Starting phenix.real_space_refine on Sat Sep 12 14:32:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lqp_63300/09_2026/9lqp_63300.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lqp_63300/09_2026/9lqp_63300.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lqp_63300/09_2026/9lqp_63300.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lqp_63300/09_2026/9lqp_63300.map" model { file = "/net/cci-nas-00/data/ceres_data/9lqp_63300/09_2026/9lqp_63300.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lqp_63300/09_2026/9lqp_63300.cif" } resolution = 3.4 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= -0.001 sd= 0.097 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 Zn 2 6.06 5 P 96 5.49 5 S 104 5.16 5 C 9844 2.51 5 N 2779 2.21 5 O 3179 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16004 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 543, 4364 Classifications: {'peptide': 543} Link IDs: {'PTRANS': 25, 'TRANS': 517} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2616 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 18, 'TRANS': 314} Chain breaks: 2 Chain: "C" Number of atoms: 4373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4373 Classifications: {'peptide': 544} Link IDs: {'PTRANS': 25, 'TRANS': 518} Chain: "D" Number of atoms: 2648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2648 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 19, 'TRANS': 318} Chain breaks: 1 Chain: "I" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 444 Inner-chain residues flagged as termini: ['pdbres=" DT I 33 "'] Classifications: {'DNA': 22} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 21} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "J" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 450 Inner-chain residues flagged as termini: ['pdbres=" DA J 33 "'] Classifications: {'DNA': 22} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 21} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "x" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 301 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "M" Number of atoms: 314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 314 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "y" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 243 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "L" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 249 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2074 SG CYS A 727 76.624 100.158 44.867 1.00 33.27 S ATOM 2095 SG CYS A 730 79.282 102.267 43.200 1.00 31.72 S ATOM 9054 SG CYS C 727 26.576 56.816 40.700 1.00 45.93 S ATOM 9075 SG CYS C 730 25.339 53.548 39.898 1.00 37.09 S Time building chain proxies: 3.40, per 1000 atoms: 0.21 Number of scatterers: 16004 At special positions: 0 Unit cell: (104.5, 152.9, 106.7, 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) Zn 2 29.99 S 104 16.00 P 96 15.00 O 3179 8.00 N 2779 7.00 C 9844 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 514.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 937 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 942 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 730 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 727 " pdb=" ZN C1101 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 730 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 937 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 942 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 727 " Number of angles added : 4 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3290 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 24 sheets defined 35.5% alpha, 16.2% beta 45 base pairs and 77 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'A' and resid 466 through 474 removed outlier: 3.532A pdb=" N THR A 474 " --> pdb=" O ILE A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 493 Processing helix chain 'A' and resid 499 through 511 removed outlier: 3.696A pdb=" N LYS A 508 " --> pdb=" O ARG A 504 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL A 509 " --> pdb=" O ASN A 505 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU A 510 " --> pdb=" O ALA A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 570 removed outlier: 4.064A pdb=" N LEU A 563 " --> pdb=" O TYR A 559 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL A 564 " --> pdb=" O ASP A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 581 Processing helix chain 'A' and resid 666 through 683 Proline residue: A 674 - end of helix Processing helix chain 'A' and resid 711 through 716 Processing helix chain 'A' and resid 733 through 741 Processing helix chain 'A' and resid 749 through 763 Processing helix chain 'A' and resid 764 through 767 removed outlier: 4.286A pdb=" N GLU A 767 " --> pdb=" O PRO A 764 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 764 through 767' Processing helix chain 'A' and resid 769 through 776 Processing helix chain 'A' and resid 792 through 813 Processing helix chain 'A' and resid 822 through 842 removed outlier: 3.708A pdb=" N ARG A 826 " --> pdb=" O SER A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 858 Processing helix chain 'A' and resid 859 through 868 Processing helix chain 'A' and resid 872 through 895 Proline residue: A 891 - end of helix Processing helix chain 'A' and resid 897 through 902 Processing helix chain 'A' and resid 902 through 924 removed outlier: 4.837A pdb=" N SER A 910 " --> pdb=" O LEU A 906 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N PHE A 911 " --> pdb=" O CYS A 907 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN A 914 " --> pdb=" O SER A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 942 Processing helix chain 'A' and resid 942 through 951 Processing helix chain 'A' and resid 953 through 957 removed outlier: 4.104A pdb=" N ALA