Starting phenix.real_space_refine on Thu Jul 2 21:08:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7dfh_30664/07_2026/7dfh_30664.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dfh_30664/07_2026/7dfh_30664.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dfh_30664/07_2026/7dfh_30664.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dfh_30664/07_2026/7dfh_30664.map" model { file = "/net/cci-nas-00/data/ceres_data/7dfh_30664/07_2026/7dfh_30664.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dfh_30664/07_2026/7dfh_30664.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7dfh_30664/07_2026/7dfh_30664.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7dfh_30664/07_2026/7dfh_30664.cif" } resolution = 2.97 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= -0.000 sd= 0.005 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 25 5.49 5 Mg 3 5.21 5 S 70 5.16 5 C 6263 2.51 5 N 1670 2.21 5 O 1947 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9980 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 7328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 908, 7328 Classifications: {'peptide': 908} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 877} Chain breaks: 2 Chain: "B" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 882 Classifications: {'peptide': 114} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 108} Chain: "C" Number of atoms: 485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 485 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "G" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 820 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain breaks: 1 Chain: "P" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 171 Classifications: {'RNA': 8} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 4} Link IDs: {'rna3p': 7} Chain: "T" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 249 Classifications: {'RNA': 12} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 8} Link IDs: {'rna3p': 11} Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 23 Unusual residues: {' MG': 3, ' ZN': 2, 'POP': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "P" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RVP%rna3p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna3p': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2429 SG CYS A 301 43.076 63.750 43.645 1.00 48.76 S ATOM 2470 SG CYS A 306 43.499 62.702 39.750 1.00 43.75 S ATOM 2502 SG CYS A 310 46.486 62.891 42.457 1.00 37.28 S ATOM 3910 SG CYS A 487 24.799 59.648 51.489 1.00 53.98 S ATOM 5163 SG CYS A 645 23.650 59.141 47.723 1.00 59.72 S ATOM 5169 SG CYS A 646 26.717 61.845 49.340 1.00 57.57 S Time building chain proxies: 2.46, per 1000 atoms: 0.25 Number of scatterers: 9980 At special positions: 0 Unit cell: (102.624, 93.003, 130.418, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 70 16.00 P 25 15.00 Mg 3 11.99 O 1947 8.00 N 1670 7.00 C 6263 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 360.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " Number of angles added : 3 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2286 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 14 sheets defined 48.5% alpha, 20.9% beta 7 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 removed outlier: 3.856A pdb=" N CYS A 12 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY A 13 " --> pdb=" O ASN A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 88 Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.699A pdb=" N LEU A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 149 Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.815A pdb=" N PHE A 157 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN A 158 " --> pdb=" O ASP A 155 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS A 159 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 200 removed outlier: 3.966A pdb=" N ASN A 177 " --> pdb=" O ARG A 173 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU A 178 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ARG A 181 " --> pdb=" O ASN A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 234 through 248 Proline residue: A 243 - end of helix removed outlier: 4.119A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 256 removed outlier: 3.506A pdb=" N THR A 252 " --> pdb=" O ARG A 249 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER A 255 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N HIS A 256 " --> pdb=" O ALA A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.850A pdb=" N HIS A 309 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 377 through 385 removed outlier: 4.505A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 447 through 454 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 479 removed outlier: 3.839A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR A 479 " --> pdb=" O VAL A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.800A pdb=" N VAL A 493 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 removed outlier: 3.682A pdb=" N LYS A 508 " --> pdb=" O PRO A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.846A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 Processing helix chain 'A' and resid 561 through 582 removed outlier: 