Starting phenix.real_space_refine on Sat Sep 12 15:08:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lqv_63306/09_2026/9lqv_63306.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lqv_63306/09_2026/9lqv_63306.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lqv_63306/09_2026/9lqv_63306.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lqv_63306/09_2026/9lqv_63306.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lqv_63306/09_2026/9lqv_63306.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lqv_63306/09_2026/9lqv_63306.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.101 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 106 5.49 5 Mg 3 5.21 5 S 104 5.16 5 C 9957 2.51 5 N 2824 2.21 5 O 3244 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 16240 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4387 Classifications: {'peptide': 545} Link IDs: {'PTRANS': 25, 'TRANS': 519} Chain breaks: 1 Chain: "B" Number of atoms: 2642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2642 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 19, 'TRANS': 317} Chain breaks: 1 Chain: "C" Number of atoms: 4397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4397 Classifications: {'peptide': 547} Link IDs: {'PTRANS': 25, 'TRANS': 521} Chain: "D" Number of atoms: 2636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2636 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 18, 'TRANS': 317} Chain breaks: 2 Chain: "I" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 207 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "J" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 229 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "x" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 602 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "M" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 292 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "y" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 573 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "L" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 270 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2064 SG CYS A 727 78.070 97.930 42.053 1.00 36.30 S ATOM 2085 SG CYS A 730 80.627 99.805 40.195 1.00 44.62 S ATOM 9103 SG CYS C 727 26.445 54.583 42.449 1.00 38.11 S ATOM 9124 SG CYS C 730 24.236 51.910 42.711 1.00 41.23 S Time building chain proxies: 3.71, per 1000 atoms: 0.23 Number of scatterers: 16240 At special positions: 0 Unit cell: (105.316, 151.916, 104.384, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 104 16.00 P 106 15.00 Mg 3 11.99 O 3244 8.00 N 2824 7.00 C 9957 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: 1.44 Conformation dependent library (CDL) restraints added in 599.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1102 " pdb="ZN ZN A1102 " - pdb=" NE2 HIS A 937 " pdb="ZN ZN A1102 " - pdb=" NE2 HIS A 942 " pdb="ZN ZN A1102 " - pdb=" SG CYS A 727 " pdb="ZN ZN A1102 " - pdb=" SG CYS A 730 " pdb=" ZN C1103 " pdb="ZN ZN C1103 " - pdb=" NE2 HIS C 937 " pdb="ZN ZN C1103 " - pdb=" NE2 HIS C 942 " pdb="ZN ZN C1103 " - pdb=" SG CYS C 727 " pdb="ZN ZN C1103 " - pdb=" SG CYS C 730 " Number of angles added : 4 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3304 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 21 sheets defined 36.4% alpha, 21.0% beta 50 base pairs and 82 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'A' and resid 469 through 474 Processing helix chain 'A' and resid 477 through 493 Processing helix chain 'A' and resid 499 through 511 removed outlier: 4.035A pdb=" N VAL A 509 " --> pdb=" O ASN A 505 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 510 " --> pdb=" O ALA A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 570 removed outlier: 3.591A pdb=" N LEU A 563 " --> pdb=" O TYR A 559 " (cutoff:3.500A) removed outlier: 3.785A 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 664 through 683 removed outlier: 3.557A pdb=" N THR A 669 " --> pdb=" O HIS A 665 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A 671 " --> pdb=" O THR A 667 " (cutoff:3.500A) Proline residue: A 674 - end of helix Processing helix chain 'A' and resid 708 through 717 Processing helix chain 'A' and resid 733 through 741 Processing helix chain 'A' and resid 749 through 763 Processing helix chain 'A' and resid 768 through 777 Processing helix chain 'A' and resid 792 through 813 Processing helix chain 'A' and resid 824 through 841 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 923 removed outlier: 5.132A pdb=" N SER A 910 " --> pdb=" O LEU A 906 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N PHE A 911 " --> pdb=" O CYS A 907 " (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: 3.873A pdb=" N ALA A 957 " --> pdb=" O GLY A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 975 Processing helix chain 'A' and resid 982 through 996 Processing helix chain 'A' and resid 996 through 1003 removed outlier: 3.619A pdb=" N PHE A1002 " --> pdb=" O TYR A 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 15 removed outlier: 