A 957 " --> pdb=" O GLY A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 975 removed outlier: 3.829A pdb=" N LYS A 966 " --> pdb=" O ASN A 962 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 967 " --> pdb=" O SER A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 996 Processing helix chain 'A' and resid 996 through 1003 removed outlier: 3.911A pdb=" N PHE A1002 " --> pdb=" O TYR A 998 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET A1003 " --> pdb=" O LEU A 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 314 Processing helix chain 'C' and resid 463 through 474 removed outlier: 3.502A pdb=" N THR C 474 " --> pdb=" O ILE C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 493 Processing helix chain 'C' and resid 499 through 511 removed outlier: 4.059A pdb=" N ASN C 505 " --> pdb=" O HIS C 501 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA C 506 " --> pdb=" O ALA C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 570 Processing helix chain 'C' and resid 571 through 581 Processing helix chain 'C' and resid 664 through 683 removed outlier: 3.632A pdb=" N THR C 669 " --> pdb=" O HIS C 665 " (cutoff:3.500A) Proline residue: C 674 - end of helix Processing helix chain 'C' and resid 708 through 717 Processing helix chain 'C' and resid 733 through 741 Processing helix chain 'C' and resid 749 through 763 Processing helix chain 'C' and resid 768 through 776 removed outlier: 4.128A pdb=" N ASP C 774 " --> pdb=" O GLU C 770 " (cutoff:3.500A) Processing helix chain 'C' and resid 792 through 813 removed outlier: 3.570A pdb=" N GLY C 813 " --> pdb=" O GLN C 809 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 842 removed outlier: 3.781A pdb=" N GLN C 830 " --> pdb=" O ARG C 826 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA C 831 " --> pdb=" O LYS C 827 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS C 836 " --> pdb=" O THR C 832 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN C 842 " --> pdb=" O ARG C 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 858 Processing helix chain 'C' and resid 859 through 867 removed outlier: 3.739A pdb=" N VAL C 863 " --> pdb=" O THR C 859 " (cutoff:3.500A) Processing helix chain 'C' and resid 873 through 895 removed outlier: 3.771A pdb=" N GLU C 877 " --> pdb=" O GLU C 873 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA C 878 " --> pdb=" O GLU C 874 " (cutoff:3.500A) Proline residue: C 891 - end of helix Processing helix chain 'C' and resid 897 through 902 Processing helix chain 'C' and resid 902 through 908 Processing helix chain 'C' and resid 909 through 923 Processing helix chain 'C' and resid 933 through 942 removed outlier: 3.534A pdb=" N THR C 939 " --> pdb=" O TYR C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 951 Processing helix chain 'C' and resid 953 through 957 Processing helix chain 'C' and resid 960 through 975 Processing helix chain 'C' and resid 982 through 995 Processing helix chain 'C' and resid 1000 through 1004 removed outlier: 3.562A pdb=" N ASN C1004 " --> pdb=" O LYS C1001 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 172 removed outlier: 3.687A pdb=" N TRP D 172 " --> pdb=" O THR D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 313 Processing sheet with id=AA1, first strand: chain 'A' and resid 518 through 519 removed outlier: 3.629A pdb=" N GLU A 518 " --> pdb=" O THR A 688 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 534 through 536 Processing sheet with id=AA3, first strand: chain 'A' and resid 653 through 654 removed outlier: 3.999A pdb=" N ARG A 621 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP A 600 " --> pdb=" O ARG A 621 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL A 595 " --> pdb=" O ARG A 703 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N THR A 705 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLU A 597 " --> pdb=" O THR A 705 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 628 through 632 removed outlier: 6.650A pdb=" N ILE A 629 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A 631 " --> pdb=" O VAL A 638 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 20 through 24 removed outlier: 5.178A pdb=" N VAL B 28 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP B 49 " --> pdb=" O LYS B 56 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N LEU B 55 " --> pdb=" O MET B 5 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N THR B 7 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N LEU B 57 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER B 2 " --> pdb=" O ARG B 343 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N PHE B 339 " --> pdb=" O VAL B 6 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR B 340 " --> pdb=" O LEU B 329 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 61 through 62 removed outlier: 7.419A pdb=" N ILE B 61 " --> pdb=" O PHE B 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 76 through 80 removed outlier: 3.569A pdb=" N ILE B 107 " --> pdb=" O LYS B 127 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 153 through 154 Processing sheet with id=AA9, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AB1, first strand: chain 'B' and resid 204 through 205 Processing sheet with id=AB2, first strand: chain 'B' and resid 208 through 212 removed outlier: 3.606A pdb=" N THR B 215 " --> pdb=" O ARG B 212 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG B 237 " --> pdb=" O ASN B 248 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN B 248 " --> pdb=" O ARG B 237 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 208 through 212 removed outlier: 3.606A pdb=" N THR B 215 " --> pdb=" O ARG B 212 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU B 233 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 262 through 264 removed outlier: 3.557A pdb=" N VAL B 