4.479A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 606 Processing helix chain 'A' and resid 627 through 640 Processing helix chain 'A' and resid 647 through 662 Processing helix chain 'A' and resid 686 through 709 Processing helix chain 'A' and resid 718 through 733 removed outlier: 3.582A pdb=" N GLU A 729 " --> pdb=" O HIS A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 752 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 778 through 791 removed outlier: 3.653A pdb=" N ASN A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 842 removed outlier: 3.557A pdb=" N ILE A 837 " --> pdb=" O ASP A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 850 Processing helix chain 'A' and resid 851 through 866 removed outlier: 4.438A pdb=" N GLU A 857 " --> pdb=" O THR A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 870 Processing helix chain 'A' and resid 874 through 895 removed outlier: 4.233A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 923 Processing helix chain 'B' and resid 79 through 98 removed outlier: 3.880A pdb=" N LEU B 98 " --> pdb=" O MET B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 109 removed outlier: 4.429A pdb=" N LEU B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 134 through 142 removed outlier: 3.735A pdb=" N TYR B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASN B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 20 removed outlier: 3.948A pdb=" N VAL C 12 " --> pdb=" O CYS C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 41 removed outlier: 3.937A pdb=" N GLN C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 62 removed outlier: 3.898A pdb=" N ALA C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N MET C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 99 removed outlier: 3.622A pdb=" N THR G 89 " --> pdb=" O SER G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 113 Processing helix chain 'G' and resid 134 through 142 Processing helix chain 'G' and resid 173 through 177 removed outlier: 4.003A pdb=" N SER G 177 " --> pdb=" O MET G 174 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 21 removed outlier: 4.408A pdb=" N ARG A 18 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ASN A 52 " --> pdb=" O ASP A 29 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASP A 29 " --> pdb=" O ASN A 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 21 removed outlier: 4.408A pdb=" N ARG A 18 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 71 " --> pdb=" O ARG A 116 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 223 through 224 removed outlier: 7.060A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.740A pdb=" N VAL A 335 " --> pdb=" O PRO A 339 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N VAL A 341 " --> pdb=" O ILE A 333 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE A 333 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N SER A 343 " --> pdb=" O ARG A 331 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ARG A 331 " --> pdb=" O SER A 343 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 329 " --> pdb=" O GLY A 345 " (cutoff:3.500A) removed outlier: 10.105A pdb=" N SER A 363 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N PHE A 334 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.740A pdb=" N VAL A 335 " --> pdb=" O PRO A 339 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N VAL A 341 " --> pdb=" O ILE A 333 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE A 333 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N SER A 343 " --> pdb=" O ARG A 331 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ARG A 331 " --> pdb=" O SER A 343 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 329 " --> pdb=" O GLY A 345 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 387 through 390 removed outlier: 6.427A pdb=" N ILE B 185 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N VAL B 159 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N THR B 187 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 387 through 390 removed outlier: 6.427A pdb=" N ILE B 185 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N VAL B 159 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N THR B 187 " --> pdb=" O GLN B 157 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL B 159 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 397 through 400 removed outlier: 6.998A pdb=" N LEU A 673 " --> pdb=" O VAL A 398 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AB1, first strand: chain 'A' and resid 541 through 544 Processing sheet with id=AB2, first strand: chain 'A' and resid 753 through 757 removed outlier: 3.516A pdb=" N SER A 754 " --> pdb=" O CYS A 765 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ALA A 762 " --> pdb=" O TRP A 617 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TRP A 617 " --> pdb=" O ALA A 762 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 816 through 822 removed outlier: 3.678A pdb=" N ASP A 825 " --> pdb=" O GLN A 822 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 127 through 132 removed outlier: 4.323A pdb=" N GLN G 158 " --> pdb=" O THR G 187 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU G 189 " --> pdb=" O ILE G 156 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ILE G 156 " --> pdb=" O LEU G 189 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 127 through 132 removed outlier: 4.323A pdb=" N GLN G 158 " --> pdb=" O THR G 187 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU G 189 " --> pdb=" O ILE G 156 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ILE G 156 " --> pdb=" O LEU G 189 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL G 159 " --> pdb=" O VAL G 167 " (cutoff:3.500A) 475 hydrogen bonds defined for protein. 