Starting phenix.real_space_refine on Thu Jul 2 21:37:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gtb_51560/07_2026/9gtb_51560.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gtb_51560/07_2026/9gtb_51560.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9gtb_51560/07_2026/9gtb_51560.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gtb_51560/07_2026/9gtb_51560.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gtb_51560/07_2026/9gtb_51560.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gtb_51560/07_2026/9gtb_51560.map" } resolution = 3.5 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= 0.003 sd= 0.063 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 3 5.49 5 S 58 5.16 5 C 6401 2.51 5 N 1698 2.21 5 O 1903 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 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: 10064 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 939, 7297 Classifications: {'peptide': 939} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 892} Chain breaks: 3 Chain: "B" Number of atoms: 2643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2643 Classifications: {'peptide': 332} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 316} Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'KXP': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'KXP:plan-1': 1, 'KXP:plan-3': 1, 'KXP:plan-4': 1, 'KXP:plan-5': 1, 'KXP:plan-6': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 2.23, per 1000 atoms: 0.22 Number of scatterers: 10064 At special positions: 0 Unit cell: (197.47, 128.31, 126.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 58 16.00 P 3 15.00 O 1903 8.00 N 1698 7.00 C 6401 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 116 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 217 " distance=2.05 Simple disulfide: pdb=" SG CYS B 258 " - pdb=" SG CYS B 315 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG B 501 " - " ASN B 283 " " NAG B 502 " - " ASN B 316 " " NAG B 503 " - " ASN B 295 " " NAG B 504 " - " ASN B 170 " " NAG B 505 " - " ASN B 228 " " NAG B 506 " - " ASN B 196 " Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 368.2 milliseconds 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2376 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 14 sheets defined 42.6% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 27 through 37 Processing helix chain 'A' and resid 38 through 41 removed outlier: 3.695A pdb=" N GLU A 41 " --> pdb=" O ARG A 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 38 through 41' Processing helix chain 'A' and resid 42 through 48 Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 71 through 75 Processing helix chain 'A' and resid 94 through 103 Processing helix chain 'A' and resid 105 through 124 Processing helix chain 'A' and resid 151 through 184 removed outlier: 3.610A pdb=" N ALA A 155 " --> pdb=" O TRP A 151 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER A 160 " --> pdb=" O ALA A 156 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N VAL A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL A 167 " --> pdb=" O CYS A 163 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 169 " --> pdb=" O VAL A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 243 removed outlier: 3.634A pdb=" N THR A 242 " --> pdb=" O GLU A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 288 removed outlier: 3.506A pdb=" N PHE A 286 " --> pdb=" O THR A 282 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 288 " --> pdb=" O ILE A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 377 removed outlier: 3.625A pdb=" N LYS A 344 " --> pdb=" O VAL A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 410 removed outlier: 3.839A pdb=" N TYR A 391 " --> pdb=" O CYS A 387 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA A 409 " --> pdb=" O VAL A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 430 removed outlier: 3.761A pdb=" N VAL A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR A 419 " --> pdb=" O PRO A 415 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS A 427 " --> pdb=" O ALA A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 445 removed outlier: 4.081A pdb=" N CYS A 442 " --> pdb=" O HIS A 438 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU A 443 " --> pdb=" O LEU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 448 No H-bonds generated for 'chain 'A' and resid 446 through 448' Processing helix chain 'A' and resid 486 through 501 Processing helix chain 'A' and resid 522 through 535 removed outlier: 3.669A pdb=" N CYS A 526 " --> pdb=" O ASN A 522 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY A 527 " --> pdb=" O LYS A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 546 removed outlier: 4.389A pdb=" N VAL A 542 " --> pdb=" O ASP A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 588 removed outlier: 4.650A pdb=" N LYS A 588 " --> pdb=" O GLU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 623 removed outlier: 3.921A pdb=" N LYS A 613 " --> pdb=" O ASP A 609 " (cutoff:3.500A) Proline residue: A 618 - end of helix Processing helix chain 'A' and resid 667 through 678 Processing helix chain 'A' and resid 689 through 700 Processing helix chain 'A' and resid 714 through 722 Processing helix chain 'A' and resid 731 through 738 removed outlier: 3.538A pdb=" N LYS A 735 " --> pdb=" O ARG A 732 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N TRP A 737 " --> pdb=" O ASP A 734 " (cutoff:3.500A) Proline residue: A 738 - end of helix Processing helix chain 'A' and resid 747 through 761 removed outlier: 3.673A pdb=" N LYS A 751 " --> pdb=" O SER A 747 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N HIS A 752 " --> pdb=" O PRO A 748 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR A 753 " --> pdb=" O THR A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 786 removed outlier: 3.554A pdb=" N ALA A 786 " --> pdb=" O ALA A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 803 removed outlier: 3.627A pdb=" N ALA A 803 " --> pdb=" O VAL A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 855 removed outlier: 3.900A pdb=" N VAL A 817 " --> pdb=" O PHE A 813 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TRP A 822 " --> pdb=" O LYS A 818 