274 " --> pdb=" O ILE B 262 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 288 through 290 Processing sheet with id=AB6, first strand: chain 'C' and resid 518 through 519 Processing sheet with id=AB7, first strand: chain 'C' and resid 534 through 536 removed outlier: 7.028A pdb=" N LEU C 655 " --> pdb=" O PHE C 557 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N PHE C 624 " --> pdb=" O PRO C 654 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N MET C 627 " --> pdb=" O GLU C 642 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N GLU C 642 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE C 629 " --> pdb=" O VAL C 640 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE C 631 " --> pdb=" O VAL C 638 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 534 through 536 removed outlier: 7.028A pdb=" N LEU C 655 " --> pdb=" O PHE C 557 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N PHE C 624 " --> pdb=" O PRO C 654 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N VAL C 620 " --> pdb=" O MET C 602 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N MET C 602 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N PHE C 622 " --> pdb=" O ASP C 600 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ASP C 600 " --> pdb=" O PHE C 622 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N PHE C 624 " --> pdb=" O SER C 598 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N SER C 598 " --> pdb=" O PHE C 624 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N VAL C 626 " --> pdb=" O LYS C 596 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LYS C 596 " --> pdb=" O VAL C 626 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG C 628 " --> pdb=" O VAL C 594 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 48 through 50 removed outlier: 7.462A pdb=" N LEU D 55 " --> pdb=" O MET D 5 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N THR D 7 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N LEU D 57 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE D 339 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL D 8 " --> pdb=" O PHE D 337 " (cutoff:3.500A) removed outlier: 9.402A pdb=" N PHE D 337 " --> pdb=" O VAL D 8 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 20 through 24 Processing sheet with id=AC2, first strand: chain 'D' and resid 61 through 62 removed outlier: 7.499A pdb=" N ILE D 61 " --> pdb=" O PHE D 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'D' and resid 76 through 79 removed outlier: 3.520A pdb=" N CYS D 78 " --> pdb=" O ILE D 92 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 130 through 131 removed outlier: 6.118A pdb=" N VAL D 130 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N SER D 194 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE D 156 " --> pdb=" O SER D 141 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER D 141 " --> pdb=" O PHE D 156 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 208 through 211 removed outlier: 4.001A pdb=" N ASP D 239 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ALA D 246 " --> pdb=" O ASP D 239 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 270 through 272 553 hydrogen bonds defined for protein. 1551 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 108 hydrogen bonds 216 hydrogen bond angles 0 basepair planarities 45 basepair parallelities 77 stacking parallelities Total time for adding SS restraints: 3.41 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4190 1.33 - 1.45: 3453 1.45 - 1.57: 8576 1.57 - 1.69: 186 1.69 - 1.81: 160 Bond restraints: 16565 Sorted by residual: bond pdb=" C GLN A 914 " pdb=" N ARG A 915 " ideal model delta sigma weight residual 1.335 1.382 -0.047 1.31e-02 5.83e+03 1.27e+01 bond pdb=" C3' DA I 19 " pdb=" O3' DA I 19 " ideal model delta sigma weight residual 1.435 1.479 -0.044 1.30e-02 5.92e+03 1.15e+01 bond pdb=" C PHE A 641 " pdb=" N GLU A 642 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.32e-02 5.74e+03 1.10e+01 bond pdb=" C3' DC x 35 " pdb=" C2' DC x 35 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DC y 24 " pdb=" C2' DC y 24 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 ... (remaining 16560 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 21452 1.26 - 2.52: 1071 2.52 - 3.78: 219 3.78 - 5.05: 37 5.05 - 6.31: 13 Bond angle restraints: 22792 Sorted by residual: angle pdb=" O4' DT y 33 " pdb=" C4' DT y 33 " pdb=" C3' DT y 33 " ideal model delta sigma weight residual 106.00 103.11 2.89 6.00e-01 2.78e+00 2.32e+01 angle pdb=" N3 DT x 42 " pdb=" C4 DT x 42 " pdb=" O4 DT x 42 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.01e+01 angle pdb=" N3 DT y 31 " pdb=" C4 DT y 31 " pdb=" O4 DT y 31 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 1.99e+01 angle pdb=" N3 DT I 18 " pdb=" C4 DT I 18 " pdb=" O4 DT I 18 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" N3 DT x 44 " pdb=" C4 DT x 44 " pdb=" O4 DT x 44 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 ... (remaining 22787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.66: 9094 31.66 - 63.33: 604 63.33 - 94.99: 17 94.99 - 126.65: 0 126.65 - 158.32: 6 Dihedral angle restraints: 9721 sinusoidal: 4612 harmonic: 5109 Sorted by residual: dihedral pdb=" CA GLU A 709 " pdb=" C GLU A 709 " pdb=" N LYS A 710 " pdb=" CA LYS A 710 " ideal model delta harmonic sigma weight residual 180.00 159.10 20.90 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA ALA A 941 " pdb=" C ALA A 941 " pdb=" N HIS A 942 " pdb=" CA HIS A 942 " ideal model delta harmonic sigma weight residual -180.00 -159.40 -20.60 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA ARG D 137 " pdb=" C ARG D 137 " pdb=" N TYR D 138 " pdb=" CA TYR D 138 " ideal model delta harmonic sigma weight residual -180.00 -160.06 -19.94 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 