Starting phenix.real_space_refine on Sat Sep 12 05:09:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k8s_36960/09_2026/8k8s_36960.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k8s_36960/09_2026/8k8s_36960.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8k8s_36960/09_2026/8k8s_36960.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k8s_36960/09_2026/8k8s_36960.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k8s_36960/09_2026/8k8s_36960.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k8s_36960/09_2026/8k8s_36960.map" } resolution = 3.06 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= 0.002 sd= 0.111 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 6 Type Number sf(0) Gaussians P 29 5.49 5 Mg 1 5.21 5 S 71 5.16 5 C 8855 2.51 5 N 2327 2.21 5 O 2679 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 114 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13962 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1004, 8201 Classifications: {'peptide': 1004} Link IDs: {'PTRANS': 37, 'TRANS': 966} Chain: "B" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1772 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 204} Chain: "C" Number of atoms: 3406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3406 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 10, 'TRANS': 407} Chain breaks: 2 Chain: "E" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 231 Classifications: {'DNA': 12} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 11} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 321 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Unusual residues: {' MG': 1, 'HF4': 1} Classifications: {'undetermined': 2, 'water': 1} Link IDs: {None: 2} Time building chain proxies: 3.03, per 1000 atoms: 0.22 Number of scatterers: 13962 At special positions: 0 Unit cell: (102.178, 129.353, 145.658, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 71 16.00 P 29 15.00 Mg 1 11.99 O 2679 8.00 N 2327 7.00 C 8855 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 584.4 milliseconds 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3142 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 20 sheets defined 39.1% alpha, 22.0% beta 11 base pairs and 22 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 44 through 48 Processing helix chain 'A' and resid 108 through 116 Processing helix chain 'A' and resid 144 through 148 removed outlier: 3.651A pdb=" N ASN A 147 " --> pdb=" O ASP A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 209 through 219 Processing helix 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 337 Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 380 through 390 removed outlier: 3.514A pdb=" N VAL A 388 " --> pdb=" O THR A 384 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 444 Processing helix chain 'A' and resid 448 through 473 removed outlier: 3.513A pdb=" N TYR A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS A 466 " --> pdb=" O ASP A 462 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 486 Processing helix chain 'A' and resid 489 through 493 Processing helix chain 'A' and resid 497 through 502 Processing helix chain 'A' and resid 502 through 514 Processing helix chain 'A' and resid 552 through 561 Processing helix chain 'A' and resid 576 through 591 removed outlier: 3.896A pdb=" N GLU A 581 " --> pdb=" O ARG A 577 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN A 589 " --> pdb=" O GLN A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 642 removed outlier: 3.993A pdb=" N ARG A 625 " --> pdb=" O GLY A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 670 removed outlier: 3.813A pdb=" N ALA A 651 " --> pdb=" O SER A 647 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR A 668 " --> pdb=" O ALA A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 703 Processing helix chain 'A' and resid 763 through 782 removed outlier: 3.654A pdb=" N SER A 767 " --> pdb=" O ASP A 763 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE A 768 " --> pdb=" O VAL A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 857 removed outlier: 3.723A pdb=" N ASN A 841 " --> pdb=" O LYS A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 883 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 905 through 918 Processing helix chain 'A' and resid 947 through 949 No H-bonds generated for 'chain 'A' and resid 947 through 949' Processing helix chain 'A' and resid 967 through 981 removed outlier: 3.787A pdb=" N TYR A 971 " --> pdb=" O PHE A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 997 Processing helix chain 'B' and resid 16 through 21 Proline residue: B 21 - end of helix Processing helix chain 'B' and resid 22 through 38 removed outlier: 3.740A pdb=" N VAL B 33 " --> pdb=" O PHE B 29 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N SER B 35 " --> pdb=" O ASN B 31 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N TRP B 36 " --> pdb=" O GLU B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 86 through 101 Processing helix chain 'B' and resid 110 through 113 removed outlier: 3.638A pdb=" N ILE B 113 " --> pdb=" O LEU B 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 110 through 113' Processing helix chain 'B' and resid 137 through 150 Processing helix chain 'B' and resid 165 through 170 removed outlier: 3.746A pdb=" N LEU B 170 " --> pdb=" O ARG B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 192 removed outlier: 4.165A pdb=" N HIS B 187 " --> pdb=" O ALA B 184 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN B 188 " --> pdb=" O ARG B 185 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N PHE B 189 " --> pdb=" O ASP B 186 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU B 190 " --> pdb=" O HIS B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 205 removed outlier: 3.536A 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 Processing helix chain 'C' and resid 27 through 43 Processing helix chain 'C' and resid 57 through 61 Processing helix chain 'C' and resid 107 through 121 Processing helix chain 'C' and resid 149 through 159 Processing helix chain 'C' and resid 177 through 187 Processing helix chain 'C' and resid 249 through 257 removed outlier: 4.274A pdb=" N LEU C 253 " --> pdb=" O ASP C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 298 Processing helix chain 'C' and resid 315 through 323 Processing helix chain 'C' and resid 330 through 332 No H-bonds generated for 'chain 'C' and resid 330 through 332' Processing helix chain 'C' and resid 333 through 339 removed outlier: 3.611A pdb=" N ASN C 339 " --> pdb=" O VAL C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 349 removed outlier: 3.638A pdb=" N ILE C 348 " --> pdb=" O VAL C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 360 Processing helix chain 'C' and resid 365 through 373 Processing helix chain 'C' and resid 391 through 396 removed outlier: 3.826A pdb=" N ASN C 396 " --> pdb=" O ASN C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 406 removed outlier: 3.652A pdb=" N ASN C 406 " --> pdb=" O THR C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 425 removed outlier: 4.119A pdb=" N PHE C 410 " --> pdb=" O ASN C 406 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG C 423 " --> pdb=" O ASP C 419 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 10 removed outlier: 5.775A pdb=" N CYS A 5 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ARG A 23 " --> pdb=" O CYS A 5 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N CYS A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 43 removed outlier: 4.117A pdb=" N GLY A 61 " --> pdb=" O MET A 88 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N LEU A 90 " --> pdb=" O PRO A 59 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLU A 92 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 5.544A 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: 6.568A pdb=" N ILE A 614 " --> pdb=" O VAL A 569 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL A 571 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE A 612 " --> pdb=" O VAL A 571 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL A 573 " --> pdb=" O SER A 610 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N SER A 610 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 4.106A 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: 6.628A pdb=" N LEU A 222 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N SER A 184 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 6.328A 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 305 Processing sheet with id=AA7, first strand: chain 'A' and resid 355 through 363 removed outlier: 5.526A pdb=" N VAL A 360 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE A 371 " --> pdb=" O VAL A 360 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN A 362 " --> pdb=" O THR A 369 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LYS A 416 " --> pdb=" O LYS A 408 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N LYS A 408 " --> pdb=" O LYS A 416 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL A 418 " --> pdb=" O ILE A 406 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 732 through 734 removed outlier: 6.868A pdb=" N PHE A 756 " --> pdb=" O VAL A 748 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLY A 750 " --> pdb=" O SER A 754 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N SER A 754 " --> pdb=" O GLY A 750 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA A 793 " --> pdb=" O ILE A 547 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ASP A 549 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N PHE A 791 " --> pdb=" O ASP A 549 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LEU A 798 " --> pdb=" O THR A 807 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N THR A 807 " --> pdb=" O LEU A 798 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N MET A 800 " --> pdb=" O LYS A 805 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N LYS A 805 " --> pdb=" O MET A 800 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 892 through 895 removed outlier: 4.603A pdb=" N TYR A 929 " --> pdb=" O ILE A 954 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 892 through 895 Processing sheet with id=AB2, first strand: chain 'B' and resid 2 through 5 Processing sheet with id=AB3, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AB4, first strand: chain 'B' and resid 115 through 120 removed outlier: 6.784A pdb=" N GLY B 115 " --> pdb=" O LYS B 60 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ARG B 61 " --> pdb=" O VAL B 154 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N TYR B 156 " --> pdb=" O ARG B 61 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N CYS B 63 " --> pdb=" O TYR B 156 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N LEU B 158 " --> pdb=" O CYS B 63 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N CYS B 65 " --> pdb=" O LEU B 158 " (cutoff:3.500A) 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 64 through 65 Processing sheet with id=AB7, first strand: chain 'C' and resid 95 through 97 Processing sheet with id=AB8, first strand: chain 'C' and resid 95 through 97 removed outlier: 7.045A pdb=" N ILE C 142 " --> pdb=" O ASP C 125 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 244 through 245 removed outlier: 3.602A pdb=" N VAL C 237 " --> pdb=" O ILE C 245 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR C 262 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 301 through 304 Processing sheet with id=AC2, first strand: chain 'C' and resid 375 through 380 removed outlier: 3.586A pdb=" N ASN C 386 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLU C 380 " --> pdb=" O VAL C 384 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N VAL C 384 " --> pdb=" O GLU C 380 " (cutoff:3.500A) 595 hydrogen bonds defined for protein. 