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY A 823 " --> pdb=" O ALA A 819 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG A 824 " --> pdb=" O VAL A 820 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TYR A 827 " --> pdb=" O GLY A 823 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE A 846 " --> pdb=" O VAL A 842 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL A 847 " --> pdb=" O VAL A 843 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR A 850 " --> pdb=" O ILE A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 882 removed outlier: 4.595A pdb=" N ALA A 876 " --> pdb=" O MET A 872 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N SER A 877 " --> pdb=" O ASP A 873 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU A 878 " --> pdb=" O THR A 874 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N THR A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 892 removed outlier: 3.922A pdb=" N LEU A 889 " --> pdb=" O THR A 886 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 890 " --> pdb=" O GLU A 887 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ARG A 892 " --> pdb=" O LEU A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 932 removed outlier: 3.677A pdb=" N MET A 907 " --> pdb=" O SER A 903 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS A 908 " --> pdb=" O ARG A 904 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR A 916 " --> pdb=" O GLY A 912 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N GLU A 929 " --> pdb=" O LEU A 925 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LYS A 930 " --> pdb=" O PHE A 926 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N MET A 931 " --> pdb=" O VAL A 927 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE A 932 " --> pdb=" O GLY A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 966 removed outlier: 3.881A pdb=" N ILE A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 970 removed outlier: 4.057A pdb=" N LYS A 970 " --> pdb=" O ASN A 967 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 967 through 970' Processing helix chain 'A' and resid 980 through 983 Processing helix chain 'A' and resid 984 through 1005 removed outlier: 3.805A pdb=" N CYS A 988 " --> pdb=" O ASN A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1037 removed outlier: 3.553A pdb=" N TRP A1019 " --> pdb=" O GLN A1015 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET A1020 " --> pdb=" O LEU A1016 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TRP A1021 " --> pdb=" O ASP A1017 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A1030 " --> pdb=" O GLY A1026 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A1037 " --> pdb=" O GLY A1033 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 86 removed outlier: 3.715A pdb=" N ARG B 85 " --> pdb=" O GLY B 81 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 81 through 86' Processing helix chain 'B' and resid 107 through 110 Processing helix chain 'B' and resid 338 through 360 removed outlier: 3.605A pdb=" N ILE B 355 " --> pdb=" O ILE B 351 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU B 360 " --> pdb=" O ILE B 356 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 213 through 215 removed outlier: 6.900A pdb=" N ARG A 270 " --> pdb=" O ILE A 229 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 247 through 250 removed outlier: 3.560A pdb=" N VAL A 248 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE A 236 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LEU A 234 " --> pdb=" O LYS A 250 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 435 through 436 removed outlier: 6.620A pdb=" N ALA A 791 " --> pdb=" O LEU A 808 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 710 through 712 removed outlier: 7.785A pdb=" N LEU A 710 " --> pdb=" O ARG A 741 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N LEU A 743 " --> pdb=" O LEU A 710 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU A 712 " --> pdb=" O LEU A 743 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ARG A 741 " --> pdb=" O VAL A 682 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE A 451 " --> pdb=" O ARG A 683 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N VAL A 685 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N SER A 453 " --> pdb=" O VAL A 685 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ALA A 450 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 474 through 476 removed outlier: 6.572A pdb=" N GLY A 659 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ALA A 469 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL A 657 " --> pdb=" O ALA A 469 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N VAL A 471 " --> pdb=" O ILE A 655 " (cutoff:3.500A) removed outlier: 10.075A pdb=" N ILE A 655 " --> pdb=" O VAL A 471 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N LEU A 652 " --> pdb=" O ASP A 633 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ASP A 633 " --> pdb=" O LEU A 652 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N CYS A 654 " --> pdb=" O TYR A 631 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N TYR A 631 " --> pdb=" O CYS A 654 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N CYS A 656 " --> pdb=" O VAL A 629 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS A 628 " --> pdb=" O GLY A 581 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLY A 581 " --> pdb=" O CYS A 628 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 474 through 476 removed outlier: 6.572A pdb=" N GLY A 659 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ALA A 469 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL A 657 " --> pdb=" O ALA A 469 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N VAL A 471 " --> pdb=" O ILE A 655 " (cutoff:3.500A) removed outlier: 10.075A pdb=" N ILE A 655 " --> pdb=" O VAL A 471 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N CYS A 654 " --> pdb=" O CYS A 591 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ILE A 593 " --> pdb=" O CYS A 654 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N CYS A 656 " --> pdb=" O ILE A 593 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 33 through 35 removed outlier: 6.820A pdb=" N PHE B 33 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL B 55 " --> pdb=" O PHE B 33 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL B 98 " --> pdb=" O ALA B 92 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 40 through 43 removed outlier: 6.315A pdb=" N GLU B 40 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N LEU B 145 " --> pdb=" O GLU B 40 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LYS B 42 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TRP B 64 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 149 through 152 removed outlier: 6.484A pdb=" N ARG B 149 " --> pdb=" O THR B 172 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 156 through 157 removed outlier: 6.569A pdb=" N VAL B 156 " --> pdb=" O LYS B 234 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N ALA B 236 " --> pdb=" O VAL B 156 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 156 through 157 removed outlier: 6.569A pdb=" N VAL B 156 " --> pdb=" O LYS B 234 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N ALA B 236 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N TYR B 263 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL B 261 " --> pdb=" O PRO B 237 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ILE B 239 " --> pdb=" O LYS B 259 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N LYS B 259 " --> pdb=" O ILE B 239 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 245 through 249 removed outlier: 4.968A pdb=" N GLU B 312 " --> pdb=" O LYS B 273 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 245 through 249 Processing sheet with id=AB5, first strand: chain 'B' and resid 254 through 256 451 hydrogen bonds defined for protein. 1269 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.80 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1798 1.32 - 1.45: 2449 1.45 - 1.57: 5914 1.57 - 1.69: 4 1.69 - 1.81: 90 Bond restraints: 10255 Sorted by residual: bond pdb=" O41 KXP A1302 " pdb=" P42 KXP A1302 " ideal model delta sigma weight residual 1.725 1.614 0.111 2.00e-02 2.50e+03 3.05e+01 bond pdb=" O36 KXP A1302 " pdb=" P37 KXP A1302 " ideal model delta sigma weight residual 1.722 1.617 0.105 2.00e-02 2.50e+03 2.78e+01 bond pdb=" C33 KXP A1302 " pdb=" O36 KXP A1302 " ideal model delta sigma weight residual 1.394 1.468 -0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C32 KXP A1302 " pdb=" O41 KXP A1302 " ideal model delta sigma weight residual 1.394 1.466 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C23 KXP A1302 " pdb=" O24 KXP A1302 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.60e+00 ... (remaining 10250 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 13567 2.11 - 4.23: 282 4.23 - 6.34: 52 6.34 - 8.45: 10 8.45 - 10.57: 2 Bond angle restraints: 13913 Sorted by residual: angle pdb=" C LYS A 553 " pdb=" N VAL A 554 " pdb=" CA VAL A 554 " ideal model delta sigma weight residual 121.97 129.11 -7.14 1.80e+00 3.09e-01 1.57e+01 angle pdb=" CA LYS B 195 " pdb=" CB LYS B 195 " pdb=" CG LYS B 195 " ideal model delta sigma weight residual 114.10 121.67 -7.57 2.00e+00 2.50e-01 1.43e+01 angle pdb=" N LEU A 535 " pdb=" CA LEU A 535 " pdb=" C LEU A 535 " ideal model delta sigma weight residual 112.72 108.51 4.21 1.14e+00 7.69e-01 1.37e+01 angle pdb=" C GLN A 537 " pdb=" N ASP A 538 " pdb=" CA ASP A 538 " ideal model delta sigma weight residual 122.09 116.69 5.40 1.48e+00 4.57e-01 1.33e+01 angle pdb=" O24 KXP A1302 " pdb=" P25 KXP A1302 " pdb=" O28 KXP A1302 " ideal model delta sigma weight residual 90.95 101.52 -10.57 3.00e+00 1.11e-01 1.24e+01 ... (remaining 13908 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.28: 6126 30.28 - 60.56: 186 60.56 - 90.83: 20 90.83 - 121.11: 6 121.11 - 151.39: 2 Dihedral angle restraints: 6340 sinusoidal: 2665 harmonic: 3675 Sorted by residual: dihedral pdb=" CB CYS B 169 " pdb=" SG CYS B 169 " pdb=" SG CYS B 217 " pdb=" CB CYS B 217 " ideal model delta sinusoidal sigma weight residual 93.00 142.99 -49.99 1 1.00e+01 1.00e-02 3.43e+01 dihedral pdb=" CA GLU B 294 " pdb=" C GLU B 294 " pdb=" N ASN B 295 " pdb=" CA ASN B 295 " ideal model delta harmonic sigma weight residual 180.00 153.29 26.71 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" C2 KXP A1302 " pdb=" C1 KXP A1302 " pdb=" C18 KXP A1302 " pdb=" O1 KXP A1302 " ideal model delta sinusoidal sigma weight residual -21.13 -172.52 151.39 1 3.00e+01 1.11e-03 2.00e+01 ... (remaining 6337 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1108 0.044 - 0.087: 396 0.087 - 0.131: 115 0.131 - 0.175: 15 0.175 - 0.218: 2 Chirality restraints: 1636 Sorted by residual: chirality pdb=" CA LEU A 529 " pdb=" N LEU A 529 " pdb=" C LEU A 529 " pdb=" CB LEU A 529 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CB ILE A1001 " pdb=" CA ILE A1001 " pdb=" CG1 ILE A1001 " pdb=" CG2 ILE A1001 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.27e-01 chirality pdb=" CA LEU A 528 " pdb=" N LEU A 528 " pdb=" C LEU A 528 " pdb=" CB LEU A 528 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.59e-01 ... (remaining 1633 not shown) Planarity restraints: 1762 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 835 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.52e+00 pdb=" C GLN A 835 " -0.041 2.00e-02 2.50e+03 pdb=" O GLN A 835 " 0.015 2.00e-02 2.50e+03 pdb=" N PHE A 836 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 570 " 0.035 5.00e-02 4.00e+02 5.29e-02 4.47e+00 pdb=" N PRO A 571 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 571 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 571 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 836 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.78e+00 pdb=" C PHE A 836 " -0.034 2.00e-02 2.50e+03 pdb=" O PHE A 836 " 0.013 2.00e-02 2.50e+03 pdb=" N GLN A 837 " 0.011 2.00e-02 2.50e+03 ... (remaining 1759 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 41 2.66 - 3.22: 10049 3.22 - 3.78: 15021 3.78 - 4.34: 20007 4.34 - 4.90: 32296 Nonbonded interactions: 77414 Sorted by model distance: nonbonded pdb=" OD2 ASP A 873 " pdb="CA CA A1301 " model vdw 2.095 3.250 nonbonded pdb=" OD1 ASN A 869 " pdb="CA CA A1301 " model vdw 2.181 3.250 nonbonded pdb=" OE1 GLU A 412 " pdb="CA CA A1301 " model vdw 2.181 3.250 nonbonded pdb=" O VAL A 410 " pdb="CA CA A1301 " model vdw 2.462 3.250 nonbonded pdb=" O PRO A 547 " pdb=" OE1 GLU A 549 " model vdw 2.544 3.040 ... (remaining 77409 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.580 Find NCS groups from input model: 0.050 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 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 : 0.006 0.111 10264 Z= 0.276 Angle : 0.774 10.566 13937 Z= 0.402 Chirality : 0.048 0.218 1636 Planarity : 0.005 0.053 1756 Dihedral : 14.749 151.391 3955 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.47 % Favored : 94.21 % Rotamer: Outliers : 2.08 % Allowed : 13.92 % Favored : 84.00 % 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: -0.71 (0.24), residues: 1261 helix: 0.13 (0.24), residues: 483 sheet: -0.05 (0.38), residues: 207 loop : -1.09 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 543 TYR 0.021 0.002 TYR B 180 PHE 0.025 0.002 PHE A 179 TRP 0.025 0.002 TRP A 642 HIS 0.016 0.002 HIS B 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00640 / 0.28 (10255) covalent geometry : angle 0.76548 / 0.40 (13913) SS BOND : bond 0.01003 / 0.56 ( 3) SS BOND : angle 1.18821 / 0.62 ( 6) hydrogen bonds : bond 0.14344 / 9.79 ( 436) hydrogen bonds : angle 6.94449 / 5.11 ( 1269) link_NAG-ASN : bond 0.00306 / 0.19 ( 6) link_NAG-ASN : angle 3.17939 / 1.84 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 TYR cc_start: 0.5614 (OUTLIER) cc_final: 0.4076 (m-80) REVERT: A 784 LYS cc_start: 0.8435 (mtmm) cc_final: 0.8143 (mtmm) REVERT: A 857 ASP cc_start: 0.7549 (t0) cc_final: 0.7267 (p0) REVERT: A 911 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7835 (mp) REVERT: B 38 MET cc_start: 0.3593 (ppp) cc_final: 0.3296 (tpt) REVERT: B 202 TYR cc_start: 0.7456 (t80) cc_final: 0.7098 (t80) REVERT: B 296 TYR cc_start: 0.8614 (OUTLIER) cc_final: 0.7853 (t80) REVERT: B 359 TYR cc_start: 0.7206 (t80) cc_final: 0.6895 (t80) outliers start: 23 outliers final: 16 residues processed: 119 average time/residue: 0.0975 time to fit residues: 16.6608 Evaluate side-chains 114 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 511 GLU Chi-restraints excluded: chain A residue 552 TYR Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 296 TYR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 335 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 50.0000 chunk 97 optimal weight: 0.0040 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 overall best weight: 1.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 837 GLN A 869 ASN ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 HIS B 220 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.215458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.155024 restraints weight = 14772.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.139449 restraints weight = 19717.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.133716 restraints weight = 13544.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.132919 restraints weight = 12704.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.133242 restraints weight = 9704.801| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.0750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10264 Z= 0.184 Angle : 0.648 7.935 13937 Z= 0.328 Chirality : 0.045 0.198 1636 Planarity : 0.004 0.056 1756 Dihedral : 11.966 130.723 1583 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.23 % Favored : 94.61 % Rotamer: Outliers : 4.97 % Allowed : 12.66 % Favored : 82.37 % 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: -0.23 (0.24), residues: 1261 helix: 0.83 (0.25), residues: 474 sheet: 0.15 (0.41), residues: 182 loop : -1.02 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 543 TYR 0.018 0.002 TYR B 180 PHE 0.017 0.001 PHE A 179 TRP 0.013 0.001 TRP A 822 HIS 0.011 0.001 HIS B 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.18 (10255) covalent geometry : angle 0.63816 / 0.33 (13913) SS BOND : bond 0.00699 / 0.39 ( 3) SS BOND : angle 1.35113 / 0.72 ( 6) hydrogen bonds : bond 0.06370 / 4.26 ( 436) hydrogen bonds : angle 5.24926 / 3.87 ( 1269) link_NAG-ASN : bond 0.00261 / 0.16 ( 6) link_NAG-ASN : angle 3.15025 / 1.80 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 100 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 503 TYR cc_start: 0.6045 (OUTLIER) cc_final: 0.4934 (m-80) REVERT: A 511 GLU cc_start: 0.4458 (OUTLIER) cc_final: 0.2821 (mp0) REVERT: A 857 ASP cc_start: 0.7506 (t0) cc_final: 0.7229 (p0) REVERT: A 911 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7689 (mp) REVERT: B 38 MET cc_start: 0.3608 (ppp) cc_final: 0.3388 (tpt) REVERT: B 202 TYR cc_start: 0.7674 (t80) cc_final: 0.7242 (t80) REVERT: B 296 TYR cc_start: 0.8669 (OUTLIER) cc_final: 0.7889 (t80) outliers start: 55 outliers final: 38 residues processed: 144 average time/residue: 0.0939 time to fit residues: 19.6310 Evaluate side-chains 137 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 95 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 511 GLU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 552 TYR Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 869 ASN Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 921 ILE Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 296 TYR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 335 HIS Chi-restraints excluded: chain B residue 358 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 124 optimal weight: 0.9990 chunk 17 optimal weight: 30.0000 chunk 7 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 111 optimal weight: 6.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 869 ASN B 220 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.213411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.150414 restraints weight = 14320.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.135039 restraints weight = 19645.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.130658 restraints weight = 13874.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.129830 restraints weight = 11671.