9718 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1723 0.041 - 0.082: 545 0.082 - 0.123: 200 0.123 - 0.164: 18 0.164 - 0.205: 3 Chirality restraints: 2489 Sorted by residual: chirality pdb=" C3' DA J 34 " pdb=" C4' DA J 34 " pdb=" O3' DA J 34 " pdb=" C2' DA J 34 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB ILE D 273 " pdb=" CA ILE D 273 " pdb=" CG1 ILE D 273 " pdb=" CG2 ILE D 273 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.17 2.00e-01 2.50e+01 7.30e-01 chirality pdb=" C3' DT y 31 " pdb=" C4' DT y 31 " pdb=" O3' DT y 31 " pdb=" C2' DT y 31 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.26e-01 ... (remaining 2486 not shown) Planarity restraints: 2594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 317 " 0.021 2.00e-02 2.50e+03 1.78e-02 7.94e+00 pdb=" CG TRP D 317 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP D 317 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP D 317 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 317 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP D 317 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 317 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 317 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 317 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 317 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA J 39 " -0.025 2.00e-02 2.50e+03 1.36e-02 5.11e+00 pdb=" N9 DA J 39 " 0.035 2.00e-02 2.50e+03 pdb=" C8 DA J 39 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DA J 39 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DA J 39 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DA J 39 " -0.004 2.00e-02 2.50e+03 pdb=" N6 DA J 39 " 0.001 2.00e-02 2.50e+03 pdb=" N1 DA J 39 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA J 39 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DA J 39 " 0.009 2.00e-02 2.50e+03 pdb=" C4 DA J 39 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 240 " -0.030 5.00e-02 4.00e+02 4.64e-02 3.45e+00 pdb=" N PRO D 241 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO D 241 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 241 " -0.026 5.00e-02 4.00e+02 ... (remaining 2591 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 836 2.73 - 3.27: 15187 3.27 - 3.81: 25913 3.81 - 4.36: 31481 4.36 - 4.90: 54252 Nonbonded interactions: 127669 Sorted by model distance: nonbonded pdb=" O ASP A 774 " pdb=" OD1 ASP A 774 " model vdw 2.185 3.040 nonbonded pdb=" O TYR A 559 " pdb=" CD1 TYR A 559 " model vdw 2.277 3.340 nonbonded pdb=" O TYR D 80 " pdb=" CD1 TYR D 80 " model vdw 2.301 3.340 nonbonded pdb=" O TRP D 317 " pdb=" CD1 TRP D 317 " model vdw 2.449 3.260 nonbonded pdb=" O TRP B 317 " pdb=" CD1 TRP B 317 " model vdw 2.464 3.260 ... (remaining 127664 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and (resid 461 through 968 or (resid 969 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name NE or name CZ or name NH \ 2)) or resid 970 through 1003 or resid 1101)) } ncs_group { reference = chain 'B' selection = (chain 'D' and (resid 1 through 241 or resid 246 through 344)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.750 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: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.750 Find NCS groups from input model: 0.180 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 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 : 0.005 0.221 16573 Z= 0.304 Angle : 0.661 12.729 22796 Z= 0.450 Chirality : 0.045 0.205 2489 Planarity : 0.004 0.046 2594 Dihedral : 18.594 158.315 6431 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.45 % Favored : 92.49 % Rotamer: Outliers : 0.06 % Allowed : 0.90 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.95 (0.21), residues: 1744 helix: 1.08 (0.23), residues: 548 sheet: -1.20 (0.31), residues: 337 loop : -1.54 (0.22), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 894 TYR 0.020 0.002 TYR C 757 PHE 0.025 0.001 PHE D 48 TRP 0.047 0.001 TRP D 317 HIS 0.008 0.001 HIS B 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.30 (16565) covalent geometry : angle 0.65248 / 0.45 (22792) hydrogen bonds : bond 0.15604 / 10.99 ( 643) hydrogen bonds : angle 7.40449 / 5.28 ( 1767) metal coordination : bond 0.13797 / 9.87 ( 8) metal coordination : angle 8.17801 / 3.79 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 209 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 571 GLU cc_start: 0.7612 (tm-30) cc_final: 0.7205 (pt0) REVERT: A 709 GLU cc_start: 0.8391 (tt0) cc_final: 0.8137 (tt0) REVERT: A 754 LEU cc_start: 0.8408 (tt) cc_final: 0.8147 (mt) REVERT: A 828 ARG cc_start: 0.7926 (tpp80) cc_final: 0.7605 (ttm-80) REVERT: B 197 LEU cc_start: 0.8558 (mt) cc_final: 0.8312 (mp) REVERT: C 534 ILE cc_start: 0.8727 (mt) cc_final: 0.8444 (tt) REVERT: C 786 GLU cc_start: 0.7934 (tt0) cc_final: 0.7618 (pm20) REVERT: C 823 LYS cc_start: 0.8377 (mmmt) cc_final: 0.8030 (tptt) REVERT: C 858 MET cc_start: 0.8668 (mmp) cc_final: 0.8149 (mmm) outliers start: 1 outliers final: 1 residues processed: 209 average time/residue: 0.1235 time to fit residues: 38.7018 Evaluate side-chains 144 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 143 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 80 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 473 ASN A 818 HIS B 23 ASN B 47 HIS B 268 ASN B 281 ASN C 515 HIS ** C 937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 4 GLN D 232 ASN D 265 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.135113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.109176 restraints weight = 23680.244| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.00 r_work: 0.3217 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16573 Z= 0.157 Angle : 0.611 11.198 22796 Z= 0.334 Chirality : 0.045 0.318 2489 Planarity : 0.004 0.040 2594 Dihedral : 