6514 (mtp) REVERT: A 413 ASN cc_start: 0.8053 (t0) cc_final: 0.7591 (t0) REVERT: A 416 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.7970 (pptt) REVERT: A 837 LYS cc_start: 0.8135 (tptt) cc_final: 0.7919 (tptp) REVERT: A 842 MET cc_start: 0.8576 (tpp) cc_final: 0.8266 (tpp) REVERT: A 859 MET cc_start: 0.6572 (mmp) cc_final: 0.6192 (mmp) REVERT: A 880 PHE cc_start: 0.8203 (t80) cc_final: 0.7951 (t80) REVERT: B 201 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7872 (mp) REVERT: C 336 ASP cc_start: 0.8232 (m-30) cc_final: 0.7862 (m-30) REVERT: C 340 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8426 (pttm) REVERT: C 388 ASN cc_start: 0.7536 (p0) cc_final: 0.7232 (p0) outliers start: 30 outliers final: 22 residues processed: 346 average time/residue: 0.3154 time to fit residues: 149.6219 Evaluate side-chains 359 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 333 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASN Chi-restraints excluded: chain A residue 84 SER 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 416 LYS Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 459 CYS 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 853 MET Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 901 LYS Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 243 LYS Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 340 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 95 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 chunk 109 optimal weight: 9.9990 chunk 123 optimal weight: 7.9990 chunk 138 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 133 optimal weight: 0.0060 overall best weight: 1.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 339 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.179215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.137612 restraints weight = 21112.909| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.48 r_work: 0.3607 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14228 Z= 0.197 Angle : 0.624 9.798 19353 Z= 0.328 Chirality : 0.045 0.223 2144 Planarity : 0.004 0.060 2357 Dihedral : 13.484 155.288 2118 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.27 % Favored : 94.60 % Rotamer: Outliers : 1.93 % Allowed : 19.01 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.18 (0.21), residues: 1612 helix: 1.33 (0.22), residues: 580 sheet: 0.42 (0.30), residues: 330 loop : -1.05 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 470 HIS 0.009 0.001 HIS A 897 PHE 0.035 0.002 PHE A 784 TYR 0.025 0.001 TYR A 681 ARG 0.007 0.000 ARG A 894 Details of bonding type rmsd hydrogen bonds : bond 0.04799 ( 598) hydrogen bonds : angle 4.22684 ( 1672) covalent geometry : bond 0.00464 (14228) covalent geometry : angle 0.62438 (19353) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8268.62 seconds wall clock time: 143 minutes 42.82 seconds (8622.82 seconds total)