1329 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 17 hydrogen bonds 30 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 2.19 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2541 1.33 - 1.45: 2117 1.45 - 1.57: 5426 1.57 - 1.69: 42 1.69 - 1.81: 105 Bond restraints: 10231 Sorted by residual: bond pdb=" O5' RVP P1201 " pdb=" P RVP P1201 " ideal model delta sigma weight residual 1.690 1.293 0.397 2.00e-02 2.50e+03 3.94e+02 bond pdb=" P G P 20 " pdb=" O5' G P 20 " ideal model delta sigma weight residual 1.593 1.389 0.204 1.50e-02 4.44e+03 1.84e+02 bond pdb=" C5' RVP P1201 " pdb=" O5' RVP P1201 " ideal model delta sigma weight residual 1.408 1.641 -0.233 2.00e-02 2.50e+03 1.35e+02 bond pdb=" O2P RVP P1201 " pdb=" P RVP P1201 " ideal model delta sigma weight residual 1.525 1.437 0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" O3' U P 19 " pdb=" P G P 20 " ideal model delta sigma weight residual 1.607 1.667 -0.060 1.50e-02 4.44e+03 1.62e+01 ... (remaining 10226 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.28: 13914 4.28 - 8.56: 58 8.56 - 12.84: 9 12.84 - 17.12: 1 17.12 - 21.40: 1 Bond angle restraints: 13983 Sorted by residual: angle pdb=" C4' U P 17 " pdb=" C3' U P 17 " pdb=" O3' U P 17 " ideal model delta sigma weight residual 113.00 125.52 -12.52 1.50e+00 4.44e-01 6.97e+01 angle pdb=" O2P RVP P1201 " pdb=" P RVP P1201 " pdb=" O5' RVP P1201 " ideal model delta sigma weight residual 105.30 126.70 -21.40 3.00e+00 1.11e-01 5.09e+01 angle pdb=" P G P 20 " pdb=" O5' G P 20 " pdb=" C5' G P 20 " ideal model delta sigma weight residual 120.90 129.72 -8.82 1.50e+00 4.44e-01 3.46e+01 angle pdb=" C2' U P 17 " pdb=" C1' U P 17 " pdb=" N1 U P 17 " ideal model delta sigma weight residual 112.00 103.61 8.39 1.50e+00 4.44e-01 3.13e+01 angle pdb=" O2' U P 17 " pdb=" C2' U P 17 " pdb=" C1' U P 17 " ideal model delta sigma weight residual 108.40 100.05 8.35 1.50e+00 4.44e-01 3.10e+01 ... (remaining 13978 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.99: 5380 16.99 - 33.99: 573 33.99 - 50.98: 92 50.98 - 67.97: 9 67.97 - 84.97: 10 Dihedral angle restraints: 6064 sinusoidal: 2531 harmonic: 3533 Sorted by residual: dihedral pdb=" CA ARG A 914 " pdb=" C ARG A 914 " pdb=" N TYR A 915 " pdb=" CA TYR A 915 " ideal model delta harmonic sigma weight residual -180.00 -150.38 -29.62 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA ASP B 99 " pdb=" C ASP B 99 " pdb=" N ASN B 100 " pdb=" CA ASN B 100 " ideal model delta harmonic sigma weight residual -180.00 -151.36 -28.64 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA ILE A 757 " pdb=" C ILE A 757 " pdb=" N LEU A 758 " pdb=" CA LEU A 758 " ideal model delta harmonic sigma weight residual 180.00 154.99 25.01 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 6061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1321 0.071 - 0.142: 235 0.142 - 0.213: 32 0.213 - 0.284: 3 0.284 - 0.355: 2 Chirality restraints: 1593 Sorted by residual: chirality pdb=" P G P 20 " pdb=" OP1 G P 20 " pdb=" OP2 G P 20 " pdb=" O5' G P 20 " both_signs ideal model delta sigma weight residual True 2.41 -2.06 0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" C3' U P 17 " pdb=" C4' U P 17 " pdb=" O3' U P 17 " pdb=" C2' U P 17 " both_signs ideal model delta sigma weight residual False -2.48 -2.13 -0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CB VAL C 53 " pdb=" CA VAL C 53 " pdb=" CG1 VAL C 53 " pdb=" CG2 VAL C 53 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 1590 not shown) Planarity restraints: 1708 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U P 17 " 0.040 2.00e-02 2.50e+03 2.25e-02 1.14e+01 pdb=" N1 U P 17 " -0.050 2.00e-02 2.50e+03 pdb=" C2 U P 17 " -0.007 2.00e-02 2.50e+03 pdb=" O2 U P 17 " -0.000 2.00e-02 2.50e+03 pdb=" N3 U P 17 " 0.001 2.00e-02 2.50e+03 pdb=" C4 U P 17 " 0.020 2.00e-02 2.50e+03 pdb=" O4 U P 17 " 0.002 2.00e-02 2.50e+03 pdb=" C5 U P 17 " 0.000 2.00e-02 2.50e+03 pdb=" C6 U P 17 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 177 " -0.038 5.00e-02 4.00e+02 5.58e-02 4.98e+00 pdb=" N PRO B 178 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 178 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 178 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 242 " -0.035 5.00e-02 4.00e+02 5.25e-02 4.41e+00 pdb=" N PRO A 243 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 243 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 243 " -0.030 5.00e-02 4.00e+02 ... (remaining 1705 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1794 2.76 - 3.29: 8800 3.29 - 3.83: 17097 3.83 - 4.36: 20535 4.36 - 4.90: 34674 Nonbonded interactions: 82900 Sorted by model distance: nonbonded pdb=" NZ LYS A 577 " pdb=" OP1 C T 13 " model vdw 2.224 3.120 nonbonded pdb=" CA ASP A 618 " pdb=" O HOH A1102 " model vdw 2.232 3.470 nonbonded pdb=" OG SER A 239 " pdb=" OD1 ASP A 465 " model vdw 2.269 3.040 nonbonded pdb=" O THR G 137 " pdb=" OG1 THR G 141 " model vdw 2.287 3.040 nonbonded pdb=" N2 G P 13 " pdb=" O2 C T 18 " model vdw 2.290 2.496 ... (remaining 82895 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 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 84 through 179 or resid 182 through 191)) selection = chain 'G' } 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: 1.540 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.200 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: 0.000 Load rotamer database and sin/cos tables:8.