3.584A pdb=" N LEU B 14 " --> pdb=" O ASN B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'B' and resid 308 through 314 Processing helix chain 'C' and resid 463 through 474 Processing helix chain 'C' and resid 477 through 493 Processing helix chain 'C' and resid 499 through 511 removed outlier: 3.925A pdb=" N ASN C 505 " --> pdb=" O HIS C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 570 Processing helix chain 'C' and resid 570 through 581 Processing helix chain 'C' and resid 664 through 683 Proline residue: C 674 - end of helix Processing helix chain 'C' and resid 708 through 716 Processing helix chain 'C' and resid 733 through 740 Processing helix chain 'C' and resid 749 through 763 removed outlier: 3.518A pdb=" N VAL C 759 " --> pdb=" O GLN C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 777 Processing helix chain 'C' and resid 792 through 813 Processing helix chain 'C' and resid 822 through 842 removed outlier: 3.636A pdb=" N ARG C 828 " --> pdb=" O GLU C 824 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN C 830 " --> pdb=" O ARG C 826 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 858 Processing helix chain 'C' and resid 859 through 868 Processing helix chain 'C' and resid 873 through 895 Proline residue: C 891 - end of helix Processing helix chain 'C' and resid 897 through 902 Processing helix chain 'C' and resid 902 through 924 removed outlier: 4.986A pdb=" N SER C 910 " --> pdb=" O LEU C 906 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N PHE C 911 " --> pdb=" O CYS C 907 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE C 924 " --> pdb=" O LEU C 920 " (cutoff:3.500A) Processing helix chain 'C' and resid 933 through 951 removed outlier: 4.209A pdb=" N VAL C 943 " --> pdb=" O THR C 939 " (cutoff:3.500A) Proline residue: C 944 - end of helix Processing helix chain 'C' and resid 958 through 975 removed outlier: 3.693A pdb=" N LYS C 966 " --> pdb=" O GLU C 962 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU C 967 " --> pdb=" O SER C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 996 Processing helix chain 'C' and resid 996 through 1002 removed outlier: 3.700A pdb=" N PHE C1002 " --> pdb=" O TYR C 998 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1005 No H-bonds generated for 'chain 'C' and resid 1003 through 1005' Processing helix chain 'D' and resid 11 through 13 No H-bonds generated for 'chain 'D' and resid 11 through 13' Processing helix chain 'D' and resid 146 through 150 removed outlier: 4.259A pdb=" N GLY D 149 " --> pdb=" O TYR D 146 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS D 150 " --> pdb=" O SER D 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 146 through 150' Processing helix chain 'D' and resid 168 through 172 removed outlier: 3.697A 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: 3.573A 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 removed outlier: 6.472A pdb=" N LEU A 655 " --> pdb=" O PHE A 557 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N PHE A 622 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LEU A 657 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL A 620 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 619 " --> pdb=" O MET A 602 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP A 600 " --> pdb=" O ARG A 621 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 534 through 536 removed outlier: 6.472A pdb=" N LEU A 655 " --> pdb=" O PHE A 557 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N PHE A 622 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LEU A 657 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL A 620 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE A 631 " --> pdb=" O LYS A 639 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N LYS A 639 " --> pdb=" O ILE A 631 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 690 through 691 Processing sheet with id=AA5, first strand: chain 'B' and resid 20 through 23 removed outlier: 4.788A pdb=" N VAL B 28 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU B 55 " --> pdb=" O MET B 5 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N THR B 7 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N LEU B 57 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER B 2 " --> pdb=" O ARG B 343 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N PHE B 339 " --> pdb=" O VAL B 6 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N VAL B 8 " --> pdb=" O PHE B 337 " (cutoff:3.500A) removed outlier: 9.953A pdb=" N PHE B 337 " --> pdb=" O VAL B 8 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 80 removed outlier: 3.817A pdb=" N ILE B 107 " --> pdb=" O LYS B 127 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR B 121 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LYS B 115 " --> pdb=" O LYS B 119 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LYS B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 144 through 145 Processing sheet with id=AA8, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AA9, first strand: chain 'B' and