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.130195 restraints weight = 9142.699| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 10264 Z= 0.250 Angle : 0.691 7.598 13937 Z= 0.353 Chirality : 0.047 0.200 1636 Planarity : 0.004 0.057 1756 Dihedral : 11.568 118.626 1579 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.31 % Favored : 94.45 % Rotamer: Outliers : 5.79 % Allowed : 14.47 % Favored : 79.75 % 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: -0.37 (0.24), residues: 1261 helix: 0.64 (0.24), residues: 475 sheet: -0.06 (0.39), residues: 190 loop : -1.00 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 536 TYR 0.016 0.001 TYR A 916 PHE 0.013 0.002 PHE A 836 TRP 0.012 0.001 TRP A 822 HIS 0.009 0.001 HIS B 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00612 / 0.25 (10255) covalent geometry : angle 0.68165 / 0.35 (13913) SS BOND : bond 0.00500 / 0.29 ( 3) SS BOND : angle 1.63371 / 0.91 ( 6) hydrogen bonds : bond 0.06952 / 4.62 ( 436) hydrogen bonds : angle 5.24610 / 3.86 ( 1269) link_NAG-ASN : bond 0.00116 / 0.07 ( 6) link_NAG-ASN : angle 3.18684 / 1.85 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 102 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7378 (tt) REVERT: A 185 ARG cc_start: 0.7569 (mmp-170) cc_final: 0.7364 (mmp80) REVERT: A 503 TYR cc_start: 0.5957 (OUTLIER) cc_final: 0.4997 (m-80) REVERT: A 511 GLU cc_start: 0.4759 (OUTLIER) cc_final: 0.2944 (pm20) REVERT: A 552 TYR cc_start: 0.5453 (OUTLIER) cc_final: 0.3801 (m-80) REVERT: A 624 LEU cc_start: 0.9014 (mp) cc_final: 0.8764 (mp) REVERT: A 857 ASP cc_start: 0.7530 (t0) cc_final: 0.7276 (p0) REVERT: B 202 TYR cc_start: 0.7932 (t80) cc_final: 0.7484 (t80) REVERT: B 296 TYR cc_start: 0.8742 (OUTLIER) cc_final: 0.8077 (t80) outliers start: 64 outliers final: 49 residues processed: 158 average time/residue: 0.0898 time to fit residues: 20.5826 Evaluate side-chains 148 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 94 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 511 GLU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 552 TYR Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain A residue 779 ASP Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 869 ASN Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 921 ILE Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 960 MET Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 296 TYR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 335 HIS Chi-restraints excluded: chain B residue 358 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 78 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 chunk 113 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 20 optimal weight: 20.0000 chunk 99 optimal weight: 4.9990 chunk 96 optimal weight: 8.9990 chunk 88 optimal weight: 0.5980 chunk 21 optimal weight: 7.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 869 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.211638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.145859 restraints weight = 14393.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.135132 restraints weight = 20259.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.124398 restraints weight = 13448.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.123401 restraints weight = 15441.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.124838 restraints weight = 10569.313| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 10264 Z= 0.330 Angle : 0.753 9.239 13937 Z= 0.385 Chirality : 0.049 0.200 1636 Planarity : 0.005 0.056 1756 Dihedral : 11.586 116.453 1579 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.87 % Favored : 93.89 % Rotamer: Outliers : 7.14 % Allowed : 14.65 % Favored : 78.21 % 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: -0.71 (0.24), residues: 1261 helix: 0.30 (0.24), residues: 477 sheet: -0.61 (0.36), residues: 223 loop : -1.01 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 180 TYR 0.024 0.002 TYR A 895 PHE 0.016 0.002 PHE A 836 TRP 0.015 0.002 TRP A 822 HIS 0.007 0.001 HIS B 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00810 / 0.33 (10255) covalent geometry : angle 0.74445 / 0.38 (13913) SS BOND : bond 0.00408 / 0.24 ( 3) SS BOND : angle 1.07419 / 0.57 ( 6) hydrogen bonds : bond 0.07514 / 4.99 ( 436) hydrogen bonds : angle 5.37645 / 3.95 ( 1269) link_NAG-ASN : bond 0.00240 / 0.15 ( 6) link_NAG-ASN : angle 3.26596 / 1.90 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 93 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7326 (tt) REVERT: A 370 TYR cc_start: 0.7461 (t80) cc_final: 0.7078 (t80) REVERT: A 503 TYR cc_start: 0.6260 (OUTLIER) cc_final: 0.5552 (m-80) REVERT: A 552 TYR cc_start: 0.5519 (OUTLIER) cc_final: 0.3881 (m-80) REVERT: A 857 ASP cc_start: 0.7536 (t0) cc_final: 0.7279 (p0) REVERT: A 920 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7929 (mp) REVERT: A 1038 THR cc_start: 0.9145 (OUTLIER) cc_final: 0.8776 (m) REVERT: B 202 TYR cc_start: 0.8255 (t80) cc_final: 0.7743 (t80) REVERT: B 296 TYR cc_start: 0.8803 (OUTLIER) cc_final: 0.8175 (t80) outliers start: 79 outliers final: 61 residues processed: 165 average time/residue: 0.0803 time to fit residues: 19.8878 Evaluate side-chains 156 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 89 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 552 TYR Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain A residue 779 ASP Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 869 ASN Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 921 ILE Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 960 MET Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 296 TYR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 335 HIS Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 358 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 3 optimal weight: 0.0770 chunk 53 optimal weight: 20.0000 chunk 52 optimal weight: 8.9990 chunk 110 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 59 optimal weight: 6.9990 chunk 95 optimal weight: 30.0000 chunk 119 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 17 optimal weight: 20.0000 overall best weight: 1.5142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 869 ASN B 220 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.215210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 108)---------------| | r_work = 0.3884 r_free = 0.3884 target = 0.138163 restraints weight = 14347.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.130015 restraints weight = 10258.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.131093 restraints weight = 8995.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.132185 restraints weight = 7467.