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 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 : 0.009 0.397 10239 Z= 0.411 Angle : 0.943 21.403 13986 Z= 0.531 Chirality : 0.055 0.355 1593 Planarity : 0.006 0.056 1708 Dihedral : 13.968 84.965 3778 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.09 % Allowed : 6.16 % Favored : 93.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.16 (0.20), residues: 1177 helix: -2.63 (0.16), residues: 523 sheet: -1.03 (0.42), residues: 142 loop : -1.63 (0.23), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 858 TYR 0.018 0.002 TYR G 149 PHE 0.022 0.002 PHE A 348 TRP 0.010 0.002 TRP A 509 HIS 0.011 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00794 / 0.39 (10231) covalent geometry : angle 0.93508 / 0.53 (13983) hydrogen bonds : bond 0.19159 / 12.59 ( 460) hydrogen bonds : angle 7.38249 / 5.07 ( 1359) metal coordination : bond 0.14038 / 6.97 ( 7) metal coordination : angle 8.48727 / 4.97 ( 3) Misc. bond : bond 0.05465 / 2.88 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 195 time to evaluate : 0.406 Fit side-chains REVERT: A 81 GLN cc_start: 0.7377 (tt0) cc_final: 0.7151 (tm-30) REVERT: A 98 LYS cc_start: 0.7773 (mtpp) cc_final: 0.7573 (tttp) REVERT: A 105 ARG cc_start: 0.6738 (mtp-110) cc_final: 0.6416 (mtp-110) REVERT: A 197 ARG cc_start: 0.7888 (ttp-170) cc_final: 0.7535 (ttp80) REVERT: A 289 TYR cc_start: 0.7869 (m-80) cc_final: 0.7493 (m-80) REVERT: A 794 MET cc_start: 0.8715 (ttp) cc_final: 0.8369 (ttp) REVERT: A 855 MET cc_start: 0.6997 (mtm) cc_final: 0.6535 (mtp) REVERT: C 18 GLN cc_start: 0.8610 (tm-30) cc_final: 0.8364 (tm130) outliers start: 1 outliers final: 0 residues processed: 196 average time/residue: 0.5067 time to fit residues: 107.7008 Evaluate side-chains 148 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 117 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 GLN A 75 HIS ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN A 177 ASN A 191 GLN A 256 HIS A 491 ASN A 570 GLN A 573 GLN A 613 HIS A 642 HIS A 705 ASN A 790 ASN A 791 ASN A 815 GLN A 892 HIS B 109 ASN B 140 ASN C 31 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.146255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.113281 restraints weight = 13346.672| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.02 r_work: 0.3314 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10239 Z= 0.129 Angle : 0.545 7.554 13986 Z= 0.295 Chirality : 0.042 0.163 1593 Planarity : 0.004 0.035 1708 Dihedral : 5.557 42.536 1565 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.08 % Allowed : 13.26 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.45 (0.23), residues: 1177 helix: -0.84 (0.21), residues: 542 sheet: -0.73 (0.42), residues: 147 loop : -0.97 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 553 TYR 0.015 0.001 TYR A 606 PHE 0.011 0.001 PHE A 652 TRP 0.012 0.001 TRP G 182 HIS 0.011 0.001 HIS A 892 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (10231) covalent geometry : angle 0.54308 / 0.29 (13983) hydrogen bonds : bond 0.04860 / 3.26 ( 460) hydrogen bonds : angle 4.73033 / 3.25 ( 1359) metal coordination : bond 0.01442 / 0.76 ( 7) metal coordination : angle 3.38565 / 1.99 ( 3) Misc. bond : bond 0.00139 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 172 time to evaluate : 0.379 Fit side-chains REVERT: A 19 LEU cc_start: 0.8269 (mt) cc_final: 0.8027 (mt) REVERT: A 41 LYS cc_start: 0.8140 (mmtt) cc_final: 0.7792 (mtmm) REVERT: A 81 GLN cc_start: 0.7645 (tt0) cc_final: 0.7323 (tm-30) REVERT: A 197 ARG cc_start: 0.8167 (ttp-170) cc_final: 0.7807 (ttp80) REVERT: A 289 TYR cc_start: 0.8237 (m-80) cc_final: 0.7737 (m-80) REVERT: A 758 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8451 (tt) REVERT: A 794 MET cc_start: 0.8999 (ttp) cc_final: 0.8742 (ttp) REVERT: A 855 MET cc_start: 0.7480 (mtm) cc_final: 0.7113 (mtm) REVERT: C 18 GLN cc_start: 0.8790 (tm-30) cc_final: 0.8563 (tm130) REVERT: G 184 LEU cc_start: 0.6348 (OUTLIER) cc_final: 0.6050 (pt) REVERT: G 189 LEU cc_start: 0.7093 (mm) cc_final: 0.6580 (pp) outliers start: 22 outliers final: 4 residues processed: 184 average time/residue: 0.4939 time to fit residues: 98.7646 Evaluate side-chains 149 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 143 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain G residue 184 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 35 optimal weight: 7.9990 chunk 82 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 69 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN C 31 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 