resid 205 through 212 removed outlier: 6.718A pdb=" N PHE B 206 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLY B 221 " --> pdb=" O PHE B 206 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 205 through 212 removed outlier: 6.718A pdb=" N PHE B 206 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLY B 221 " --> pdb=" O PHE B 206 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU B 233 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 262 through 267 removed outlier: 3.507A pdb=" N THR B 266 " --> pdb=" O GLU B 270 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N GLU B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 534 through 536 removed outlier: 6.835A pdb=" N LEU C 655 " --> pdb=" O PHE C 557 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N PHE C 622 " --> pdb=" O LEU C 655 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LEU C 657 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL C 620 " --> pdb=" O LEU C 657 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE C 631 " --> pdb=" O LYS C 639 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N LYS C 639 " --> pdb=" O ILE C 631 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 534 through 536 removed outlier: 6.835A pdb=" N LEU C 655 " --> pdb=" O PHE C 557 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N PHE C 622 " --> pdb=" O LEU C 655 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LEU C 657 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL C 620 " --> pdb=" O LEU C 657 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP C 600 " --> pdb=" O ARG C 621 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL C 594 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE C 629 " --> pdb=" O THR C 592 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N THR C 592 " --> pdb=" O ILE C 629 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 46 through 50 removed outlier: 7.746A pdb=" N LEU D 55 " --> pdb=" O MET D 5 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N THR D 7 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N LEU D 57 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N PHE D 339 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL D 8 " --> pdb=" O PHE D 337 " (cutoff:3.500A) removed outlier: 9.523A pdb=" N PHE D 337 " --> pdb=" O VAL D 8 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 15 through 24 removed outlier: 9.324A pdb=" N GLY D 18 " --> pdb=" O GLN D 33 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N GLN D 33 " --> pdb=" O GLY D 18 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 61 through 62 removed outlier: 6.879A pdb=" N ILE D 61 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N THR D 121 " --> pdb=" O ALA D 113 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 76 through 79 removed outlier: 3.874A pdb=" N ILE D 107 " --> pdb=" O LYS D 127 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 130 through 131 removed outlier: 6.156A pdb=" N VAL D 130 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N SER D 194 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL D 145 " --> pdb=" O MET D 152 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 159 through 161 Processing sheet with id=AC2, first strand: chain 'D' and resid 208 through 211 removed outlier: 4.330A pdb=" N LEU D 233 " --> pdb=" O LEU D 252 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 262 through 265 removed outlier: 4.308A pdb=" N CYS D 287 " --> pdb=" O MET D 302 " (cutoff:3.500A) 628 hydrogen bonds defined for protein. 1767 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 121 hydrogen bonds 242 hydrogen bond angles 0 basepair planarities 50 basepair parallelities 82 stacking parallelities Total time for adding SS restraints: 3.80 Time building geometry restraints manager: 1.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2909 1.33 - 1.45: 4699 1.45 - 1.57: 8848 1.57 - 1.69: 205 1.69 - 1.81: 160 Bond restraints: 16821 Sorted by residual: bond pdb=" O3' DA x 40 " pdb=" P DC x 41 " ideal model delta sigma weight residual 1.607 1.543 0.064 1.20e-02 6.94e+03 2.88e+01 bond pdb=" C ARG C 628 " pdb=" N ILE C 629 " ideal model delta sigma weight residual 1.331 1.283 0.048 1.24e-02 6.50e+03 1.51e+01 bond pdb=" CA TYR A 928 " pdb=" C TYR A 928 " ideal model delta sigma weight residual 1.523 1.473 0.050 1.34e-02 5.57e+03 1.41e+01 bond pdb=" C3' DA I 22 " pdb=" C2' DA I 22 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.32e+01 bond pdb=" C LYS B 150 " pdb=" N SER B 151 " ideal model delta sigma weight residual 1.331 1.284 0.047 1.38e-02 5.25e+03 1.17e+01 ... (remaining 16816 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 22266 1.71 - 3.42: 795 3.42 - 5.13: 106 5.13 - 6.84: 10 6.84 - 8.54: 1 Bond angle restraints: 23178 Sorted by residual: angle pdb=" O4' DT I 26 " pdb=" C4' DT I 26 " pdb=" C3' DT I 26 " ideal model delta sigma weight residual 106.00 102.13 3.87 6.00e-01 2.78e+00 4.17e+01 angle pdb=" N3 DT x 52 " pdb=" C4 DT x 52 " pdb=" O4 DT x 52 " ideal model delta sigma weight residual 119.90 122.74 -2.84 6.00e-01 2.78e+00 2.24e+01 angle pdb=" O4' DG y 34 " pdb=" C4' DG y 34 " pdb=" C3' DG y 34 " ideal model delta sigma weight residual 106.00 103.17 2.83 6.00e-01 2.78e+00 2.23e+01 angle pdb=" N3 DT y 31 " pdb=" C4 DT y 31 " pdb=" O4 DT y 31 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.01e+01 angle pdb=" N3 DT y 42 " pdb=" C4 DT y 42 " pdb=" O4 DT y 42 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.97e+01 ... (remaining 23173 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.75: 9382 35.75 - 71.51: 455 71.51 - 107.26: 4 107.26 - 143.01: 4 143.01 - 178.76: 8 Dihedral angle restraints: 9853 sinusoidal: 4724 harmonic: 5129 Sorted by residual: dihedral pdb=" CA GLN A 520 " pdb=" C GLN A 520 " pdb=" N PRO A 521 " pdb=" CA PRO A 521 " ideal model delta harmonic sigma weight residual 180.00 156.36 23.64 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA LYS A 823 " pdb=" C LYS A 823 " pdb=" N GLU A 824 " pdb=" CA GLU A 824 " ideal model delta harmonic sigma weight residual 180.00 156.50 23.50 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA PHE D 156 " pdb=" C PHE D 156 " pdb=" N GLY D 157 " pdb=" CA GLY D 157 " ideal model delta harmonic sigma weight residual 180.00 -158.22 -21.78 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 9850 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2212 0.074 - 0.149: 308 0.149 - 0.223: 8 0.223 - 0.298: 1 0.298 - 0.372: 2 Chirality restraints: 2531 Sorted by residual: chirality pdb=" P DT I 26 " pdb=" OP1 DT I 26 " pdb=" OP2 DT I 26 " pdb=" O5' DT I 26 " both_signs ideal model delta sigma weight residual True 2.34 -2.71 -0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" P DT I 27 " pdb=" OP1 DT I 27 " pdb=" OP2 DT I 27 " pdb=" O5' DT I 27 " both_signs ideal model delta sigma weight residual True 2.34 -2.67 -0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" CA LYS A 925 " pdb=" N LYS A 925 " pdb=" C LYS A 925 " pdb=" CB LYS A 925 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 2528 not shown) Planarity restraints: 2614 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 317 " -0.022 2.00e-02 2.50e+03 2.18e-02 1.18e+01 pdb=" CG TRP B 317 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP B 317 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP B 317 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 317 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 317 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 317 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 317 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 317 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP B 317 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 927 " 0.274 9.50e-02 1.11e+02 1.23e-01 9.27e+00 pdb=" NE ARG A 927 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 927 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 927 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 927 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 583 " -0.011 2.00e-02 2.50e+03 2.22e-02 4.92e+00 pdb=" C LEU A 583 " 0.038 2.00e-02 2.50e+03 pdb=" O LEU A 583 " -0.014 2.00e-02 2.50e+03 pdb=" N ASP A 584 " -0.013 2.00e-02 2.50e+03 ... (remaining 2611 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 19 2.59 - 3.17: 13000 3.17 - 3.74: 25658 3.74 - 4.32: 37108 4.32 - 4.90: 60381 Nonbonded interactions: 136166 Sorted by model distance: nonbonded pdb=" OP2 DC x 46 " pdb="MG MG C1101 " model vdw 2.009 2.170 nonbonded pdb=" OD2 ASP C 708 " pdb="MG MG C1102 " model vdw 2.015 2.170 nonbonded pdb=" CE1 TYR C 559 " pdb=" CD1 LEU C 563 " model vdw 2.360 3.760 nonbonded pdb=" OE2 GLU A 803 " pdb=" OH TYR A 928 " model vdw 2.414 3.040 nonbonded pdb=" SG CYS C 727 " pdb=" CD2 HIS C 937 " model vdw 2.476 2.896 ... (remaining 136161 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' and resid 461 through 1101) selection = (chain 'C' and (resid 461 through 633 or resid 636 through 1101)) } ncs_group { reference = (chain 'B' and (resid 1 through 240 or resid 244 through 344)) selection = (chain 'D' and (resid 1 through 81 or resid 89 through 344)) } ncs_group { reference = chain 'L' selection = (chain 'M' and resid 1 through 13) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.490 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 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 0.247 16829 Z= 0.353 Angle : 0.714 9.561 23182 Z= 0.496 Chirality : 0.048 0.372 2531 Planarity : 0.005 0.123 2614 Dihedral : 18.391 178.765 6549 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 0.06 % Allowed : 0.71 % Favored : 99.23 % 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: -0.54 (0.21), residues: 1749 helix: 1.00 (0.22), residues: 561 sheet: -0.65 (0.30), residues: 326 loop : -1.13 (0.22), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 284 TYR 0.026 0.002 TYR A 757 PHE 0.025 0.002 PHE C 936 TRP 0.057 0.002 TRP B 317 HIS 0.008 0.001 HIS C 937 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.35 (16821) covalent geometry : angle 0.70617 / 0.50 (23178) hydrogen bonds : bond 0.14076 / 9.23 ( 723) hydrogen