Starting phenix.real_space_refine on Fri Sep 11 16:23:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7dfh_30664/09_2026/7dfh_30664.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dfh_30664/09_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_30664/09_2026/7dfh_30664.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dfh_30664/09_2026/7dfh_30664.map" model { file = "/net/cci-nas-00/data/ceres_data/7dfh_30664/09_2026/7dfh_30664.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dfh_30664/09_2026/7dfh_30664.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7dfh_30664/09_2026/7dfh_30664.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7dfh_30664/09_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-2.2.1-6174/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: {'RNAv2': 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: {'RNAv2': 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: 2.05, per 1000 atoms: 0.21 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: 0.81 Conformation dependent library (CDL) restraints added in 284.5 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: 1.15 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: 1.94 Time building geometry restraints manager: 1.07 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 1.593 1.293 0.300 1.50e-02 4.44e+03 3.99e+02 bond pdb=" C5' RVP P1201 " pdb=" O5' RVP P1201 " ideal model delta sigma weight residual 1.420 1.641 -0.221 1.50e-02 4.44e+03 2.16e+02 bond pdb=" P G P 20 " pdb=" O5' G P 20 " ideal model delta sigma weight residual 1.593 1.389 0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" O3' U P 19 " pdb=" P G P 20 " ideal model delta sigma weight residual 1.607 1.667 -0.060 1.20e-02 6.94e+03 2.53e+01 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 ... (remaining 10226 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.28: 13914 4.28 - 8.56: 57 8.56 - 12.84: 8 12.84 - 17.12: 3 17.12 - 21.40: 1 Bond angle restraints: 13983 Sorted by residual: angle pdb=" C5' RVP P1201 " pdb=" C4' RVP P1201 " pdb=" O4' RVP P1201 " ideal model delta sigma weight residual 109.80 124.68 -14.88 1.50e+00 4.44e-01 9.84e+01 angle pdb=" C3' RVP P1201 " pdb=" C4' RVP P1201 " pdb=" C5' RVP P1201 " ideal model delta sigma weight residual 116.00 102.83 13.17 1.50e+00 4.44e-01 7.71e+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=" N SER A 759 " pdb=" CA SER A 759 " pdb=" C SER A 759 " ideal model delta sigma weight residual 111.02 116.65 -5.63 1.22e+00 6.72e-01 2.13e+01 angle pdb=" C4' RVP P1201 " pdb=" C5' RVP P1201 " pdb=" O5' RVP P1201 " ideal model delta sigma weight residual 111.50 118.34 -6.84 1.50e+00 4.44e-01 2.08e+01 ... (remaining 13978 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.99: 5361 16.99 - 33.99: 578 33.99 - 50.98: 105 50.98 - 67.97: 10 67.97 - 84.97: 10 Dihedral angle restraints: 6064 sinusoidal: 2531 harmonic: 3533 Sorted by residual: dihedral pdb=" C4' U P 17 " pdb=" C3' U P 17 " pdb=" C2' U P 17 " pdb=" C1' U P 17 " ideal model delta sinusoidal sigma weight residual 36.34 8.01 28.33 1 3.10e+00 1.04e-01 1.20e+02 dihedral pdb=" O4' U P 17 " pdb=" C2' U P 17 " pdb=" C1' U P 17 " pdb=" C3' U P 17 " ideal model delta sinusoidal sigma weight residual 25.59 -4.22 29.81 3 3.80e+00 6.93e-02 7.32e+01 dihedral pdb=" O5' G P 20 " pdb=" C5' G P 20 " pdb=" C4' G P 20 " pdb=" C3' G P 20 " ideal model delta sinusoidal sigma weight residual 60.00 6.45 53.55 3 6.40e+00 2.44e-02 5.06e+01 ... (remaining 6061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1311 0.073 - 0.146: 235 0.146 - 0.219: 35 0.219 - 0.292: 11 0.292 - 0.365: 1 Chirality restraints: 1593 Sorted by residual: 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 -2.50 -2.13 -0.36 2.00e-01 2.50e+01 3.33e+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 chirality pdb=" P C T 7 " pdb=" OP1 C T 7 " pdb=" OP2 C T 7 " pdb=" O5' C T 7 " both_signs ideal model delta sigma weight residual True 2.17 -2.42 -0.25 2.00e-01 2.50e+01 1.58e+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: 1.170 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.750 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:6.