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.132308 restraints weight = 6673.963| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10264 Z= 0.166 Angle : 0.644 8.912 13937 Z= 0.322 Chirality : 0.044 0.196 1636 Planarity : 0.004 0.056 1756 Dihedral : 10.883 108.048 1576 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.15 % Favored : 94.61 % Rotamer: Outliers : 5.24 % Allowed : 17.00 % Favored : 77.76 % 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: 1261 helix: 0.72 (0.24), residues: 477 sheet: -0.57 (0.36), residues: 222 loop : -0.90 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 180 TYR 0.023 0.001 TYR B 180 PHE 0.011 0.001 PHE A 849 TRP 0.012 0.001 TRP B 183 HIS 0.015 0.001 HIS B 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (10255) covalent geometry : angle 0.63413 / 0.32 (13913) SS BOND : bond 0.00368 / 0.21 ( 3) SS BOND : angle 0.48439 / 0.25 ( 6) hydrogen bonds : bond 0.06016 / 4.02 ( 436) hydrogen bonds : angle 5.02393 / 3.71 ( 1269) link_NAG-ASN : bond 0.00220 / 0.13 ( 6) link_NAG-ASN : angle 3.17375 / 1.85 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 97 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7324 (tt) REVERT: A 370 TYR cc_start: 0.7442 (t80) cc_final: 0.7107 (t80) REVERT: A 503 TYR cc_start: 0.6040 (OUTLIER) cc_final: 0.5354 (m-80) REVERT: A 857 ASP cc_start: 0.7430 (t0) cc_final: 0.7192 (p0) REVERT: A 1038 THR cc_start: 0.9128 (OUTLIER) cc_final: 0.8775 (m) REVERT: B 179 MET cc_start: 0.7761 (ttp) cc_final: 0.7460 (ppp) REVERT: B 202 TYR cc_start: 0.8179 (t80) cc_final: 0.7807 (t80) REVERT: B 206 LYS cc_start: 0.7863 (mmmt) cc_final: 0.7308 (mtpt) REVERT: B 296 TYR cc_start: 0.8744 (OUTLIER) cc_final: 0.8128 (t80) REVERT: B 345 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.8014 (mt) outliers start: 58 outliers final: 48 residues processed: 147 average time/residue: 0.0764 time to fit residues: 16.6665 Evaluate side-chains 148 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 95 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 552 TYR Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 779 ASP Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 921 ILE Chi-restraints excluded: chain A residue 956 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 180 TYR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 296 TYR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 335 HIS Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 358 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 1 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 43 optimal weight: 8.9990 chunk 121 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 chunk 95 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 14 optimal weight: 20.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.215611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.154495 restraints weight = 14805.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.139200 restraints weight = 21344.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.133648 restraints weight = 14605.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.133837 restraints weight = 12029.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.134080 restraints weight = 10412.420| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10264 Z= 0.161 Angle : 0.633 9.529 13937 Z= 0.314 Chirality : 0.044 0.183 1636 Planarity : 0.004 0.056 1756 Dihedral : 10.498 108.806 1576 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.63 % Favored : 94.13 % Rotamer: Outliers : 6.24 % Allowed : 16.37 % Favored : 77.40 % 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: -0.25 (0.24), residues: 1261 helix: 0.86 (0.24), residues: 483 sheet: -0.50 (0.37), residues: 210 loop : -0.86 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 180 TYR 0.025 0.001 TYR B 180 PHE 0.010 0.001 PHE A 179 TRP 0.013 0.001 TRP B 183 HIS 0.007 0.001 HIS B 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 (10255) covalent geometry : angle 0.62395 / 0.31 (13913) SS BOND : bond 0.00509 / 0.29 ( 3) SS BOND : angle 0.37518 / 0.18 ( 6) hydrogen bonds : bond 0.05732 / 3.83 ( 436) hydrogen bonds : angle 4.87263 / 3.58 ( 1269) link_NAG-ASN : bond 0.00195 / 0.12 ( 6) link_NAG-ASN : angle 3.08936 / 1.82 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 97 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7346 (tt) REVERT: A 370 TYR cc_start: 0.7440 (t80) cc_final: 0.7184 (t80) REVERT: A 503 TYR cc_start: 0.6107 (OUTLIER) cc_final: 0.5525 (m-80) REVERT: A 1038 THR cc_start: 0.9166 (OUTLIER) cc_final: 0.8812 (m) REVERT: B 202 TYR cc_start: 0.8195 (t80) cc_final: 0.7874 (t80) REVERT: B 296 TYR cc_start: 0.8759 (OUTLIER) cc_final: 0.8063 (t80) REVERT: B 345 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8019 (mt) outliers start: 69 outliers final: 57 residues processed: 160 average time/residue: 0.0911 time to fit residues: 21.7188 Evaluate side-chains 154 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 92 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 552 TYR Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 749 THR Chi-restraints excluded: chain A residue 779 ASP Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 869 ASN Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 921 ILE Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 956 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 180 TYR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 296 TYR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 335 HIS Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 358 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 121 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 6 optimal weight: 0.0670 chunk 83 optimal weight: 0.0470 chunk 53 optimal weight: 10.0000 chunk 85 optimal weight: 0.5980 chunk 88 optimal weight: 0.5980 chunk 37 optimal weight: 0.3980 chunk 14 optimal weight: 20.0000 overall best weight: 0.3416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 972 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.219963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.146439 restraints weight = 14349.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.137178 restraints weight = 9591.