158 GLN ** 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 = 0.3825 r_free = 0.3825 target = 0.145210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.112371 restraints weight = 13359.756| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.17 r_work: 0.3290 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10239 Z= 0.147 Angle : 0.533 7.112 13986 Z= 0.287 Chirality : 0.042 0.153 1593 Planarity : 0.003 0.029 1708 Dihedral : 5.215 36.301 1565 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.46 % Allowed : 15.15 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.24), residues: 1177 helix: -0.10 (0.22), residues: 544 sheet: -0.66 (0.43), residues: 132 loop : -0.74 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 116 TYR 0.015 0.001 TYR A 606 PHE 0.012 0.001 PHE A 313 TRP 0.013 0.001 TRP G 182 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (10231) covalent geometry : angle 0.53154 / 0.29 (13983) hydrogen bonds : bond 0.04557 / 3.10 ( 460) hydrogen bonds : angle 4.36924 / 2.98 ( 1359) metal coordination : bond 0.01071 / 0.56 ( 7) metal coordination : angle 2.75056 / 1.61 ( 3) Misc. bond : bond 0.00001 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.357 Fit side-chains REVERT: A 19 LEU cc_start: 0.8266 (mt) cc_final: 0.8021 (mt) REVERT: A 41 LYS cc_start: 0.8064 (mmtt) cc_final: 0.7784 (mtmm) REVERT: A 81 GLN cc_start: 0.7682 (tt0) cc_final: 0.7365 (tm-30) REVERT: A 197 ARG cc_start: 0.8171 (ttp-170) cc_final: 0.7919 (ttp80) REVERT: A 289 TYR cc_start: 0.8241 (m-80) cc_final: 0.7912 (m-80) REVERT: A 758 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8443 (tt) REVERT: A 794 MET cc_start: 0.9057 (ttp) cc_final: 0.8747 (ttp) REVERT: A 802 GLU cc_start: 0.7587 (tp30) cc_final: 0.7299 (tm-30) REVERT: A 855 MET cc_start: 0.7552 (mtm) cc_final: 0.7220 (mtm) REVERT: A 895 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7545 (pt) REVERT: B 93 THR cc_start: 0.8470 (m) cc_final: 0.8233 (p) REVERT: C 18 GLN cc_start: 0.8837 (tm-30) cc_final: 0.8589 (tm130) REVERT: G 184 LEU cc_start: 0.6262 (OUTLIER) cc_final: 0.6001 (pt) REVERT: G 189 LEU cc_start: 0.7040 (mm) cc_final: 0.6559 (pp) outliers start: 26 outliers final: 9 residues processed: 168 average time/residue: 0.4846 time to fit residues: 88.6603 Evaluate side-chains 156 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain G residue 184 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 12 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 115 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 0.3980 chunk 77 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 ASN A 573 GLN A 875 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.144235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.111788 restraints weight = 13718.280| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.05 r_work: 0.3258 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10239 Z= 0.114 Angle : 0.501 6.517 13986 Z= 0.267 Chirality : 0.041 0.154 1593 Planarity : 0.003 0.027 1708 Dihedral : 4.950 34.257 1565 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.37 % Allowed : 16.86 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.24), residues: 1177 helix: 0.25 (0.23), residues: 550 sheet: -0.57 (0.43), residues: 132 loop : -0.58 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 116 TYR 0.012 0.001 TYR A 156 PHE 0.011 0.001 PHE A 652 TRP 0.012 0.001 TRP G 182 HIS 0.006 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (10231) covalent geometry : angle 0.49954 / 0.27 (13983) hydrogen bonds : bond 0.04157 / 2.84 ( 460) hydrogen bonds : angle 4.15822 / 2.83 ( 1359) metal coordination : bond 0.00770 / 0.40 ( 7) metal coordination : angle 2.77382 / 1.63 ( 3) Misc. bond : bond 0.00024 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 0.390 Fit side-chains REVERT: A 40 ASP cc_start: 0.7536 (p0) cc_final: 0.7315 (p0) REVERT: A 81 GLN cc_start: 0.7496 (tt0) cc_final: 0.7166 (tm-30) REVERT: A 257 VAL cc_start: 0.8144 (OUTLIER) cc_final: 0.7853 (m) REVERT: A 370 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7053 (tp30) REVERT: A 758 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8158 (tt) REVERT: A 794 MET cc_start: 0.9118 (ttp) cc_final: 0.8764 (ttp) REVERT: A 855 MET cc_start: 0.7543 (mtm) cc_final: 0.7188 (mtp) REVERT: A 859 PHE cc_start: 0.8704 (m-80) cc_final: 0.8444 (m-80) REVERT: A 895 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7591 (pt) REVERT: C 18 GLN cc_start: 0.8786 (tm-30) cc_final: 0.8398 (tm130) REVERT: G 189 LEU cc_start: 0.7017 (mm) cc_final: 0.6525 (pp) outliers start: 25 outliers final: 10 residues processed: 179 average time/residue: 0.4584 time to fit residues: 89.5435 Evaluate side-chains 161 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 403 ASN Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 573 GLN Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain G residue 184 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 19 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 96 optimal weight: 0.0870 chunk 22 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 overall best weight: 2.