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.470 ------------------------------------------------------------------------------- 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 : 0.008 0.300 10239 Z= 0.413 Angle : 0.958 21.403 13986 Z= 0.528 Chirality : 0.059 0.365 1593 Planarity : 0.006 0.056 1708 Dihedral : 14.251 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 0.00748 / 0.39 (10231) covalent geometry : angle 0.94954 / 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 : 0.286 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: 0.4514 time to fit residues: 96.0197 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 : 0.390 ------------------------------------------------------------------------------- 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: 1.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 117 optimal weight: 4.9990 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 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.145930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.112882 restraints weight = 13361.176| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.03 r_work: 0.3310 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10239 Z= 0.130 Angle : 0.570 7.392 13986 Z= 0.301 Chirality : 0.044 0.213 1593 Planarity : 0.004 0.039 1708 Dihedral : 7.013 49.924 1565 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.99 % Allowed : 13.45 % Favored : 84.56 % 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: -1.47 (0.22), residues: 1177 helix: -0.85 (0.21), residues: 542 sheet: -0.73 (0.42), residues: 147 loop : -1.00 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 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 0.010 0.001 HIS A 892 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (10231) covalent geometry : angle 0.56762 / 0.30 (13983) hydrogen bonds : bond 0.04945 / 3.33 ( 460) hydrogen bonds : angle 4.77866 / 3.29 ( 1359) metal coordination : bond 0.01604 / 0.84 ( 7) metal coordination : angle 3.65807 / 2.15 ( 3) Misc. bond : bond 0.00065 / 0.03 ( 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 192 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 171 time to evaluate : 0.279 Fit side-chains REVERT: A 19 LEU cc_start: 0.8295 (mt) cc_final: 0.8019 (mt) REVERT: A 41 LYS cc_start: 0.8143 (mmtt) cc_final: 0.7791 (mtmm) REVERT: A 81 GLN cc_start: 0.7636 (tt0) cc_final: 0.7314 (tm-30) REVERT: A 197 ARG cc_start: 0.8190 (ttp-170) cc_final: 0.7827 (ttp80) REVERT: A 289 TYR cc_start: 0.8250 (m-80) cc_final: 0.7748 (m-80) REVERT: A 758 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8395 (tt) REVERT: A 794 MET cc_start: 0.9003 (ttp) cc_final: 0.8750 (ttp) REVERT: A 855 MET cc_start: 0.7484 (mtm) cc_final: 0.7126 (mtm) REVERT: C 18 GLN cc_start: 0.8784 (tm-30) cc_final: 0.8559 (tm130) REVERT: G 184 LEU cc_start: 0.6437 (OUTLIER) cc_final: 0.6154 (pt) REVERT: G 189 LEU cc_start: 0.7008 (mm) cc_final: 0.6491 (pp) outliers start: 21 outliers final: 3 residues processed: 182 average time/residue: 0.4574 time to fit residues: 90.4169 Evaluate side-chains 149 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 144 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 82 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 108 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 69 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 ASN B 104 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.146943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.114235 restraints weight = 13336.812| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.23 r_work: 0.3314 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1899 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= 0.122 Angle : 0.534 7.082 13986 Z= 0.280 Chirality : 0.043 0.187 1593 Planarity : 0.003 0.029 1708 Dihedral : 6.581 50.763 1565 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.65 % Allowed : 14.49 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.24), residues: 1177 helix: -0.10 (0.22), residues: 551 sheet: -0.63 (0.43), residues: 132 loop : -0.69 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 116 TYR 0.013 0.001 TYR A 156 PHE 0.011 0.001 PHE A 652 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 0.00268 / 0.12 (10231) covalent geometry : angle 0.53235 / 0.28 (13983) hydrogen bonds : bond 0.04369 / 2.97 ( 460) hydrogen bonds : angle 4.29998 / 2.94 ( 1359) metal coordination : bond 0.00866 / 0.46 ( 7) metal coordination : angle 2.62965 / 1.54 ( 3) Misc. bond : bond 0.00015 / 