1656 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 29 hydrogen bonds 58 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 22 stacking parallelities Total time for adding SS restraints: 2.06 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2226 1.31 - 1.43: 3915 1.43 - 1.56: 8011 1.56 - 1.68: 58 1.68 - 1.81: 108 Bond restraints: 14318 Sorted by residual: bond pdb=" C3' HF4 A1102 " pdb=" C4' HF4 A1102 " ideal model delta sigma weight residual 1.531 1.342 0.189 2.00e-02 2.50e+03 8.90e+01 bond pdb=" C4' HF4 A1102 " pdb=" O4' HF4 A1102 " ideal model delta sigma weight residual 1.427 1.600 -0.173 2.00e-02 2.50e+03 7.52e+01 bond pdb=" C5 HF4 A1102 " pdb=" C6 HF4 A1102 " ideal model delta sigma weight residual 1.349 1.493 -0.144 2.00e-02 2.50e+03 5.19e+01 bond pdb=" C2 HF4 A1102 " pdb=" N3 HF4 A1102 " ideal model delta sigma weight residual 1.348 1.472 -0.124 2.00e-02 2.50e+03 3.84e+01 bond pdb=" C4 HF4 A1102 " pdb=" N3 HF4 A1102 " ideal model delta sigma weight residual 1.319 1.435 -0.116 2.00e-02 2.50e+03 3.39e+01 ... (remaining 14313 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 19237 2.52 - 5.04: 217 5.04 - 7.56: 10 7.56 - 10.08: 2 10.08 - 12.60: 2 Bond angle restraints: 19468 Sorted by residual: angle pdb=" N GLY A 570 " pdb=" CA GLY A 570 " pdb=" C GLY A 570 " ideal model delta sigma weight residual 110.63 117.99 -7.36 1.45e+00 4.76e-01 2.58e+01 angle pdb=" N3 DT E 18 " pdb=" C4 DT E 18 " pdb=" O4 DT E 18 " ideal model delta sigma weight residual 119.90 122.61 -2.71 6.00e-01 2.78e+00 2.04e+01 angle pdb=" O4' DT E 23 " pdb=" C4' DT E 23 " pdb=" C3' DT E 23 " ideal model delta sigma weight residual 106.00 103.39 2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" O3A HF4 A1102 " pdb=" PB HF4 A1102 " pdb=" O3B HF4 A1102 " ideal model delta sigma weight residual 97.36 109.96 -12.60 3.00e+00 1.11e-01 1.77e+01 angle pdb=" N3 DT F 15 " pdb=" C4 DT F 15 " pdb=" O4 DT F 15 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 ... (remaining 19463 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.86: 8297 26.86 - 53.72: 246 53.72 - 80.59: 48 80.59 - 107.45: 9 107.45 - 134.31: 2 Dihedral angle restraints: 8602 sinusoidal: 3733 harmonic: 4869 Sorted by residual: dihedral pdb=" C5' HF4 A1102 " pdb=" O5' HF4 A1102 " pdb=" PA HF4 A1102 " pdb=" O1A HF4 A1102 " ideal model delta sinusoidal sigma weight residual -166.00 -31.69 -134.31 1 3.00e+01 1.11e-03 1.81e+01 dihedral pdb=" C5' HF4 A1102 " pdb=" O5' HF4 A1102 " pdb=" PA HF4 A1102 " pdb=" O2A HF4 A1102 " ideal model delta sinusoidal sigma weight residual -34.81 -151.24 116.43 1 3.00e+01 1.11e-03 1.54e+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 180.00 160.57 19.43 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 8599 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1646 0.061 - 0.122: 380 0.122 - 0.183: 125 0.183 - 0.244: 3 0.244 - 0.305: 1 Chirality restraints: 2155 Sorted by residual: chirality pdb=" C3' HF4 A1102 " pdb=" C2' HF4 A1102 " pdb=" C4' HF4 A1102 " pdb=" O3' HF4 A1102 " both_signs ideal model delta sigma weight residual False -2.73 -2.42 -0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CA VAL A 794 " pdb=" N VAL A 794 " pdb=" C VAL A 794 " pdb=" CB VAL A 794 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.36e-01 chirality pdb=" CA VAL A 259 " pdb=" N VAL A 259 " pdb=" C VAL A 259 " pdb=" CB VAL A 259 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.22e-01 ... (remaining 2152 not shown) Planarity restraints: 2376 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 289 " 0.011 2.00e-02 2.50e+03 2.13e-02 4.53e+00 pdb=" C VAL C 289 " -0.037 2.00e-02 2.50e+03 pdb=" O VAL C 289 " 0.014 2.00e-02 2.50e+03 pdb=" N ILE C 290 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 20 " -0.028 5.00e-02 4.00e+02 4.19e-02 2.80e+00 pdb=" N PRO B 21 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 21 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 21 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 502 " -0.006 2.00e-02 2.50e+03 1.21e-02 1.46e+00 pdb=" C ILE A 502 " 0.021 2.00e-02 2.50e+03 pdb=" O ILE A 502 " -0.008 2.00e-02 2.50e+03 pdb=" N LYS A 503 " -0.007 2.00e-02 2.50e+03 ... (remaining 2373 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 13 2.45 - 3.07: 8987 3.07 - 3.68: 19549 3.68 - 4.29: 31716 4.29 - 4.90: 50834 Nonbonded interactions: 111099 Sorted by model distance: nonbonded pdb="MG MG A1101 " pdb=" O1B HF4 A1102 " model vdw 1.842 2.170 nonbonded pdb=" OD2 ASP A 753 " pdb="MG MG A1101 " model vdw 1.847 2.170 nonbonded pdb=" O TYR A 550 " pdb="MG MG A1101 " model vdw 2.008 2.170 nonbonded pdb="MG MG A1101 " pdb=" O1G HF4 A1102 " model vdw 2.284 2.170 nonbonded pdb=" OD1 ASP A 549 " pdb="MG MG A1101 " model vdw 2.350 2.170 ... (remaining 111094 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.380 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 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 : 0.010 0.189 14318 Z= 0.534 Angle : 0.736 12.604 19468 Z= 0.485 Chirality : 0.056 0.305 2155 Planarity : 0.003 0.042 2376 Dihedral : 12.912 134.310 5460 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 0.