21.172 159.754 2982 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.34 % Favored : 92.55 % Rotamer: Outliers : 1.16 % Allowed : 7.20 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.86 (0.21), residues: 1744 helix: 1.19 (0.23), residues: 552 sheet: -1.06 (0.29), residues: 360 loop : -1.56 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 828 TYR 0.017 0.002 TYR C 757 PHE 0.014 0.001 PHE D 189 TRP 0.013 0.001 TRP D 317 HIS 0.007 0.001 HIS B 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 (16565) covalent geometry : angle 0.60291 / 0.33 (22792) hydrogen bonds : bond 0.04610 / 3.10 ( 643) hydrogen bonds : angle 5.57765 / 3.93 ( 1767) metal coordination : bond 0.01986 / 1.50 ( 8) metal coordination : angle 7.36939 / 3.64 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 571 GLU cc_start: 0.7787 (tm-30) cc_final: 0.6972 (pt0) REVERT: A 709 GLU cc_start: 0.8391 (tt0) cc_final: 0.8103 (tt0) REVERT: B 197 LEU cc_start: 0.8617 (mt) cc_final: 0.8338 (mp) REVERT: B 269 ASP cc_start: 0.7850 (t0) cc_final: 0.7518 (t0) REVERT: C 508 LYS cc_start: 0.8079 (mmtm) cc_final: 0.7808 (mmtt) REVERT: C 534 ILE cc_start: 0.9009 (mt) cc_final: 0.8704 (tt) REVERT: C 786 GLU cc_start: 0.8253 (tt0) cc_final: 0.7568 (pm20) REVERT: D 232 ASN cc_start: 0.6704 (OUTLIER) cc_final: 0.6391 (p0) outliers start: 18 outliers final: 13 residues processed: 159 average time/residue: 0.1040 time to fit residues: 25.8392 Evaluate side-chains 142 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 765 TYR Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 249 CYS Chi-restraints excluded: chain C residue 841 MET Chi-restraints excluded: chain D residue 4 GLN Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 138 TYR Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 250 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 82 optimal weight: 10.0000 chunk 44 optimal weight: 0.3980 chunk 36 optimal weight: 0.0870 chunk 175 optimal weight: 9.9990 chunk 136 optimal weight: 0.2980 chunk 166 optimal weight: 0.8980 chunk 116 optimal weight: 0.8980 chunk 162 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 177 optimal weight: 9.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 818 HIS B 47 HIS C 912 ASN ** C 937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.136126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.110146 restraints weight = 23911.769| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.02 r_work: 0.3233 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16573 Z= 0.128 Angle : 0.567 9.260 22796 Z= 0.312 Chirality : 0.043 0.320 2489 Planarity : 0.004 0.038 2594 Dihedral : 21.150 161.348 2982 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.22 % Favored : 92.72 % Rotamer: Outliers : 1.41 % Allowed : 8.42 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.74 (0.21), residues: 1744 helix: 1.32 (0.23), residues: 552 sheet: -0.96 (0.29), residues: 358 loop : -1.53 (0.23), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 828 TYR 0.018 0.001 TYR B 338 PHE 0.019 0.001 PHE D 187 TRP 0.011 0.001 TRP D 317 HIS 0.007 0.001 HIS B 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.13 (16565) covalent geometry : angle 0.56188 / 0.31 (22792) hydrogen bonds : bond 0.03970 / 2.65 ( 643) hydrogen bonds : angle 5.22184 / 3.65 ( 1767) metal coordination : bond 0.02177 / 1.71 ( 8) metal coordination : angle 6.03674 / 2.98 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.631 Fit side-chains revert: symmetry clash REVERT: A 529 ARG cc_start: 0.7984 (mmm-85) cc_final: 0.7781 (mtp85) REVERT: A 709 GLU cc_start: 0.8380 (tt0) cc_final: 0.8107 (tt0) REVERT: B 197 LEU cc_start: 0.8563 (mt) cc_final: 0.8302 (mp) REVERT: B 269 ASP cc_start: 0.7887 (t0) cc_final: 0.7532 (t0) REVERT: C 508 LYS cc_start: 0.8058 (mmtm) cc_final: 0.7783 (mmtt) REVERT: C 534 ILE cc_start: 0.8995 (mt) cc_final: 0.8664 (tt) REVERT: C 786 GLU cc_start: 0.8209 (tt0) cc_final: 0.7505 (pm20) REVERT: D 281 ASN cc_start: 0.8174 (OUTLIER) cc_final: 0.7811 (t0) REVERT: D 282 GLN cc_start: 0.7059 (tm-30) cc_final: 0.6847 (tm-30) outliers start: 22 outliers final: 14 residues processed: 155 average time/residue: 0.1190 time to fit residues: 28.6437 Evaluate side-chains 145 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain A residue 765 TYR Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 249 CYS Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 841 MET Chi-restraints excluded: chain C residue 850 ASN Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 281 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 80 optimal weight: 2.9990 chunk 55 optimal weight: 0.0870 chunk 15 optimal weight: 0.0570 chunk 63 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 129 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 809 GLN C 588 ASN ** C 937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.135754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.109735 restraints weight = 23488.144| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.01 r_work: 0.3233 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16573 Z= 0.121 Angle : 0.549 8.934 22796 Z= 0.302 Chirality : 0.043 0.319 2489 Planarity : 0.004 0.078 2594 Dihedral : 21.138 161.144 2980 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.77 % Favored : 93.12 % Rotamer: Outliers : 1.48 % Allowed : 8.94 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.62 (0.21), residues: 1744 helix: 1.43 (0.23), residues: 549 sheet: -0.87 (0.29), residues: 356 loop : -1.48 (0.22), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 828 TYR 0.020 0.001 TYR A 757 PHE 0.013 0.001 PHE B 189 TRP 0.009 0.001 TRP D 317 HIS 0.007 0.001 HIS A 818 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (16565) covalent geometry : angle 0.54435 / 0.30 (22792) hydrogen bonds : bond 0.03768 / 2.50 ( 643) hydrogen