0.01 ( 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 188 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 0.257 Fit side-chains REVERT: A 19 LEU cc_start: 0.8240 (mt) cc_final: 0.8017 (mt) REVERT: A 41 LYS cc_start: 0.8065 (mmtt) cc_final: 0.7779 (mtmm) REVERT: A 81 GLN cc_start: 0.7684 (tt0) cc_final: 0.7365 (tm-30) REVERT: A 758 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8274 (tt) REVERT: A 794 MET cc_start: 0.9027 (ttp) cc_final: 0.8740 (ttp) REVERT: A 855 MET cc_start: 0.7530 (mtm) cc_final: 0.7240 (mtm) REVERT: A 895 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7582 (pt) REVERT: C 18 GLN cc_start: 0.8811 (tm-30) cc_final: 0.8562 (tm130) REVERT: G 189 LEU cc_start: 0.7031 (mm) cc_final: 0.6574 (pp) outliers start: 28 outliers final: 11 residues processed: 174 average time/residue: 0.4348 time to fit residues: 82.3698 Evaluate side-chains 155 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 THR 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 119 ILE 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 169 LEU 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: 0.9980 chunk 14 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 67 optimal weight: 0.2980 chunk 105 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 = 0.3761 r_free = 0.3761 target = 0.142327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.109454 restraints weight = 13756.600| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.08 r_work: 0.3232 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 10239 Z= 0.155 Angle : 0.551 6.495 13986 Z= 0.287 Chirality : 0.044 0.202 1593 Planarity : 0.003 0.025 1708 Dihedral : 6.534 50.123 1565 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.12 % Allowed : 16.19 % Favored : 80.68 % 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: -0.41 (0.24), residues: 1177 helix: 0.24 (0.23), residues: 544 sheet: -0.61 (0.42), residues: 132 loop : -0.60 (0.27), 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 0.011 0.001 PHE A 440 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 0.00355 / 0.16 (10231) covalent geometry : angle 0.54933 / 0.29 (13983) hydrogen bonds : bond 0.04484 / 3.07 ( 460) hydrogen bonds : angle 4.24362 / 2.89 ( 1359) metal coordination : bond 0.00922 / 0.49 ( 7) metal coordination : angle 2.76667 / 1.62 ( 3) Misc. bond : bond 0.00002 / 0.00 ( 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 183 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 150 time to evaluate : 0.408 Fit side-chains REVERT: A 19 LEU cc_start: 0.8296 (mt) cc_final: 0.8072 (mt) REVERT: A 40 ASP cc_start: 0.7522 (p0) cc_final: 0.7298 (p0) REVERT: A 81 GLN cc_start: 0.7510 (tt0) cc_final: 0.7174 (tm-30) REVERT: A 257 VAL cc_start: 0.8200 (OUTLIER) cc_final: 0.7902 (m) REVERT: A 370 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7040 (tp30) REVERT: A 758 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8260 (tt) REVERT: A 794 MET cc_start: 0.9137 (ttp) cc_final: 0.8751 (ttp) REVERT: A 895 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7577 (pt) REVERT: C 18 GLN cc_start: 0.8771 (tm-30) cc_final: 0.8374 (tm130) REVERT: G 189 LEU cc_start: 0.7026 (mm) cc_final: 0.6529 (pp) outliers start: 33 outliers final: 11 residues processed: 170 average time/residue: 0.4274 time to fit residues: 79.3096 Evaluate side-chains 156 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 0.277 ------------------------------------------------------------------------------- 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 119 ILE 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 153 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 19 optimal weight: 3.9990 chunk 50 optimal weight: 0.2980 chunk 63 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 112 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 22 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 90 optimal weight: 20.0000 chunk 4 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 ** 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 = 0.3813 r_free = 0.3813 target = 0.144587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.110696 restraints weight = 13462.040| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.10 r_work: 0.3276 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10239 Z= 0.163 Angle : 0.554 6.313 13986 