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.19 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.46 (0.20), residues: 1631 helix: -0.14 (0.20), residues: 546 sheet: 0.02 (0.27), residues: 354 loop : -0.43 (0.23), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 625 TYR 0.001 0.000 TYR A 653 PHE 0.001 0.000 PHE A 630 TRP 0.001 0.000 TRP B 19 HIS 0.001 0.000 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00967 / 0.53 (14318) covalent geometry : angle 0.73633 / 0.49 (19468) hydrogen bonds : bond 0.21564 / 14.79 ( 612) hydrogen bonds : angle 6.76417 / 4.75 ( 1714) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 407 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 ASP cc_start: 0.7898 (m-30) cc_final: 0.7556 (m-30) REVERT: A 534 PHE cc_start: 0.8316 (m-80) cc_final: 0.8030 (m-10) REVERT: A 753 ASP cc_start: 0.7862 (t0) cc_final: 0.7265 (p0) REVERT: A 797 ASN cc_start: 0.7580 (m-40) cc_final: 0.7222 (t0) REVERT: B 48 LYS cc_start: 0.7603 (mmtt) cc_final: 0.7315 (mttm) REVERT: C 32 ASN cc_start: 0.6408 (m-40) cc_final: 0.6097 (m-40) REVERT: C 228 ILE cc_start: 0.6451 (pt) cc_final: 0.6229 (pt) outliers start: 0 outliers final: 0 residues processed: 407 average time/residue: 0.1285 time to fit residues: 72.7716 Evaluate side-chains 215 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.0970 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.0060 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 HIS ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 839 HIS C 134 ASN C 415 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.231696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.185846 restraints weight = 16132.816| |-----------------------------------------------------------------------------| r_work (start): 0.4120 rms_B_bonded: 4.05 r_work: 0.3583 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14318 Z= 0.154 Angle : 0.617 7.664 19468 Z= 0.337 Chirality : 0.045 0.221 2155 Planarity : 0.004 0.045 2376 Dihedral : 14.199 132.204 2136 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.64 % Favored : 97.30 % Rotamer: Outliers : 1.32 % Allowed : 7.85 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.17 (0.21), residues: 1631 helix: 0.87 (0.21), residues: 562 sheet: 0.23 (0.28), residues: 341 loop : -0.45 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 292 TYR 0.019 0.002 TYR A 971 PHE 0.027 0.002 PHE A 838 TRP 0.008 0.001 TRP A 470 HIS 0.010 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (14318) covalent geometry : angle 0.61711 / 0.34 (19468) hydrogen bonds : bond 0.06319 / 4.31 ( 612) hydrogen bonds : angle 4.90203 / 3.45 ( 1714) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 238 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.7364 (tp30) cc_final: 0.6995 (pt0) REVERT: A 131 TYR cc_start: 0.7221 (m-80) cc_final: 0.6959 (m-80) REVERT: A 257 ASP cc_start: 0.8312 (m-30) cc_final: 0.8101 (m-30) REVERT: A 303 ASN cc_start: 0.8285 (m110) cc_final: 0.7908 (m-40) REVERT: A 387 LYS cc_start: 0.7177 (ttpp) cc_final: 0.6792 (ttpt) REVERT: A 404 LYS cc_start: 0.8287 (tttt) cc_final: 0.7894 (tmtt) REVERT: A 709 ASN cc_start: 0.8337 (p0) cc_final: 0.7936 (p0) REVERT: A 819 SER cc_start: 0.8561 (m) cc_final: 0.8299 (t) REVERT: A 842 MET cc_start: 0.7639 (mpp) cc_final: 0.7225 (mpp) REVERT: B 32 GLU cc_start: 0.6904 (tt0) cc_final: 0.6663 (tt0) REVERT: C 32 ASN cc_start: 0.6185 (m-40) cc_final: 0.5861 (m-40) REVERT: C 95 MET cc_start: 0.6191 (tpp) cc_final: 0.5830 (tpp) REVERT: C 317 LYS cc_start: 0.8791 (tttt) cc_final: 0.8145 (mmtm) REVERT: C 375 MET cc_start: 0.5973 (ttm) cc_final: 0.5753 (ttm) outliers start: 20 outliers final: 16 residues processed: 254 average time/residue: 0.1276 time to fit residues: 46.7283 Evaluate side-chains 202 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 186 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASN Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 394 CYS Chi-restraints excluded: chain C residue 408 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 20 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 133 optimal weight: 9.9990 chunk 97 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 109 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 225 GLN B 52 GLN B 59 ASN B 111 ASN C 374 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.229608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.184386 restraints weight = 16183.004| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 4.05 r_work: 0.3531 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14318 Z= 0.139 Angle : 0.544 8.431 19468 Z= 0.299 Chirality : 0.043 0.215 2155 Planarity : 0.004 0.053 2376 Dihedral : 13.935 137.070 2136 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.72 % Allowed : 9.31 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.17 (0.21), residues: 1631 helix: 0.96 (0.22), residues: 562 sheet: 0.25 (0.28), residues: 333 loop : -0.54 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 16 TYR 0.020 0.001 TYR A 554 PHE 0.018 0.002 PHE A 9 TRP 0.007 0.001 TRP A 470 HIS 0.006 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (14318) covalent geometry : angle 0.54358 / 0.30 (19468) hydrogen bonds : bond 0.05339 / 3.66 ( 612) hydrogen bonds : angle 4.62300 / 3.25 ( 1714) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 194 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 TYR cc_start: 0.7356 (m-80) cc_final: 0.7074 (m-80) REVERT: A 387 LYS cc_start: 0.7231 (ttpp) cc_final: 0.6775 (ttpt) REVERT: A 404 LYS cc_start: 0.8390 (tttt) cc_final: 0.7942 (tmtt) REVERT: A 709 ASN cc_start: 0.8232 (p0) cc_final: 0.7946 (p0) REVERT: A 725 ASP cc_start: 0.6284 (t0) cc_final: 0.5799 (p0) REVERT: A 819 SER cc_start: 0.8613 (m) cc_final: 0.8355 (t) REVERT: A 996 MET cc_start: 0.7375 (tpt) cc_final: 0.6228 (tpt) REVERT: B 126 LYS cc_start: 0.8066 (ttmt) cc_final: 0.7572 (tptp) REVERT: C 32 ASN cc_start: 0.6243 (m-40) cc_final: 0.5960 (m-40) REVERT: C 95 MET cc_start: 0.6447 (tpp) cc_final: 0.5991 (tpp) REVERT: C 118 LEU cc_start: 0.2776 (OUTLIER) cc_final: 0.2560 (mp) outliers start: 26 outliers final: 19 residues processed: 212 average time/residue: 0.1132 time to fit residues: 34.9257 Evaluate side-chains 189 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASN Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 315 ASN Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 908 MET Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 394 CYS Chi-restraints excluded: chain C residue 408 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 7 optimal weight: 0.0040 chunk 157 optimal weight: 3.9990 chunk 132 optimal weight: 40.0000 chunk 158 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 139 optimal weight: 30.0000 chunk 103 optimal weight: 0.8980 chunk 143 optimal weight: 10.0000 chunk 119 optimal weight: 0.8980 chunk 156 optimal weight: 4.9990 overall best weight: 1.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 915 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.226419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.171695 restraints weight = 16114.472| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 1.94 r_work: 0.3660 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.118 14318 Z= 0.149 Angle : 0.552 8.245 19468 Z= 0.298 Chirality : 0.043 0.157 2155 Planarity : 0.004 0.059 2376 Dihedral : 13.913 136.092 2136 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.38 % Allowed : 9.50 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.06 (0.21), residues: 1631 helix: 0.92 (0.22), residues: 557 sheet: 0.12 (0.28), residues: 341 loop : -0.61 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 674 TYR 0.026 0.002 TYR A 554 PHE 0.015 0.002 PHE A 838 TRP 0.008 0.001 TRP A 470 HIS 0.005 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (14318) covalent geometry : angle 0.55221 / 0.30 (19468) hydrogen bonds : bond 0.04868 / 3.32 ( 612) hydrogen bonds : angle 4.53466 / 3.18 ( 1714) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 185 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: A 131 TYR cc_start: 0.7380 (m-80) cc_final: 0.7021 (m-80) REVERT: A 147 ASN cc_start: 0.7911 (OUTLIER) cc_final: 0.7325 (t0) REVERT: A 313 MET cc_start: 0.6917 (mmt) cc_final: 0.6071 (mmt) REVERT: A 387 LYS cc_start: 0.7252 (ttpp) cc_final: 0.6870 (ttpt) REVERT: A 404 LYS cc_start: 0.8394 (tttt) cc_final: 0.7955 (tmtt) REVERT: A 462 ASP cc_start: 0.8041 (m-30) cc_final: 0.7770 (m-30) REVERT: A 709 ASN cc_start: 0.8267 (p0) cc_final: 0.7992 (p0) REVERT: A 711 MET cc_start: 0.7721 (ppp) cc_final: 0.7143 (ppp) REVERT: A 725 ASP cc_start: 0.6526 (t0) cc_final: 0.5872 (p0) REVERT: A 819 SER cc_start: 0.8584 (m) cc_final: 0.8341 (t) REVERT: A 996 MET cc_start: 0.7362 (tpt) cc_final: 0.6969 (tpp) REVERT: B 126 LYS cc_start: 0.8166 (ttmt) cc_final: 0.7673 (tptp) REVERT: C 32 ASN cc_start: 0.6379 (m-40) cc_final: 0.6093 (m-40) REVERT: C 118 LEU cc_start: 0.2717 (OUTLIER) cc_final: 0.2456 (mp) REVERT: C 184 MET cc_start: 0.5797 (tpp) cc_final: 0.5486 (tpp) outliers start: 36 outliers final: 25 residues processed: 208 average time/residue: 0.1096 time to fit residues: 33.9720 Evaluate side-chains 195 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASN Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 394 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 69 optimal weight: 2.9990 chunk 72 optimal weight: 0.0020 chunk 78 optimal weight: 0.6980 chunk 36 optimal weight: 8.9990 chunk 100 optimal weight: 9.9990 chunk 109 optimal weight: 2.9990 chunk 125 optimal weight: 0.4980 chunk 142 optimal weight: 40.0000 chunk 84 optimal weight: 6.9990 chunk 129 optimal weight: 8.9990 chunk 117 optimal weight: 5.9990 overall best weight: 1.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 HIS B 133 HIS ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.224486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.169254 restraints weight = 16076.673| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 1.92 r_work: 0.3621 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3478 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14318 Z= 0.165 Angle : 0.559 9.109 19468 Z= 0.300 Chirality : 0.044 0.163 2155 Planarity : 0.004 0.069 2376 Dihedral : 13.955 139.652 2136 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.38 % Allowed : 10.63 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.17 (0.20), residues: 1631 helix: 0.76 (0.22), residues: 560 sheet: -0.03 (0.28), residues: 327 loop : -0.76 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 197 TYR 0.025 0.002 TYR A 554 PHE 0.019 0.002 PHE A 9 TRP 0.008 0.001 TRP A 470 HIS 0.006 0.001 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (14318) covalent geometry : angle 0.55859 / 0.30 (19468) hydrogen bonds : bond 0.05035 / 3.40 ( 612) hydrogen bonds : angle 4.55416 / 3.19 ( 1714) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 174 time to evaluate : 0.547 Fit side-chains revert: symmetry clash REVERT: A 80 ASP cc_start: 0.7598 (m-30) cc_final: 0.7139 (t70) REVERT: A 131 TYR cc_start: 0.7428 (m-80) cc_final: 0.7048 (m-80) REVERT: A 147 ASN cc_start: 0.7971 (OUTLIER) cc_final: 0.7393 (t0) REVERT: A 313 MET cc_start: 0.7022 (mmt) cc_final: 0.6229 (mmt) REVERT: A 387 LYS cc_start: 0.7325 (ttpp) cc_final: 0.6941 (ttpt) REVERT: A 709 ASN cc_start: 0.8298 (p0) cc_final: 0.8059 (p0) REVERT: A 711 MET cc_start: 0.7727 (ppp) cc_final: 0.7156 (ppp) REVERT: A 725 ASP cc_start: 0.6660 (t0) cc_final: 0.5973 (p0) REVERT: A 842 MET cc_start: 0.7703 (mpp) cc_final: 