bonds : angle 5.05075 / 3.53 ( 1767) metal coordination : bond 0.01654 / 1.28 ( 8) metal coordination : angle 5.42160 / 2.58 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 0.429 Fit side-chains revert: symmetry clash REVERT: A 529 ARG cc_start: 0.8023 (mmm-85) cc_final: 0.7812 (mtp85) REVERT: A 757 TYR cc_start: 0.8565 (t80) cc_final: 0.7930 (t80) REVERT: B 197 LEU cc_start: 0.8533 (mt) cc_final: 0.8276 (mp) REVERT: B 269 ASP cc_start: 0.7878 (t0) cc_final: 0.7507 (t0) REVERT: C 534 ILE cc_start: 0.8982 (mt) cc_final: 0.8662 (tt) REVERT: C 584 ASP cc_start: 0.7348 (m-30) cc_final: 0.6691 (m-30) REVERT: C 786 GLU cc_start: 0.8216 (tt0) cc_final: 0.7478 (pm20) REVERT: D 282 GLN cc_start: 0.7216 (tm-30) cc_final: 0.6723 (tm-30) outliers start: 23 outliers final: 15 residues processed: 155 average time/residue: 0.1003 time to fit residues: 24.7371 Evaluate side-chains 144 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 249 CYS Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 850 ASN Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 279 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 100 optimal weight: 0.2980 chunk 6 optimal weight: 1.9990 chunk 156 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 165 optimal weight: 0.0970 chunk 80 optimal weight: 0.3980 chunk 146 optimal weight: 0.6980 chunk 133 optimal weight: 2.9990 chunk 95 optimal weight: 0.0000 chunk 61 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 overall best weight: 0.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 818 HIS C 588 ASN ** C 937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.137146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.111130 restraints weight = 23445.797| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.02 r_work: 0.3254 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16573 Z= 0.108 Angle : 0.535 8.911 22796 Z= 0.293 Chirality : 0.042 0.318 2489 Planarity : 0.004 0.061 2594 Dihedral : 21.089 161.493 2980 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.42 % Favored : 93.46 % Rotamer: Outliers : 1.67 % Allowed : 9.97 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.51 (0.21), residues: 1744 helix: 1.53 (0.23), residues: 549 sheet: -0.81 (0.29), residues: 352 loop : -1.41 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 828 TYR 0.018 0.001 TYR B 338 PHE 0.013 0.001 PHE B 183 TRP 0.007 0.001 TRP C 893 HIS 0.005 0.001 HIS B 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.11 (16565) covalent geometry : angle 0.53072 / 0.29 (22792) hydrogen bonds : bond 0.03518 / 2.32 ( 643) hydrogen bonds : angle 4.90733 / 3.42 ( 1767) metal coordination : bond 0.01592 / 1.26 ( 8) metal coordination : angle 5.30672 / 2.55 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 529 ARG cc_start: 0.8055 (mmm-85) cc_final: 0.7848 (mtp85) REVERT: A 598 SER cc_start: 0.8799 (p) cc_final: 0.8471 (p) REVERT: A 757 TYR cc_start: 0.8583 (t80) cc_final: 0.8077 (t80) REVERT: B 197 LEU cc_start: 0.8512 (mt) cc_final: 0.8276 (mp) REVERT: B 233 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.8014 (tp) REVERT: B 269 ASP cc_start: 0.7850 (t0) cc_final: 0.7432 (t0) REVERT: C 534 ILE cc_start: 0.8991 (mt) cc_final: 0.8685 (tt) REVERT: C 584 ASP cc_start: 0.7289 (m-30) cc_final: 0.6712 (m-30) REVERT: C 633 HIS cc_start: 0.7363 (t-90) cc_final: 0.6672 (t70) REVERT: C 786 GLU cc_start: 0.8191 (tt0) cc_final: 0.7690 (pm20) REVERT: C 826 ARG cc_start: 0.8712 (ttm110) cc_final: 0.8165 (mtt90) REVERT: D 281 ASN cc_start: 0.7817 (OUTLIER) cc_final: 0.7540 (t0) REVERT: D 282 GLN cc_start: 0.7031 (tm-30) cc_final: 0.6429 (tm-30) outliers start: 26 outliers final: 14 residues processed: 155 average time/residue: 0.1089 time to fit residues: 26.7498 Evaluate side-chains 146 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 249 CYS Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 281 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 174 optimal weight: 20.0000 chunk 40 optimal weight: 0.0970 chunk 180 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 119 optimal weight: 0.0970 chunk 181 optimal weight: 8.9990 chunk 134 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 121 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 588 ASN ** C 937 HIS ** 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 = 0.3715 r_free = 0.3715 target = 0.136998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.110957 restraints weight = 23682.920| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.01 r_work: 0.3247 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16573 Z= 0.117 Angle : 0.531 8.526 22796 Z= 0.291 Chirality : 0.042 0.319 2489 Planarity : 0.004 0.054 2594 Dihedral : 21.102 161.425 2980 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.59 % Favored : 93.29 % Rotamer: Outliers : 1.86 % Allowed : 9.90 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.47 (0.21), residues: 1744 helix: 1.55 (0.23), residues: 548 sheet: -0.75 (0.30), residues: 344 loop : -1.39 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 828 TYR 0.015 0.001 TYR B 338 PHE 0.013 0.001 PHE B 48 TRP 0.008 0.001 TRP D 307 HIS 0.005 0.001 HIS B 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.12 (16565) covalent geometry : angle 0.52694 / 0.29 (22792) hydrogen bonds : bond 0.03531 / 2.32 ( 643) hydrogen bonds : angle 4.82867 / 3.36 ( 1767) metal coordination : bond 0.01568 / 1.23 ( 8) metal coordination : angle 5.21386 / 2.55 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: A 529 ARG cc_start: 0.8036 (mmm-85) cc_final: 0.7824 (mtp85) REVERT: A 757 TYR cc_start: 0.8578 (t80) cc_final: 0.8163 (t80) REVERT: B 197 LEU cc_start: 0.8322 (mt) cc_final: 0.8075 (mp) REVERT: B 233 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.8029 (tp) REVERT: B 269 ASP cc_start: 0.7936 (t0) cc_final: 0.7538 (t0) REVERT: C 534 