Z= 0.287 Chirality : 0.045 0.201 1593 Planarity : 0.003 0.030 1708 Dihedral : 6.548 50.770 1565 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.37 % Allowed : 18.28 % Favored : 79.36 % 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: -0.27 (0.24), residues: 1177 helix: 0.36 (0.23), residues: 545 sheet: -0.59 (0.42), residues: 132 loop : -0.53 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 513 TYR 0.014 0.001 TYR A 606 PHE 0.012 0.001 PHE A 859 TRP 0.011 0.001 TRP G 182 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (10231) covalent geometry : angle 0.55260 / 0.29 (13983) hydrogen bonds : bond 0.04507 / 3.09 ( 460) hydrogen bonds : angle 4.22927 / 2.87 ( 1359) metal coordination : bond 0.00937 / 0.50 ( 7) metal coordination : angle 2.79762 / 1.64 ( 3) Misc. bond : bond 0.00004 / 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 167 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8261 (mt) cc_final: 0.8060 (mt) REVERT: A 27 SER cc_start: 0.8193 (t) cc_final: 0.7627 (p) REVERT: A 40 ASP cc_start: 0.7507 (p0) cc_final: 0.7200 (p0) REVERT: A 81 GLN cc_start: 0.7645 (tt0) cc_final: 0.7321 (tm-30) REVERT: A 370 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7169 (tp30) REVERT: A 758 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8384 (tt) REVERT: A 794 MET cc_start: 0.9137 (ttp) cc_final: 0.8775 (ttp) REVERT: A 855 MET cc_start: 0.7592 (mtm) cc_final: 0.7134 (mtp) REVERT: A 895 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7606 (pt) REVERT: C 18 GLN cc_start: 0.8844 (tm-30) cc_final: 0.8542 (tm130) REVERT: G 189 LEU cc_start: 0.7159 (mm) cc_final: 0.6642 (pp) outliers start: 25 outliers final: 13 residues processed: 158 average time/residue: 0.4160 time to fit residues: 72.0536 Evaluate side-chains 153 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.225 ------------------------------------------------------------------------------- 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 895 LEU Chi-restraints excluded: chain B residue 119 ILE 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 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 153 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: 6.9990 chunk 38 optimal weight: 3.9990 chunk 110 optimal weight: 0.0770 chunk 56 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 overall best weight: 1.3942 ------------------------------------------------------------------------------- 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 = 0.3757 r_free = 0.3757 target = 0.141938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.109078 restraints weight = 13713.726| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.07 r_work: 0.3219 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10239 Z= 0.151 Angle : 0.548 7.028 13986 Z= 0.284 Chirality : 0.045 0.211 1593 Planarity : 0.003 0.029 1708 Dihedral : 6.524 51.202 1565 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.46 % Allowed : 18.47 % Favored : 79.07 % 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: 0.40 (0.23), residues: 548 sheet: -0.62 (0.42), residues: 132 loop : -0.43 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 513 TYR 0.012 0.001 TYR A 606 PHE 0.011 0.001 PHE A 859 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 0.00348 / 0.15 (10231) covalent geometry : angle 0.54631 / 0.28 (13983) hydrogen bonds : bond 0.04429 / 3.04 ( 460) hydrogen bonds : angle 4.18522 / 2.84 ( 1359) metal coordination : bond 0.00879 / 0.46 ( 7) metal coordination : angle 2.81854 / 1.65 ( 3) Misc. bond : bond 0.00002 / 0.00 ( 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 171 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 SER cc_start: 0.8133 (t) cc_final: 0.7546 (p) REVERT: A 40 ASP cc_start: 0.7524 (p0) cc_final: 0.7173 (p0) REVERT: A 81 GLN cc_start: 0.7553 (tt0) cc_final: 0.7326 (tm-30) REVERT: A 370 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7110 (tp30) REVERT: A 666 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.7441 (ttm) REVERT: A 758 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8317 (tt) REVERT: A 794 MET cc_start: 0.9161 (ttp) cc_final: 0.8771 (ttp) REVERT: A 859 PHE cc_start: 0.8744 (m-80) cc_final: 0.8441 (m-80) REVERT: A 895 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7558 (pt) REVERT: C 18 GLN cc_start: 0.8782 (tm-30) cc_final: 0.8448 (tm130) REVERT: G 189 LEU cc_start: 0.7109 (mm) cc_final: 0.6604 (pp) outliers start: 26 outliers final: 14 residues processed: 165 average time/residue: 0.4179 time to fit residues: 75.6353 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 : 0.229 ------------------------------------------------------------------------------- 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 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 885 LEU Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain B residue 119 ILE 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 G residue 99 ASP Chi-restraints excluded: chain G residue 153 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 83 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 105 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 ** 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 = 0.3854 r_free = 0.3854 target = 0.147695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.115424 restraints weight = 13237.302| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.00 r_work: 0.3310 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2327 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= 0.118 Angle : 0.531 7.854 13986 Z= 0.274 Chirality : 0.043 0.178 1593 Planarity : 0.003 0.029 1708 Dihedral : 6.409 51.906 1565 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.18 % Allowed : 19.13 % Favored : 78.69 % 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: -0.10 (0.24), residues: 1177 helix: 0.50 (0.23), residues: 549 sheet: -0.61 (0.42), residues: 132 loop : -0.40 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 513 TYR 0.012 0.001 TYR A 788 PHE 0.010 0.001 PHE A 652 TRP 0.011 0.001 TRP G 182 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (10231) covalent geometry : angle 0.52961 / 0.27 (13983) hydrogen bonds : bond 0.04149 / 2.84 ( 460) hydrogen bonds : angle 4.07429 / 2.77 ( 1359) metal coordination : bond 0.00741 / 0.39 ( 7) metal coordination : angle 2.72903 / 1.60 ( 3) Misc. bond : bond 0.00010 / 0.01 ( 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 178 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 27 SER cc_start: 0.8075 (t) cc_final: 0.7494 (p) REVERT: A 40 ASP cc_start: 0.7492 (p0) cc_final: 0.7084 (p0) REVERT: A 81 GLN cc_start: 0.7606 (tt0) cc_final: 0.7397 (tm-30) REVERT: A 156 TYR cc_start: 0.8279 (t80) cc_final: 0.7925 (t80) REVERT: A 370 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7206 (tp30) REVERT: A 553 ARG cc_start: 0.7319 (OUTLIER) cc_final: 0.7048 (ptm160) REVERT: A 794 MET cc_start: 0.9122 (ttp) cc_final: 0.8765 (ttp) REVERT: A 855 MET cc_start: 0.7588 (mtm) cc_final: 0.6825 (mtm) REVERT: A 859 PHE cc_start: 0.8698 (m-80) cc_final: 0.8371 (m-80) REVERT: A 893 ASP cc_start: 0.6732 (m-30) cc_final: 0.6510 (t0) REVERT: A 895 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7695 (pt) REVERT: C 18 GLN cc_start: 0.8776 (tm-30) cc_final: 0.8440 (tm130) REVERT: G 189 LEU cc_start: 0.7154 (mm) cc_final: 0.6669 (pp) outliers start: 23 outliers final: 13 residues processed: 172 average time/residue: 0.4122 time to fit residues: 77.6799 Evaluate side-chains 158 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.270 ------------------------------------------------------------------------------- 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 553 ARG 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 C residue 45 THR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain G residue 99 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 22 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 102 optimal weight: 0.5980 chunk 89 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 93 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.142748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.109961 restraints weight = 13585.409| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.06 r_work: 0.3247 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2366 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= 0.146 Angle : 0.553 9.946 13986 Z= 0.285 Chirality : 0.045 0.185 1593 Planarity : 0.003 0.026 1708 Dihedral : 6.423 52.008 1565 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.18 % Allowed : 19.22 % Favored : 78.60 % 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: -0.13 (0.24), residues: 1177 helix: 0.46 (0.23), residues: 550 sheet: -0.61 (0.42), residues: 132 loop : -0.40 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 513 TYR 0.016 0.001 TYR A 289 PHE 0.021 0.001 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 0.00338 / 0.15 (10231) covalent geometry : angle 0.55136 / 0.28 (13983) hydrogen bonds : bond 0.04343 / 2.97 ( 460) hydrogen bonds : angle 4.10475 / 2.80 ( 1359) metal coordination : bond 0.00783 / 0.41 ( 7) metal coordination : angle 2.63299 / 1.54 ( 3) Misc. bond : bond 0.00008 / 0.00 ( 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 168 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: A 27 SER cc_start: 0.8001 (t) cc_final: 0.7424 (p) REVERT: A 40 ASP cc_start: 0.7383 (p0) cc_final: 0.7028 (p0) REVERT: A 81 GLN cc_start: 0.7505 (tt0) cc_final: 0.7275 (tm-30) REVERT: A 370 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7071 (tp30) REVERT: A 553 ARG cc_start: 0.7273 (OUTLIER) cc_final: 0.7040 (ptm160) REVERT: A 758 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8250 (tt) REVERT: A 794 MET cc_start: 0.9170 (ttp) cc_final: 0.8763 (ttp) REVERT: A 855 MET cc_start: 0.7552 (mtm) cc_final: 0.6808 (mtm) REVERT: A 859 PHE cc_start: 0.8702 (m-80) cc_final: 0.8379 (m-80) REVERT: A 895 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7644 (pt) REVERT: C 18 GLN cc_start: 0.8747 (tm-30) cc_final: 0.8361 (tm130) REVERT: G 189 LEU cc_start: 0.7084 (mm) cc_final: 0.6598 (pp) outliers start: 23 outliers final: 15 residues processed: 163 average time/residue: 0.4060 time to fit residues: 72.4894 Evaluate side-chains 158 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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 553 ARG 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 767 ASN 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 G residue 99 ASP Chi-restraints excluded: chain G residue 122 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 26 optimal weight: 2.9990 chunk 31 optimal weight: 0.0870 chunk 111 optimal weight: 7.9990 chunk 21 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 54 optimal weight: 7.9990 chunk 99 optimal weight: 0.0370 chunk 110 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 overall best weight: 0.5636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.147811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.115354 restraints weight = 13258.997| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.12 r_work: 0.3343 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10239 Z= 0.109 Angle : 0.538 12.663 13986 Z= 0.275 Chirality : 0.043 0.164 1593 Planarity : 0.003 0.026 1708 Dihedral : 6.325 52.555 1565 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.08 % Allowed : 19.70 % Favored : 78.22 % 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: 0.05 (0.24), residues: 1177 helix: 0.61 (0.23), residues: 555 sheet: -0.57 (0.42), residues: 132 loop : -0.31 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 513 TYR 0.015 0.001 TYR A 289 PHE 0.011 0.001 PHE A 396 TRP 0.011 0.001 TRP A 916 HIS 0.006 0.000 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (10231) covalent geometry : angle 0.53696 / 0.27 (13983) hydrogen bonds : bond 0.04064 / 2.77 ( 460) hydrogen bonds : angle 3.99675 / 2.72 ( 1359) metal coordination : bond 0.00659 / 0.34 ( 7) metal coordination : angle 2.69343 / 1.58 ( 3) Misc. bond : bond 0.00007 / 0.00 ( 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 170 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.267 Fit side-chains REVERT: A 27 SER cc_start: 0.8012 (t) cc_final: 0.7489 (p) REVERT: A 40 ASP cc_start: 0.7259 (p0) cc_final: 0.6905 (p0) REVERT: A 156 TYR cc_start: 0.8156 (t80) cc_final: 0.7827 (t80) REVERT: A 370 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7203 (tp30) REVERT: A 514 LEU cc_start: 0.9167 (tt) cc_final: 0.8964 (tm) REVERT: A 553 ARG cc_start: 0.7325 (OUTLIER) cc_final: 0.7075 (ptm160) REVERT: A 794 MET cc_start: 0.9076 (ttp) cc_final: 0.8747 (ttp) REVERT: A 855 MET cc_start: 0.7547 (mtm) cc_final: 0.7022 (mtm) REVERT: A 859 PHE cc_start: 0.8675 (m-80) cc_final: 0.8376 (m-80) REVERT: A 895 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7699 (pt) REVERT: A 914 ARG cc_start: 0.5427 (mpt180) cc_final: 0.5203 (mmt180) REVERT: C 18 GLN cc_start: 0.8809 (tm-30) cc_final: 0.8499 (tm130) REVERT: G 189 LEU cc_start: 