0.7434 (mmt) REVERT: A 996 MET cc_start: 0.7322 (tpt) cc_final: 0.6898 (tpp) REVERT: B 126 LYS cc_start: 0.8279 (ttmt) cc_final: 0.7784 (tptp) REVERT: C 32 ASN cc_start: 0.6278 (m-40) cc_final: 0.5879 (m-40) REVERT: C 95 MET cc_start: 0.6315 (tpp) cc_final: 0.5933 (tpp) REVERT: C 118 LEU cc_start: 0.2622 (OUTLIER) cc_final: 0.2382 (mp) REVERT: C 184 MET cc_start: 0.5579 (tpp) cc_final: 0.5312 (tpp) outliers start: 36 outliers final: 29 residues processed: 200 average time/residue: 0.1117 time to fit residues: 33.5194 Evaluate side-chains 187 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASN Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 908 MET Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 394 CYS Chi-restraints excluded: chain C residue 408 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 34 optimal weight: 2.9990 chunk 47 optimal weight: 0.1980 chunk 74 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 83 optimal weight: 10.0000 chunk 50 optimal weight: 0.8980 chunk 94 optimal weight: 0.0020 chunk 18 optimal weight: 2.9990 chunk 138 optimal weight: 40.0000 chunk 82 optimal weight: 0.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 134 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.226222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.172294 restraints weight = 15994.615| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 2.10 r_work: 0.3632 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14318 Z= 0.115 Angle : 0.508 7.352 19468 Z= 0.277 Chirality : 0.043 0.270 2155 Planarity : 0.004 0.061 2376 Dihedral : 13.762 138.180 2136 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.38 % Allowed : 11.02 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.03 (0.21), residues: 1631 helix: 0.97 (0.22), residues: 559 sheet: -0.16 (0.27), residues: 360 loop : -0.66 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 167 TYR 0.013 0.001 TYR A 300 PHE 0.016 0.001 PHE C 368 TRP 0.010 0.001 TRP A 470 HIS 0.005 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 (14318) covalent geometry : angle 0.50825 / 0.28 (19468) hydrogen bonds : bond 0.04296 / 2.93 ( 612) hydrogen bonds : angle 4.41472 / 3.10 ( 1714) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 174 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: A 80 ASP cc_start: 0.7572 (m-30) cc_final: 0.7137 (t70) REVERT: A 131 TYR cc_start: 0.7427 (m-80) cc_final: 0.7136 (m-80) REVERT: A 147 ASN cc_start: 0.8031 (OUTLIER) cc_final: 0.7479 (t0) REVERT: A 313 MET cc_start: 0.6964 (mmt) cc_final: 0.6216 (mmt) REVERT: A 485 THR cc_start: 0.8531 (m) cc_final: 0.8292 (m) REVERT: A 709 ASN cc_start: 0.8265 (p0) cc_final: 0.7963 (p0) REVERT: A 711 MET cc_start: 0.7688 (ppp) cc_final: 0.7146 (ppp) REVERT: A 725 ASP cc_start: 0.6753 (t0) cc_final: 0.5904 (p0) REVERT: A 819 SER cc_start: 0.8426 (m) cc_final: 0.8153 (t) REVERT: A 834 ASP cc_start: 0.7368 (t0) cc_final: 0.7131 (p0) REVERT: A 842 MET cc_start: 0.7659 (mpp) cc_final: 0.7381 (mmt) REVERT: A 996 MET cc_start: 0.7253 (tpt) cc_final: 0.6788 (tpp) REVERT: B 80 GLU cc_start: 0.6845 (tm-30) cc_final: 0.6502 (tm-30) REVERT: B 126 LYS cc_start: 0.8288 (ttmt) cc_final: 0.7796 (tptp) REVERT: C 32 ASN cc_start: 0.6369 (m-40) cc_final: 0.6062 (m-40) REVERT: C 95 MET cc_start: 0.6294 (tpp) cc_final: 0.5863 (tpp) REVERT: C 118 LEU cc_start: 0.2626 (OUTLIER) cc_final: 0.2373 (mp) REVERT: C 184 MET cc_start: 0.5826 (tpp) cc_final: 0.5606 (tpp) REVERT: C 228 ILE cc_start: 0.7562 (OUTLIER) cc_final: 0.7319 (pt) outliers start: 36 outliers final: 25 residues processed: 200 average time/residue: 0.1083 time to fit residues: 32.4337 Evaluate side-chains 185 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASN Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 908 MET Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 394 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 119 optimal weight: 8.9990 chunk 142 optimal weight: 50.0000 chunk 93 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 chunk 71 optimal weight: 0.7980 chunk 109 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 442 GLN C 134 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.221903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.166847 restraints weight = 15918.634| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 1.84 r_work: 0.3604 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14318 Z= 0.180 Angle : 0.567 9.856 19468 Z= 0.304 Chirality : 0.045 0.228 2155 Planarity : 0.005 0.060 2376 Dihedral : 13.942 141.671 2136 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.44 % Allowed : 11.42 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 (0.20), residues: 1631 helix: 0.75 (0.22), residues: 565 sheet: -0.18 (0.28), residues: 338 loop : -0.86 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 674 TYR 0.017 0.002 TYR A 162 PHE 0.015 0.002 PHE A 756 TRP 0.020 0.002 TRP C 43 HIS 0.007 0.001 HIS A 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (14318) covalent geometry : angle 0.56743 / 0.30 (19468) hydrogen bonds : bond 0.05027 / 3.41 ( 612) hydrogen bonds : angle 4.52123 / 3.17 ( 1714) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 161 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: A 80 ASP cc_start: 0.7546 (m-30) cc_final: 0.7166 (t70) REVERT: A 88 MET cc_start: 0.7453 (mmm) cc_final: 0.7200 (mmm) REVERT: A 131 TYR cc_start: 0.7486 (m-80) cc_final: 0.7103 (m-80) REVERT: A 147 ASN cc_start: 0.8049 (OUTLIER) cc_final: 0.7472 (t0) REVERT: A 709 ASN cc_start: 0.8360 (p0) cc_final: 0.8115 (p0) REVERT: A 711 MET cc_start: 0.7777 (ppp) cc_final: 0.7233 (ppp) REVERT: A 725 ASP cc_start: 0.6883 (t0) cc_final: 0.5977 (p0) REVERT: A 842 