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 ASN A 573 GLN A 773 GLN C 31 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.142237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.109717 restraints weight = 13474.301| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.09 r_work: 0.3251 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10239 Z= 0.221 Angle : 0.581 5.940 13986 Z= 0.310 Chirality : 0.045 0.166 1593 Planarity : 0.003 0.025 1708 Dihedral : 5.258 34.391 1565 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.31 % Allowed : 16.86 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.24), residues: 1177 helix: 0.18 (0.22), residues: 543 sheet: -0.68 (0.42), residues: 132 loop : -0.58 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 513 TYR 0.016 0.002 TYR A 606 PHE 0.016 0.002 PHE A 396 TRP 0.013 0.001 TRP G 182 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.22 (10231) covalent geometry : angle 0.57969 / 0.31 (13983) hydrogen bonds : bond 0.04914 / 3.37 ( 460) hydrogen bonds : angle 4.33511 / 2.95 ( 1359) metal coordination : bond 0.01136 / 0.60 ( 7) metal coordination : angle 2.91853 / 1.69 ( 3) Misc. bond : bond 0.00001 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 139 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 40 ASP cc_start: 0.7550 (p0) cc_final: 0.7248 (p0) REVERT: A 81 GLN cc_start: 0.7705 (tt0) cc_final: 0.7399 (tm-30) REVERT: A 370 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7239 (tp30) REVERT: A 666 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.7634 (ttm) REVERT: A 758 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8505 (tt) REVERT: A 794 MET cc_start: 0.9135 (ttp) cc_final: 0.8775 (ttp) REVERT: A 892 HIS cc_start: 0.7888 (t-90) cc_final: 0.7535 (t-90) REVERT: A 895 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7592 (pt) REVERT: C 18 GLN cc_start: 0.8888 (tm-30) cc_final: 0.8598 (tm130) REVERT: G 184 LEU cc_start: 0.6408 (OUTLIER) cc_final: 0.6132 (pt) REVERT: G 189 LEU cc_start: 0.7000 (mm) cc_final: 0.6613 (pp) outliers start: 35 outliers final: 13 residues processed: 160 average time/residue: 0.4702 time to fit residues: 81.9346 Evaluate side-chains 155 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 403 ASN Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 184 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 4 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 48 optimal weight: 0.0470 chunk 25 optimal weight: 0.0070 chunk 55 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 ASN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 158 GLN ** 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 = 0.3847 r_free = 0.3847 target = 0.147190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.115168 restraints weight = 13367.612| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.02 r_work: 0.3313 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10239 Z= 0.115 Angle : 0.509 7.085 13986 Z= 0.271 Chirality : 0.041 0.157 1593 Planarity : 0.003 0.029 1708 Dihedral : 4.917 33.802 1565 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.89 % Allowed : 18.28 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.24), residues: 1177 helix: 0.45 (0.23), residues: 544 sheet: -0.58 (0.42), residues: 132 loop : -0.45 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 513 TYR 0.013 0.001 TYR A 788 PHE 0.010 0.001 PHE A 652 TRP 0.010 0.001 TRP A 916 HIS 0.006 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (10231) covalent geometry : angle 0.50752 / 0.27 (13983) hydrogen bonds : bond 0.04166 / 2.85 ( 460) hydrogen bonds : angle 4.10869 / 2.79 ( 1359) metal coordination : bond 0.00769 / 0.40 ( 7) metal coordination : angle 2.79315 / 1.64 ( 3) Misc. bond : bond 0.00022 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 27 SER cc_start: 0.8164 (t) cc_final: 0.7610 (p) REVERT: A 40 ASP cc_start: 0.7498 (p0) cc_final: 0.7144 (p0) REVERT: A 81 GLN cc_start: 0.7609 (tt0) cc_final: 0.7400 (tm-30) REVERT: A 370 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7217 (tp30) REVERT: A 553 ARG cc_start: 0.7452 (ttt90) cc_final: 0.7233 (ptm160) REVERT: A 794 MET cc_start: 0.9116 (ttp) cc_final: 0.8768 (ttp) REVERT: A 855 MET cc_start: 0.7529 (OUTLIER) cc_final: 0.6919 (mtm) REVERT: A 859 PHE cc_start: 0.8723 (m-80) cc_final: 0.8376 (m-80) REVERT: A 895 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7718 (pt) REVERT: C 18 GLN cc_start: 0.8861 (tm-30) cc_final: 0.8539 (tm130) REVERT: G 189 LEU cc_start: 0.7181 (mm) cc_final: 0.6685 (pp) outliers start: 20 outliers final: 10 residues processed: 159 average time/residue: 0.4481 time to fit residues: 77.8682 Evaluate side-chains 152 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain G residue 184 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 51 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 chunk 83 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 ASN C 31 GLN C 36 HIS C 37 ASN ** G 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.141620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.109142 restraints weight = 13439.527| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.08 r_work: 0.3252 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10239 Z= 0.229 Angle : 0.589 8.905 13986 Z= 0.313 Chirality : 0.046 0.241 1593 Planarity : 0.003 0.026 1708 Dihedral : 5.328 39.047 1565 