ILE cc_start: 0.8970 (mt) cc_final: 0.8662 (tt) REVERT: C 584 ASP cc_start: 0.7282 (m-30) cc_final: 0.6701 (m-30) REVERT: C 633 HIS cc_start: 0.7369 (t-90) cc_final: 0.6699 (t70) REVERT: C 786 GLU cc_start: 0.8212 (tt0) cc_final: 0.7724 (pm20) REVERT: C 826 ARG cc_start: 0.8712 (ttm110) cc_final: 0.8276 (mtt90) REVERT: D 27 GLN cc_start: 0.8670 (mt0) cc_final: 0.8374 (mt0) REVERT: D 282 GLN cc_start: 0.7408 (tm-30) cc_final: 0.6669 (tm-30) outliers start: 29 outliers final: 20 residues processed: 150 average time/residue: 0.1082 time to fit residues: 25.7433 Evaluate side-chains 149 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 249 CYS Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 531 ASP Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 138 TYR Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 279 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 2.9990 chunk 86 optimal weight: 0.3980 chunk 84 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 115 optimal weight: 0.0670 chunk 118 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 588 ASN ** C 937 HIS ** 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 = 0.3708 r_free = 0.3708 target = 0.136492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.110299 restraints weight = 23479.301| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.01 r_work: 0.3238 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16573 Z= 0.123 Angle : 0.538 8.702 22796 Z= 0.293 Chirality : 0.042 0.321 2489 Planarity : 0.004 0.050 2594 Dihedral : 21.118 161.551 2980 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.94 % Favored : 92.95 % Rotamer: Outliers : 1.67 % Allowed : 10.42 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.44 (0.21), residues: 1744 helix: 1.57 (0.23), residues: 548 sheet: -0.70 (0.30), residues: 344 loop : -1.38 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 828 TYR 0.015 0.001 TYR B 338 PHE 0.013 0.001 PHE B 183 TRP 0.008 0.001 TRP D 317 HIS 0.006 0.001 HIS B 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (16565) covalent geometry : angle 0.53319 / 0.29 (22792) hydrogen bonds : bond 0.03561 / 2.34 ( 643) hydrogen bonds : angle 4.76762 / 3.32 ( 1767) metal coordination : bond 0.01596 / 1.24 ( 8) metal coordination : angle 5.44765 / 2.73 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: A 757 TYR cc_start: 0.8671 (t80) cc_final: 0.8308 (t80) REVERT: B 197 LEU cc_start: 0.8307 (mt) cc_final: 0.8067 (mp) REVERT: B 233 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7967 (tp) REVERT: B 269 ASP cc_start: 0.7939 (t0) cc_final: 0.7542 (t0) REVERT: C 534 ILE cc_start: 0.8969 (mt) cc_final: 0.8679 (tt) REVERT: C 584 ASP cc_start: 0.7254 (m-30) cc_final: 0.6678 (m-30) REVERT: C 633 HIS cc_start: 0.7377 (t-90) cc_final: 0.6658 (t70) REVERT: C 786 GLU cc_start: 0.8212 (tt0) cc_final: 0.7740 (pm20) REVERT: D 27 GLN cc_start: 0.8663 (mt0) cc_final: 0.8345 (mt0) outliers start: 26 outliers final: 17 residues processed: 150 average time/residue: 0.1095 time to fit residues: 26.0431 Evaluate side-chains 143 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 249 CYS Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 279 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 95 optimal weight: 0.3980 chunk 84 optimal weight: 1.9990 chunk 67 optimal weight: 0.3980 chunk 119 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 495 GLN C 588 ASN ** C 937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.132530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.105860 restraints weight = 23665.804| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.03 r_work: 0.3168 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16573 Z= 0.190 Angle : 0.609 9.985 22796 Z= 0.328 Chirality : 0.045 0.321 2489 Planarity : 0.004 0.047 2594 Dihedral : 21.325 161.432 2980 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.40 % Favored : 92.55 % Rotamer: Outliers : 1.74 % Allowed : 11.00 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.62 (0.21), residues: 1744 helix: 1.41 (0.23), residues: 548 sheet: -0.75 (0.30), residues: 341 loop : -1.51 (0.22), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 826 TYR 0.019 0.002 TYR A 725 PHE 0.015 0.002 PHE B 48 TRP 0.013 0.001 TRP D 317 HIS 0.010 0.001 HIS B 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 (16565) covalent geometry : angle 0.60081 / 0.33 (22792) hydrogen bonds : bond 0.04273 / 2.81 ( 643) hydrogen bonds : angle 4.82804 / 3.38 ( 1767) metal coordination : bond 0.02030 / 1.53 ( 8) metal coordination : angle 7.43527 / 3.99 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: B 197 LEU cc_start: 0.8506 (mt) cc_final: 0.8222 (mp) REVERT: B 233 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7971 (tp) REVERT: B 269 ASP cc_start: 0.7985 (t0) cc_final: 0.7622 (t0) REVERT: C 534 ILE cc_start: 0.8957 (mt) cc_final: 0.8720 (tt) REVERT: C 786 GLU cc_start: 0.8300 (tt0) cc_final: 0.7777 (pm20) outliers start: 27 outliers final: 18 residues processed: 144 average time/residue: 0.1146 time to fit residues: 26.1206 Evaluate side-chains 140 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 765 TYR Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 249 CYS Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 531 ASP Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 146 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 99 optimal weight: 0.0970 chunk 72 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 179 optimal weight: 7.9990 chunk 53 optimal weight: 0.3980 chunk 59 optimal weight: 0.9980 chunk 98 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 151 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 818 HIS C 588 ASN ** C 937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.135059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.108821 restraints