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7626 (mmt) REVERT: A 996 MET cc_start: 0.7174 (tpt) cc_final: 0.6773 (tpp) REVERT: B 80 GLU cc_start: 0.6784 (tm-30) cc_final: 0.6518 (tm-30) REVERT: B 126 LYS cc_start: 0.8256 (ttmt) cc_final: 0.7869 (tptp) REVERT: B 174 VAL cc_start: 0.8068 (OUTLIER) cc_final: 0.7848 (m) REVERT: C 32 ASN cc_start: 0.6262 (m-40) cc_final: 0.5976 (m-40) REVERT: C 87 PHE cc_start: 0.5629 (m-80) cc_final: 0.5346 (m-80) REVERT: C 95 MET cc_start: 0.6310 (tpp) cc_final: 0.5898 (tpp) REVERT: C 118 LEU cc_start: 0.2687 (OUTLIER) cc_final: 0.2415 (mp) outliers start: 37 outliers final: 29 residues processed: 186 average time/residue: 0.1058 time to fit residues: 30.0532 Evaluate side-chains 191 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 158 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASN Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 812 SER Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 908 MET Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 394 CYS Chi-restraints excluded: chain C residue 408 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 113 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 67 optimal weight: 0.2980 chunk 89 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 131 optimal weight: 0.4980 chunk 55 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 55 GLN B 111 ASN C 134 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.225119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.171622 restraints weight = 15932.383| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 2.06 r_work: 0.3609 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14318 Z= 0.118 Angle : 0.522 8.755 19468 Z= 0.280 Chirality : 0.043 0.217 2155 Planarity : 0.004 0.059 2376 Dihedral : 13.779 139.677 2136 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.51 % Allowed : 11.95 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.09 (0.21), residues: 1631 helix: 0.93 (0.22), residues: 565 sheet: -0.05 (0.27), residues: 348 loop : -0.79 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 674 TYR 0.014 0.001 TYR A 300 PHE 0.013 0.001 PHE A 200 TRP 0.011 0.001 TRP A 470 HIS 0.004 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (14318) covalent geometry : angle 0.52169 / 0.28 (19468) hydrogen bonds : bond 0.04261 / 2.90 ( 612) hydrogen bonds : angle 4.38340 / 3.08 ( 1714) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 166 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 80 ASP cc_start: 0.7543 (m-30) cc_final: 0.7117 (t70) REVERT: A 131 TYR cc_start: 0.7490 (m-80) cc_final: 0.7077 (m-80) REVERT: A 147 ASN cc_start: 0.8137 (OUTLIER) cc_final: 0.7556 (t0) REVERT: A 485 THR cc_start: 0.8581 (m) cc_final: 0.8307 (m) REVERT: A 709 ASN cc_start: 0.8313 (p0) cc_final: 0.8080 (p0) REVERT: A 711 MET cc_start: 0.7797 (ppp) cc_final: 0.7327 (ppp) REVERT: A 725 ASP cc_start: 0.6958 (t0) cc_final: 0.5958 (p0) REVERT: A 842 MET cc_start: 0.7721 (OUTLIER) cc_final: 0.7406 (mmt) REVERT: A 996 MET cc_start: 0.7202 (tpt) cc_final: 0.6778 (tpp) REVERT: B 80 GLU cc_start: 0.6620 (tm-30) cc_final: 0.6391 (tm-30) REVERT: B 126 LYS cc_start: 0.8242 (ttmt) cc_final: 0.7800 (tptp) REVERT: C 32 ASN cc_start: 0.6186 (m-40) cc_final: 0.5898 (m-40) REVERT: C 87 PHE cc_start: 0.5543 (m-80) cc_final: 0.5270 (m-80) REVERT: C 95 MET cc_start: 0.6459 (tpp) cc_final: 0.6067 (tpp) REVERT: C 118 LEU cc_start: 0.2631 (OUTLIER) cc_final: 0.2375 (mp) REVERT: C 186 ARG cc_start: 0.6805 (mmt180) cc_final: 0.6579 (mmt180) outliers start: 38 outliers final: 30 residues processed: 194 average time/residue: 0.1010 time to fit residues: 30.0838 Evaluate side-chains 192 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 159 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASN Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 812 SER Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 908 MET Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 394 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 83 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 17 optimal weight: 0.0470 chunk 91 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 19 optimal weight: 0.0370 chunk 116 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 100 optimal weight: 10.0000 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 109 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.224621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.171035 restraints weight = 15998.273| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 2.08 r_work: 0.3603 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14318 Z= 0.133 Angle : 0.535 7.772 19468 Z= 0.286 Chirality : 0.043 0.202 2155 Planarity : 0.004 0.057 2376 Dihedral : 13.759 140.190 2136 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.31 % Allowed : 12.48 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1631 helix: 0.94 (0.22), residues: 566 sheet: -0.06 (0.27), residues: 349 loop : -0.80 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 135 TYR 0.013 0.001 TYR A 554 PHE 0.013 0.001 PHE A 9 TRP 0.012 0.001 TRP C 43 HIS 0.006 0.001 HIS A 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (14318) covalent geometry : angle 0.53510 / 0.29 (19468) hydrogen bonds : bond 0.04342 / 2.95 ( 612) hydrogen bonds : angle 4.37098 / 3.07 ( 1714) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 162 time to evaluate : 0.560 Fit side-chains revert: symmetry clash REVERT: A 80 ASP cc_start: 0.7581 (m-30) cc_final: 0.7143 (t70) REVERT: A 131 TYR cc_start: 0.7526 (m-80) cc_final: 0.7146 (m-80) REVERT: A 147 ASN cc_start: 0.8120 (OUTLIER) cc_final: 0.7538 (t0) REVERT: A 588 LEU cc_start: 0.8735 (mp) cc_final: 0.8479 (mp) REVERT: A 