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.75 % Allowed : 18.37 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.24), residues: 1177 helix: 0.30 (0.23), residues: 544 sheet: -0.67 (0.42), residues: 132 loop : -0.52 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 513 TYR 0.016 0.002 TYR A 748 PHE 0.017 0.002 PHE A 859 TRP 0.011 0.001 TRP G 182 HIS 0.005 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.23 (10231) covalent geometry : angle 0.58707 / 0.31 (13983) hydrogen bonds : bond 0.04945 / 3.39 ( 460) hydrogen bonds : angle 4.32860 / 2.94 ( 1359) metal coordination : bond 0.01036 / 0.55 ( 7) metal coordination : angle 2.93528 / 1.70 ( 3) Misc. bond : bond 0.00004 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 40 ASP cc_start: 0.7591 (p0) cc_final: 0.7232 (p0) REVERT: A 81 GLN cc_start: 0.7714 (tt0) cc_final: 0.7511 (tm-30) REVERT: A 160 LYS cc_start: 0.7044 (tptt) cc_final: 0.6768 (mmmt) REVERT: A 370 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.7266 (tp30) REVERT: A 553 ARG cc_start: 0.7517 (ttt90) cc_final: 0.7291 (ptm160) REVERT: A 758 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8558 (tt) REVERT: A 794 MET cc_start: 0.9125 (ttp) cc_final: 0.8749 (ttp) REVERT: A 855 MET cc_start: 0.7576 (OUTLIER) cc_final: 0.7118 (mtm) REVERT: A 893 ASP cc_start: 0.6705 (m-30) cc_final: 0.6482 (t0) REVERT: A 895 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7725 (pt) REVERT: B 82 LYS cc_start: 0.5512 (mptt) cc_final: 0.5309 (mppt) REVERT: C 18 GLN cc_start: 0.8891 (tm-30) cc_final: 0.8584 (tm130) REVERT: G 184 LEU cc_start: 0.6339 (OUTLIER) cc_final: 0.6088 (pt) REVERT: G 189 LEU cc_start: 0.7012 (mm) cc_final: 0.6635 (pp) outliers start: 29 outliers final: 14 residues processed: 155 average time/residue: 0.4424 time to fit residues: 75.0886 Evaluate side-chains 154 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 184 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 22 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 35 optimal weight: 0.0030 chunk 7 optimal weight: 6.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 ASN ** G 158 GLN ** 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 = 0.3851 r_free = 0.3851 target = 0.147512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.115395 restraints weight = 13245.550| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.01 r_work: 0.3310 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10239 Z= 0.114 Angle : 0.513 10.526 13986 Z= 0.271 Chirality : 0.042 0.156 1593 Planarity : 0.003 0.033 1708 Dihedral : 4.888 39.013 1565 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.08 % Allowed : 19.41 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.24), residues: 1177 helix: 0.52 (0.23), residues: 546 sheet: -0.62 (0.42), residues: 132 loop : -0.40 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 513 TYR 0.014 0.001 TYR A 788 PHE 0.010 0.001 PHE A 313 TRP 0.010 0.001 TRP A 916 HIS 0.005 0.001 HIS A 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (10231) covalent geometry : angle 0.51116 / 0.27 (13983) hydrogen bonds : bond 0.04129 / 2.83 ( 460) hydrogen bonds : angle 4.08588 / 2.78 ( 1359) metal coordination : bond 0.00634 / 0.33 ( 7) metal coordination : angle 2.71401 / 1.60 ( 3) Misc. bond : bond 0.00021 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: A 27 SER cc_start: 0.8098 (t) cc_final: 0.7546 (p) REVERT: A 40 ASP cc_start: 0.7519 (p0) cc_final: 0.7188 (p0) REVERT: A 81 GLN cc_start: 0.7621 (tt0) cc_final: 0.7417 (tm-30) REVERT: A 156 TYR cc_start: 0.8218 (t80) cc_final: 0.7874 (t80) REVERT: A 370 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7245 (tp30) REVERT: A 553 ARG cc_start: 0.7371 (ttt90) cc_final: 0.7093 (ptm160) REVERT: A 794 MET cc_start: 0.9097 (ttp) cc_final: 0.8751 (ttp) REVERT: A 855 MET cc_start: 0.7522 (OUTLIER) cc_final: 0.6929 (mtp) REVERT: A 859 PHE cc_start: 0.8744 (m-80) cc_final: 0.8386 (m-80) REVERT: A 895 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7706 (pt) REVERT: C 18 GLN cc_start: 0.8855 (tm-30) cc_final: 0.8535 (tm130) REVERT: G 189 LEU cc_start: 0.7200 (mm) cc_final: 0.6727 (pp) outliers start: 22 outliers final: 15 residues processed: 164 average time/residue: 0.4023 time to fit residues: 72.3931 Evaluate side-chains 157 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain G residue 184 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 26 optimal weight: 4.9990 chunk 31 optimal weight: 0.0050 chunk 111 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 62 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 overall best weight: 2.