0.7132 (mm) cc_final: 0.6694 (pp) outliers start: 22 outliers final: 13 residues processed: 165 average time/residue: 0.4300 time to fit residues: 77.6970 Evaluate side-chains 155 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 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 548 ILE Chi-restraints excluded: chain A residue 553 ARG 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 893 ASP 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 153 LEU 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: 0.0370 chunk 3 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.7658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.148158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.115287 restraints weight = 13192.421| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.13 r_work: 0.3330 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10239 Z= 0.119 Angle : 0.564 15.614 13986 Z= 0.288 Chirality : 0.044 0.164 1593 Planarity : 0.003 0.030 1708 Dihedral : 6.279 52.874 1565 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.61 % Allowed : 20.93 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.25), residues: 1177 helix: 0.70 (0.23), residues: 548 sheet: -0.50 (0.42), residues: 132 loop : -0.21 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 513 TYR 0.014 0.001 TYR A 289 PHE 0.029 0.001 PHE A 396 TRP 0.010 0.001 TRP A 916 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (10231) covalent geometry : angle 0.56280 / 0.29 (13983) hydrogen bonds : bond 0.04086 / 2.78 ( 460) hydrogen bonds : angle 4.00464 / 2.73 ( 1359) metal coordination : bond 0.00689 / 0.36 ( 7) metal coordination : angle 2.62132 / 1.54 ( 3) Misc. bond : bond 0.00032 / 0.02 ( 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 157 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 0.284 Fit side-chains REVERT: A 27 SER cc_start: 0.8003 (t) cc_final: 0.7474 (p) REVERT: A 40 ASP cc_start: 0.7174 (p0) cc_final: 0.6851 (p0) REVERT: A 156 TYR cc_start: 0.8088 (t80) cc_final: 0.7788 (t80) REVERT: A 370 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7191 (tp30) REVERT: A 553 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.7117 (ptm160) REVERT: A 794 MET cc_start: 0.9094 (ttp) cc_final: 0.8773 (ttp) REVERT: A 855 MET cc_start: 0.7536 (mtm) cc_final: 0.7050 (mtm) REVERT: A 859 PHE cc_start: 0.8670 (m-80) cc_final: 0.8412 (m-80) REVERT: A 895 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7693 (pt) REVERT: G 90 MET cc_start: 0.7383 (ptt) cc_final: 0.7109 (ttp) REVERT: G 174 MET cc_start: 0.5880 (mtm) cc_final: 0.5677 (mtt) REVERT: G 189 LEU cc_start: 0.7135 (mm) cc_final: 0.6711 (pp) outliers start: 17 outliers final: 12 residues processed: 154 average time/residue: 0.4029 time to fit residues: 68.1283 Evaluate side-chains 149 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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 553 ARG 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 53 VAL Chi-restraints excluded: chain G residue 153 LEU 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: 0.6980 chunk 76 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.145449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.111603 restraints weight = 13398.037| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.08 r_work: 0.3288 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10239 Z= 0.166 Angle : 0.609 19.901 13986 Z= 0.309 Chirality : 0.045 0.183 1593 Planarity : 0.003 0.034 1708 Dihedral : 6.438 52.652 1565 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.80 % Allowed : 21.40 % Favored : 76.80 % 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: 0.07 (0.24), residues: 1177 helix: 0.59 (0.23), residues: 548 sheet: -0.54 (0.42), residues: 132 loop : -0.25 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 513 TYR 0.017 0.001 TYR A 289 PHE 0.027 0.001 PHE A 396 TRP 0.010 0.001 TRP G 182 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (10231) covalent geometry : angle 0.60763 / 0.31 (13983) hydrogen bonds : bond 0.04462 / 3.05 ( 460) hydrogen bonds : angle 4.11280 / 2.80 ( 1359) metal coordination : bond 0.00736 / 0.39 ( 7) metal coordination : angle 2.58609 / 1.51 ( 3) Misc. bond : bond 0.00028 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3025.56 seconds wall clock time: 52 minutes 24.21 seconds (3144.21 seconds total)