weight = 23505.702| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.98 r_work: 0.3211 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16573 Z= 0.124 Angle : 0.552 9.404 22796 Z= 0.299 Chirality : 0.043 0.325 2489 Planarity : 0.004 0.044 2594 Dihedral : 21.175 162.446 2980 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.25 % Favored : 93.69 % Rotamer: Outliers : 1.29 % Allowed : 12.03 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.52 (0.21), residues: 1744 helix: 1.51 (0.23), residues: 549 sheet: -0.79 (0.30), residues: 356 loop : -1.42 (0.22), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 826 TYR 0.018 0.001 TYR B 338 PHE 0.014 0.001 PHE B 189 TRP 0.011 0.001 TRP C 893 HIS 0.013 0.001 HIS C 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (16565) covalent geometry : angle 0.54686 / 0.30 (22792) hydrogen bonds : bond 0.03602 / 2.38 ( 643) hydrogen bonds : angle 4.73338 / 3.31 ( 1767) metal coordination : bond 0.01784 / 1.39 ( 8) metal coordination : angle 5.91388 / 2.94 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.570 Fit side-chains revert: symmetry clash REVERT: A 757 TYR cc_start: 0.8760 (t80) cc_final: 0.8335 (t80) REVERT: B 197 LEU cc_start: 0.8355 (mt) cc_final: 0.8095 (mp) REVERT: B 233 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7992 (tp) REVERT: C 534 ILE cc_start: 0.8919 (mt) cc_final: 0.8683 (tt) REVERT: C 584 ASP cc_start: 0.7257 (m-30) cc_final: 0.6571 (m-30) REVERT: C 786 GLU cc_start: 0.8202 (tt0) cc_final: 0.7757 (pm20) outliers start: 20 outliers final: 15 residues processed: 143 average time/residue: 0.1147 time to fit residues: 26.1997 Evaluate side-chains 143 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 249 CYS Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 185 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 79 optimal weight: 0.0980 chunk 49 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 77 optimal weight: 5.9990 chunk 82 optimal weight: 0.0470 chunk 4 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 127 optimal weight: 4.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 818 HIS C 588 ASN ** C 937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.135820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.109622 restraints weight = 23568.867| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.00 r_work: 0.3227 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16573 Z= 0.115 Angle : 0.545 10.869 22796 Z= 0.294 Chirality : 0.042 0.324 2489 Planarity : 0.004 0.044 2594 Dihedral : 21.129 162.382 2980 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.31 % Favored : 93.58 % Rotamer: Outliers : 1.22 % Allowed : 12.28 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.45 (0.21), residues: 1744 helix: 1.55 (0.23), residues: 549 sheet: -0.72 (0.29), residues: 356 loop : -1.38 (0.22), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 826 TYR 0.017 0.001 TYR B 338 PHE 0.012 0.001 PHE B 48 TRP 0.012 0.001 TRP A 519 HIS 0.008 0.001 HIS A 818 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (16565) covalent geometry : angle 0.54016 / 0.29 (22792) hydrogen bonds : bond 0.03498 / 2.31 ( 643) hydrogen bonds : angle 4.68147 / 3.27 ( 1767) metal coordination : bond 0.01657 / 1.30 ( 8) metal coordination : angle 5.64868 / 2.84 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 1.078 Fit side-chains revert: symmetry clash REVERT: A 757 TYR cc_start: 0.8677 (t80) cc_final: 0.8305 (t80) REVERT: B 197 LEU cc_start: 0.8441 (mt) cc_final: 0.8175 (mp) REVERT: B 233 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7988 (tp) REVERT: C 534 ILE cc_start: 0.8893 (mt) cc_final: 0.8661 (tt) REVERT: C 584 ASP cc_start: 0.7250 (m-30) cc_final: 0.6654 (m-30) REVERT: C 633 HIS cc_start: 0.7303 (t-90) cc_final: 0.6524 (t70) REVERT: C 786 GLU cc_start: 0.8198 (tt0) cc_final: 0.7739 (pm20) REVERT: D 285 MET cc_start: 0.9224 (mmm) cc_final: 0.8983 (mmm) outliers start: 19 outliers final: 15 residues processed: 139 average time/residue: 0.1172 time to fit residues: 26.0793 Evaluate side-chains 140 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 249 CYS Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 185 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 126 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 152 optimal weight: 0.0970 chunk 109 optimal weight: 0.6980 chunk 156 optimal weight: 4.9990 chunk 121 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 59 optimal weight: 0.0470 chunk 41 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 818 HIS C 588 ASN ** C 937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.136290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.110185 restraints weight = 23281.556| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.99 r_work: 0.3237 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16573 Z= 0.113 Angle : 0.539 9.795 22796 Z= 0.291 Chirality : 0.042 0.324 2489 Planarity : 0.003 0.043 2594 Dihedral : 21.112 162.400 2980 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.19 % Favored : 93.69 % Rotamer: Outliers : 1.16 % Allowed : 12.28 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.21), residues: 1744 helix: 1.57 (0.23), residues: 549 sheet: -0.67 (0.30), residues: 355 loop : -1.36 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 826 TYR 0.017 0.001 TYR B 338 PHE 0.013 0.001 PHE B 183 TRP 0.015 0.001 TRP A 519 HIS 0.008 0.001 HIS A 818 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (16565) covalent geometry : angle 0.53390 / 0.29 (22792) hydrogen bonds : bond 0.03463 / 2.29 ( 643) hydrogen bonds : angle 4.64850 / 3.24 ( 1767) metal coordination : bond 0.01580 / 1.24 ( 8) metal coordination : angle 5.37112 / 2.69 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3468.88 seconds wall clock time: 60 minutes 21.57 seconds (3621.57 seconds total)