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.143961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.111605 restraints weight = 13300.841| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.00 r_work: 0.3258 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10239 Z= 0.204 Angle : 0.585 13.889 13986 Z= 0.308 Chirality : 0.045 0.169 1593 Planarity : 0.003 0.034 1708 Dihedral : 5.240 44.169 1565 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.18 % Allowed : 19.89 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.24), residues: 1177 helix: 0.43 (0.23), residues: 545 sheet: -0.69 (0.42), residues: 132 loop : -0.48 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 513 TYR 0.016 0.001 TYR A 289 PHE 0.021 0.002 PHE A 396 TRP 0.010 0.001 TRP G 182 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.20 (10231) covalent geometry : angle 0.58327 / 0.31 (13983) hydrogen bonds : bond 0.04791 / 3.29 ( 460) hydrogen bonds : angle 4.25507 / 2.90 ( 1359) metal coordination : bond 0.01038 / 0.55 ( 7) metal coordination : angle 2.90023 / 1.69 ( 3) Misc. bond : bond 0.00013 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 SER cc_start: 0.8183 (t) cc_final: 0.7597 (p) REVERT: A 40 ASP cc_start: 0.7559 (p0) cc_final: 0.7266 (p0) REVERT: A 81 GLN cc_start: 0.7688 (tt0) cc_final: 0.7475 (tm-30) REVERT: A 370 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7253 (tp30) REVERT: A 553 ARG cc_start: 0.7379 (ttt90) cc_final: 0.7166 (ptm160) REVERT: A 666 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.7280 (ttm) REVERT: A 758 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8516 (tt) REVERT: A 794 MET cc_start: 0.9132 (ttp) cc_final: 0.8746 (ttp) REVERT: A 855 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.7145 (mtp) REVERT: A 895 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7699 (pt) REVERT: C 18 GLN cc_start: 0.8839 (tm-30) cc_final: 0.8525 (tm130) REVERT: G 184 LEU cc_start: 0.6279 (OUTLIER) cc_final: 0.6000 (pt) REVERT: G 189 LEU cc_start: 0.7163 (mm) cc_final: 0.6703 (pp) outliers start: 23 outliers final: 15 residues processed: 157 average time/residue: 0.4370 time to fit residues: 75.4015 Evaluate side-chains 159 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain G residue 184 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 41 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.145247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.113115 restraints weight = 13127.028| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.00 r_work: 0.3278 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10239 Z= 0.164 Angle : 0.571 16.367 13986 Z= 0.300 Chirality : 0.044 0.172 1593 Planarity : 0.003 0.037 1708 Dihedral : 5.149 46.168 1565 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.99 % Allowed : 20.17 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.24), residues: 1177 helix: 0.45 (0.23), residues: 549 sheet: -0.72 (0.42), residues: 132 loop : -0.46 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 513 TYR 0.017 0.001 TYR A 289 PHE 0.014 0.001 PHE A 313 TRP 0.009 0.001 TRP G 182 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (10231) covalent geometry : angle 0.56897 / 0.30 (13983) hydrogen bonds : bond 0.04507 / 3.09 ( 460) hydrogen bonds : angle 4.20360 / 2.87 ( 1359) metal coordination : bond 0.00894 / 0.47 ( 7) metal coordination : angle 2.99089 / 1.75 ( 3) Misc. bond : bond 0.00022 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2354 Ramachandran restraints generated. 1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 SER cc_start: 0.8146 (t) cc_final: 0.7561 (p) REVERT: A 40 ASP cc_start: 0.7525 (p0) cc_final: 0.7182 (p0) REVERT: A 156 TYR cc_start: 0.8144 (t80) cc_final: 0.7837 (t80) REVERT: A 370 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7214 (tp30) REVERT: A 553 ARG cc_start: 0.7351 (ttt90) cc_final: 0.7142 (ptm160) REVERT: A 758 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8450 (tt) REVERT: A 794 MET cc_start: 0.9150 (ttp) cc_final: 0.8778 (ttp) REVERT: A 855 MET cc_start: 0.7518 (OUTLIER) cc_final: 0.6966 (mtp) REVERT: A 859 PHE cc_start: 0.8752 (m-80) cc_final: 0.8475 (m-80) REVERT: A 895 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7686 (pt) REVERT: C 18 GLN cc_start: 0.8822 (tm-30) cc_final: 0.8508 (tm130) REVERT: G 184 LEU cc_start: 0.6259 (OUTLIER) cc_final: 0.5988 (pt) REVERT: G 189 LEU cc_start: 0.7143 (mm) cc_final: 0.6690 (pp) outliers start: 21 outliers final: 13 residues processed: 157 average time/residue: 0.4315 time to fit residues: 74.2145 Evaluate side-chains 158 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain G residue 184 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 101 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.143875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.111638 restraints weight = 13330.396| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.01 r_work: 0.3259 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 10239 Z= 0.197 Angle : 0.611 20.345 13986 Z= 0.319 Chirality : 0.045 0.180 1593 Planarity : 0.003 0.034 1708 Dihedral : 5.266 49.839 1565 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.99 % Allowed : 20.27 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.24), residues: 1177 helix: 0.39 (0.23), residues: 554 sheet: -0.77 (0.42), residues: 132 loop : -0.54 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 513 TYR 0.018 0.001 TYR A 289 PHE 0.019 0.002 PHE A 313 TRP 0.009 0.001 TRP G 182 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 (10231) covalent geometry : angle 0.60962 / 0.32 (13983) hydrogen bonds : bond 0.04721 / 3.23 ( 460) hydrogen bonds : angle 4.28281 / 2.92 ( 1359) metal coordination : bond 0.00901 / 0.48 ( 7) metal coordination : angle 2.94527 / 1.72 ( 3) Misc. bond : bond 0.00015 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3360.37 seconds wall clock time: 58 minutes 11.08 seconds (3491.08 seconds total)