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.137903 restraints weight = 7963.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.139166 restraints weight = 6885.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.139330 restraints weight = 6014.086| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 10264 Z= 0.110 Angle : 0.612 11.190 13937 Z= 0.299 Chirality : 0.043 0.190 1636 Planarity : 0.004 0.056 1756 Dihedral : 9.685 104.196 1576 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.52 % Favored : 95.40 % Rotamer: Outliers : 3.62 % Allowed : 19.62 % Favored : 76.76 % 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 (0.25), residues: 1261 helix: 1.40 (0.25), residues: 480 sheet: -0.36 (0.36), residues: 220 loop : -0.84 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 180 TYR 0.027 0.001 TYR B 180 PHE 0.010 0.001 PHE A 86 TRP 0.017 0.001 TRP B 183 HIS 0.005 0.001 HIS B 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (10255) covalent geometry : angle 0.60111 / 0.30 (13913) SS BOND : bond 0.00439 / 0.25 ( 3) SS BOND : angle 0.34378 / 0.18 ( 6) hydrogen bonds : bond 0.04266 / 2.85 ( 436) hydrogen bonds : angle 4.53928 / 3.31 ( 1269) link_NAG-ASN : bond 0.00223 / 0.14 ( 6) link_NAG-ASN : angle 3.20287 / 1.92 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 106 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7159 (tt) REVERT: A 370 TYR cc_start: 0.7387 (t80) cc_final: 0.7171 (t80) REVERT: A 503 TYR cc_start: 0.6094 (OUTLIER) cc_final: 0.5562 (m-80) REVERT: A 611 MET cc_start: 0.8125 (tmm) cc_final: 0.7896 (tmm) REVERT: A 1038 THR cc_start: 0.9102 (OUTLIER) cc_final: 0.8766 (m) REVERT: B 202 TYR cc_start: 0.8303 (t80) cc_final: 0.7951 (t80) REVERT: B 206 LYS cc_start: 0.7841 (mmmt) cc_final: 0.7375 (mtpt) REVERT: B 296 TYR cc_start: 0.8698 (OUTLIER) cc_final: 0.7958 (t80) outliers start: 40 outliers final: 27 residues processed: 140 average time/residue: 0.0926 time to fit residues: 19.0303 Evaluate side-chains 131 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 552 TYR Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 921 ILE Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 180 TYR Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 296 TYR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 335 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 74 optimal weight: 0.2980 chunk 44 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 752 HIS ** A 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.216748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.153615 restraints weight = 14242.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.135111 restraints weight = 18028.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.132693 restraints weight = 12707.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.132563 restraints weight = 9175.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.132804 restraints weight = 8311.326| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10264 Z= 0.152 Angle : 0.627 10.662 13937 Z= 0.308 Chirality : 0.044 0.191 1636 Planarity : 0.004 0.056 1756 Dihedral : 9.404 107.519 1567 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.23 % Favored : 94.69 % Rotamer: Outliers : 3.53 % Allowed : 19.62 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.24), residues: 1261 helix: 1.19 (0.24), residues: 485 sheet: -0.38 (0.36), residues: 220 loop : -0.81 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 180 TYR 0.031 0.001 TYR B 180 PHE 0.009 0.001 PHE A 86 TRP 0.007 0.001 TRP B 183 HIS 0.005 0.001 HIS B 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (10255) covalent geometry : angle 0.61791 / 0.31 (13913) SS BOND : bond 0.00393 / 0.23 ( 3) SS BOND : angle 0.42654 / 0.21 ( 6) hydrogen bonds : bond 0.05256 / 3.51 ( 436) hydrogen bonds : angle 4.66012 / 3.39 ( 1269) link_NAG-ASN : bond 0.00262 / 0.15 ( 6) link_NAG-ASN : angle 2.98167 / 1.78 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 100 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7184 (tt) REVERT: A 503 TYR cc_start: 0.6211 (OUTLIER) cc_final: 0.5759 (m-80) REVERT: A 911 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7740 (mp) REVERT: A 1038 THR cc_start: 0.9121 (OUTLIER) cc_final: 0.8782 (m) REVERT: B 202 TYR cc_start: 0.8319 (t80) cc_final: 0.7929 (t80) REVERT: B 206 LYS cc_start: 0.7988 (mmmt) cc_final: 0.7340 (mtpt) REVERT: B 296 TYR cc_start: 0.8782 (OUTLIER) cc_final: 0.7905 (t80) outliers start: 39 outliers final: 33 residues processed: 133 average time/residue: 0.0946 time to fit residues: 18.4210 Evaluate side-chains 133 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 95 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 552 TYR Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 921 ILE Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 180 TYR Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 296 TYR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 335 HIS Chi-restraints excluded: chain B residue 358 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 98 optimal weight: 0.0030 chunk 39 optimal weight: 6.9990 chunk 105 optimal weight: 20.0000 chunk 108 optimal weight: 10.0000 chunk 75 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 101 optimal weight: 20.0000 chunk 97 optimal weight: 9.9990 chunk 121 optimal weight: 0.6980 chunk 53 optimal weight: 0.1980 chunk 85 optimal weight: 0.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.219398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.143211 restraints weight = 14390.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.135267 restraints weight = 10235.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.136560 restraints weight = 7846.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.137562 restraints weight = 6584.