709 ASN cc_start: 0.8329 (p0) cc_final: 0.8097 (p0) REVERT: A 711 MET cc_start: 0.7784 (ppp) cc_final: 0.7318 (ppp) REVERT: A 725 ASP cc_start: 0.7019 (t0) cc_final: 0.5998 (p0) REVERT: A 842 MET cc_start: 0.7730 (OUTLIER) cc_final: 0.7513 (mmt) REVERT: A 996 MET cc_start: 0.7089 (tpt) cc_final: 0.6722 (tpp) REVERT: B 126 LYS cc_start: 0.8278 (ttmt) cc_final: 0.7841 (tptp) REVERT: C 32 ASN cc_start: 0.6219 (m-40) cc_final: 0.5949 (m-40) REVERT: C 87 PHE cc_start: 0.5564 (m-80) cc_final: 0.5327 (m-80) REVERT: C 95 MET cc_start: 0.6483 (tpp) cc_final: 0.6052 (tpp) REVERT: C 118 LEU cc_start: 0.2658 (OUTLIER) cc_final: 0.2395 (mp) REVERT: C 186 ARG cc_start: 0.6829 (mmt180) cc_final: 0.6588 (mmt180) outliers start: 35 outliers final: 28 residues processed: 185 average time/residue: 0.1166 time to fit residues: 32.8826 Evaluate side-chains 187 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASN Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 812 SER Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 908 MET Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 394 CYS Chi-restraints excluded: chain C residue 408 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 88 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 119 optimal weight: 9.9990 chunk 80 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 35 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 109 ASN ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.225730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.170607 restraints weight = 16036.923| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 1.89 r_work: 0.3647 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3509 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 14318 Z= 0.116 Angle : 0.515 7.068 19468 Z= 0.279 Chirality : 0.042 0.170 2155 Planarity : 0.004 0.056 2376 Dihedral : 13.628 139.273 2136 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.91 % Allowed : 13.00 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.00 (0.21), residues: 1631 helix: 1.03 (0.22), residues: 565 sheet: -0.09 (0.28), residues: 347 loop : -0.72 (0.23), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 674 TYR 0.013 0.001 TYR A 300 PHE 0.013 0.001 PHE A 9 TRP 0.011 0.001 TRP C 43 HIS 0.004 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (14318) covalent geometry : angle 0.51513 / 0.28 (19468) hydrogen bonds : bond 0.04010 / 2.73 ( 612) hydrogen bonds : angle 4.32513 / 3.03 ( 1714) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: A 80 ASP cc_start: 0.7468 (m-30) cc_final: 0.7079 (t70) REVERT: A 131 TYR cc_start: 0.7484 (m-80) cc_final: 0.7119 (m-80) REVERT: A 147 ASN cc_start: 0.8203 (OUTLIER) cc_final: 0.7652 (t0) REVERT: A 313 MET cc_start: 0.7011 (mmt) cc_final: 0.6392 (mmt) REVERT: A 588 LEU cc_start: 0.8636 (mp) cc_final: 0.8409 (mp) REVERT: A 709 ASN cc_start: 0.8293 (p0) cc_final: 0.8050 (p0) REVERT: A 711 MET cc_start: 0.7696 (ppp) cc_final: 0.7271 (ppp) REVERT: A 725 ASP cc_start: 0.6722 (t0) cc_final: 0.5953 (p0) REVERT: A 842 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.7457 (mmt) REVERT: A 996 MET cc_start: 0.7090 (tpt) cc_final: 0.6727 (tpp) REVERT: B 91 GLU cc_start: 0.5908 (mm-30) cc_final: 0.5343 (mt-10) REVERT: B 126 LYS cc_start: 0.8288 (ttmt) cc_final: 0.7831 (tptp) REVERT: C 32 ASN cc_start: 0.6220 (m-40) cc_final: 0.5940 (m-40) REVERT: C 87 PHE cc_start: 0.5558 (m-80) cc_final: 0.5323 (m-80) REVERT: C 95 MET cc_start: 0.6497 (tpp) cc_final: 0.6051 (tpp) REVERT: C 118 LEU cc_start: 0.2683 (OUTLIER) cc_final: 0.2423 (mp) REVERT: C 184 MET cc_start: 0.5246 (tpp) cc_final: 0.4991 (tpp) outliers start: 29 outliers final: 25 residues processed: 190 average time/residue: 0.0968 time to fit residues: 28.4617 Evaluate side-chains 189 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASN Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 812 SER Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 908 MET Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 394 CYS Chi-restraints excluded: chain C residue 408 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 48 optimal weight: 0.3980 chunk 95 optimal weight: 7.9990 chunk 134 optimal weight: 5.9990 chunk 150 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 118 optimal weight: 0.0020 chunk 50 optimal weight: 0.5980 chunk 120 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 138 optimal weight: 0.5980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 109 ASN ** C 134 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 = 0.4488 r_free = 0.4488 target = 0.225858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.171312 restraints weight = 15989.597| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 1.94 r_work: 0.3650 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3510 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14318 Z= 0.108 Angle : 0.511 11.930 19468 Z= 0.274 Chirality : 0.042 0.160 2155 Planarity : 0.004 0.056 2376 Dihedral : 13.510 139.032 2136 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.58 % Allowed : 13.40 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.07 (0.21), residues: 1631 helix: 1.10 (0.22), residues: 566 sheet: -0.04 (0.28), residues: 346 loop : -0.69 (0.23), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 674 TYR 0.014 0.001 TYR A 300 PHE 0.013 0.001 PHE A 9 TRP 0.011 0.001 TRP C 43 HIS 0.004 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (14318) covalent geometry : angle 0.51061 / 0.27 (19468) hydrogen bonds : bond 0.03846 / 2.61 ( 612) hydrogen bonds : angle 4.25643 / 2.98 ( 1714) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4272.94 seconds wall clock time: 73 minutes 38.72 seconds (4418.72 seconds total)