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.137859 restraints weight = 5932.396| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 10264 Z= 0.111 Angle : 0.614 11.266 13937 Z= 0.299 Chirality : 0.042 0.210 1636 Planarity : 0.004 0.056 1756 Dihedral : 8.992 104.830 1567 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.76 % Favored : 95.16 % Rotamer: Outliers : 3.07 % Allowed : 20.34 % Favored : 76.58 % 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 (0.25), residues: 1261 helix: 1.43 (0.25), residues: 483 sheet: -0.36 (0.38), residues: 207 loop : -0.78 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 180 TYR 0.032 0.001 TYR B 180 PHE 0.010 0.001 PHE A 86 TRP 0.011 0.001 TRP A1019 HIS 0.005 0.001 HIS B 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (10255) covalent geometry : angle 0.60531 / 0.30 (13913) SS BOND : bond 0.00443 / 0.25 ( 3) SS BOND : angle 0.37130 / 0.18 ( 6) hydrogen bonds : bond 0.04391 / 2.94 ( 436) hydrogen bonds : angle 4.52414 / 3.29 ( 1269) link_NAG-ASN : bond 0.00273 / 0.17 ( 6) link_NAG-ASN : angle 2.91673 / 1.74 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7209 (tt) REVERT: A 370 TYR cc_start: 0.7373 (t80) cc_final: 0.7122 (t80) REVERT: A 503 TYR cc_start: 0.6168 (OUTLIER) cc_final: 0.5699 (m-80) REVERT: A 611 MET cc_start: 0.8188 (tmm) cc_final: 0.7936 (tmm) REVERT: A 1038 THR cc_start: 0.9107 (OUTLIER) cc_final: 0.8761 (m) REVERT: B 202 TYR cc_start: 0.8315 (t80) cc_final: 0.7910 (t80) REVERT: B 205 ASN cc_start: 0.7842 (m110) cc_final: 0.7577 (p0) REVERT: B 206 LYS cc_start: 0.7979 (mmmt) cc_final: 0.7235 (mmmt) REVERT: B 296 TYR cc_start: 0.8756 (OUTLIER) cc_final: 0.7850 (t80) outliers start: 34 outliers final: 27 residues processed: 130 average time/residue: 0.0843 time to fit residues: 16.4417 Evaluate side-chains 131 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 552 TYR Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 921 ILE Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 180 TYR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 296 TYR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 335 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 25 optimal weight: 0.9990 chunk 110 optimal weight: 7.9990 chunk 67 optimal weight: 0.0270 chunk 54 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 220 HIS ** 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 = 0.4615 r_free = 0.4615 target = 0.214151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.136656 restraints weight = 14251.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.126151 restraints weight = 10581.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.127358 restraints weight = 9224.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.128168 restraints weight = 8156.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.128060 restraints weight = 7859.911| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 10264 Z= 0.244 Angle : 0.692 11.032 13937 Z= 0.346 Chirality : 0.046 0.171 1636 Planarity : 0.004 0.058 1756 Dihedral : 9.322 112.668 1567 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.31 % Favored : 94.53 % Rotamer: Outliers : 3.35 % Allowed : 19.89 % Favored : 76.76 % 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: -0.22 (0.24), residues: 1261 helix: 0.83 (0.24), residues: 491 sheet: -0.43 (0.36), residues: 219 loop : -0.85 (0.27), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 180 TYR 0.030 0.001 TYR B 180 PHE 0.012 0.001 PHE A 849 TRP 0.010 0.001 TRP A 867 HIS 0.005 0.001 HIS B 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00599 / 0.24 (10255) covalent geometry : angle 0.68389 / 0.34 (13913) SS BOND : bond 0.00435 / 0.25 ( 3) SS BOND : angle 0.51990 / 0.25 ( 6) hydrogen bonds : bond 0.06460 / 4.30 ( 436) hydrogen bonds : angle 4.85015 / 3.53 ( 1269) link_NAG-ASN : bond 0.00218 / 0.14 ( 6) link_NAG-ASN : angle 3.07013 / 1.82 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 97 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7212 (tt) REVERT: A 503 TYR cc_start: 0.6171 (OUTLIER) cc_final: 0.5796 (m-80) REVERT: A 619 MET cc_start: 0.8057 (mmt) cc_final: 0.7772 (mmm) REVERT: A 1038 THR cc_start: 0.9156 (OUTLIER) cc_final: 0.8804 (m) REVERT: B 202 TYR cc_start: 0.8393 (t80) cc_final: 0.8001 (t80) REVERT: B 206 LYS cc_start: 0.7920 (mmmt) cc_final: 0.7232 (mmmt) REVERT: B 296 TYR cc_start: 0.8864 (OUTLIER) cc_final: 0.7904 (t80) outliers start: 37 outliers final: 31 residues processed: 129 average time/residue: 0.0905 time to fit residues: 17.2388 Evaluate side-chains 131 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 96 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 552 TYR Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 921 ILE Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 180 TYR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 296 TYR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 335 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 56 optimal weight: 0.0980 chunk 104 optimal weight: 30.0000 chunk 30 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 24 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 778 ASN ** A 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.218052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.143884 restraints weight = 14415.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.134090 restraints weight = 10268.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.135198 restraints weight = 8765.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.136174 restraints weight = 7368.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.136495 restraints weight = 6631.175| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10264 Z= 0.126 Angle : 0.629 10.812 13937 Z= 0.309 Chirality : 0.043 0.214 1636 Planarity : 0.004 0.058 1756 Dihedral : 8.841 105.290 1566 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.76 % Favored : 95.16 % Rotamer: Outliers : 3.25 % Allowed : 20.52 % Favored : 76.22 % 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: 0.07 (0.24), residues: 1261 helix: 1.28 (0.24), residues: 484 sheet: -0.44 (0.38), residues: 207 loop : -0.80 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 180 TYR 0.030 0.001 TYR B 180 PHE 0.009 0.001 PHE A 86 TRP 0.009 0.001 TRP A 822 HIS 0.004 0.001 HIS B 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (10255) covalent geometry : angle 0.62023 / 0.31 (13913) SS BOND : bond 0.00440 / 0.25 ( 3) SS BOND : angle 0.37169 / 0.19 ( 6) hydrogen bonds : bond 0.04905 / 3.28 ( 436) hydrogen bonds : angle 4.56459 / 3.31 ( 1269) link_NAG-ASN : bond 0.00212 / 0.13 ( 6) link_NAG-ASN : angle 2.92114 / 1.74 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2226.62 seconds wall clock time: 39 minutes 2.53 seconds (2342.53 seconds total)