bonds : angle 7.53039 / 5.19 ( 2009) metal coordination : bond 0.10627 / 8.50 ( 8) metal coordination : angle 8.17776 / 3.82 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 255 time to evaluate : 0.577 Fit side-chains revert: symmetry clash REVERT: A 897 CYS cc_start: 0.8379 (t) cc_final: 0.7892 (t) REVERT: D 115 LYS cc_start: 0.8346 (ptpt) cc_final: 0.7751 (tttt) REVERT: D 343 ARG cc_start: 0.8166 (ttp80) cc_final: 0.7659 (tmt170) outliers start: 1 outliers final: 1 residues processed: 256 average time/residue: 0.1219 time to fit residues: 47.8244 Evaluate side-chains 179 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 178 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 317 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.0170 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.7624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 501 HIS A 609 HIS B 313 HIS C 473 ASN C 934 ASN D 53 ASN D 94 HIS D 324 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.146493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.120736 restraints weight = 21474.202| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.54 r_work: 0.3351 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.0834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16829 Z= 0.140 Angle : 0.609 8.449 23182 Z= 0.337 Chirality : 0.047 0.330 2531 Planarity : 0.004 0.044 2614 Dihedral : 21.615 179.065 3085 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.90 % Allowed : 7.05 % Favored : 92.05 % 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: -0.23 (0.21), residues: 1749 helix: 1.22 (0.22), residues: 570 sheet: -0.39 (0.29), residues: 350 loop : -1.00 (0.23), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 949 TYR 0.020 0.001 TYR A 757 PHE 0.014 0.001 PHE B 48 TRP 0.009 0.001 TRP A 760 HIS 0.011 0.001 HIS A 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.14 (16821) covalent geometry : angle 0.60633 / 0.34 (23178) hydrogen bonds : bond 0.04362 / 2.92 ( 723) hydrogen bonds : angle 5.83628 / 4.02 ( 2009) metal coordination : bond 0.01183 / 0.90 ( 8) metal coordination : angle 3.96680 / 1.79 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 195 time to evaluate : 0.602 Fit side-chains revert: symmetry clash REVERT: A 897 CYS cc_start: 0.8331 (t) cc_final: 0.7833 (t) REVERT: B 152 MET cc_start: 0.8499 (mmt) cc_final: 0.8199 (mmt) REVERT: D 80 TYR cc_start: 0.7678 (t80) cc_final: 0.7377 (t80) REVERT: D 115 LYS cc_start: 0.8492 (ptpt) cc_final: 0.7834 (tttt) REVERT: D 343 ARG cc_start: 0.8101 (ttp80) cc_final: 0.7727 (tpt90) outliers start: 14 outliers final: 9 residues processed: 203 average time/residue: 0.1245 time to fit residues: 38.5180 Evaluate side-chains 186 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 177 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 576 GLU Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain D residue 191 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 105 optimal weight: 5.9990 chunk 180 optimal weight: 20.0000 chunk 138 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 chunk 7 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 175 optimal weight: 30.0000 chunk 21 optimal weight: 2.9990 chunk 161 optimal weight: 8.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 47 HIS ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN B 282 GLN B 324 ASN C 495 GLN C 975 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.135870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.109282 restraints weight = 22042.476| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.74 r_work: 0.3166 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 16829 Z= 0.274 Angle : 0.697 10.135 23182 Z= 0.378 Chirality : 0.051 0.334 2531 Planarity : 0.005 0.047 2614 Dihedral : 21.884 179.980 3083 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 1.54 % Allowed : 9.29 % Favored : 89.17 % 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: -0.54 (0.20), residues: 1749 helix: 0.89 (0.21), residues: 568 sheet: -0.36 (0.29), residues: 340 loop : -1.21 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 713 TYR 0.028 0.002 TYR A 757 PHE 0.019 0.002 PHE C 916 TRP 0.011 0.002 TRP B 36 HIS 0.012 0.002 HIS B 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00631 / 0.27 (16821) covalent geometry : angle 0.69387 / 0.38 (23178) hydrogen bonds : bond 0.05006 / 3.37 ( 723) hydrogen bonds : angle 5.62137 / 3.91 ( 2009) metal coordination : bond 0.01698 / 1.30 ( 8) metal coordination : angle 5.38432 / 2.18 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 179 time to evaluate : 0.711 Fit side-chains revert: symmetry clash REVERT: A 897 CYS cc_start: 0.8579 (t) cc_final: 0.7812 (t) REVERT: B 52 GLN cc_start: 0.7959 (tm-30) cc_final: 0.7724 (tm-30) REVERT: B 152 MET cc_start: 0.8538 (mmt) cc_final: 0.8184 (mmt) REVERT: B 317 TRP cc_start: 0.9093 (OUTLIER) cc_final: 0.8656 (p90) REVERT: C 650 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8137 (pp) REVERT: C 873 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7740 (tm-30) REVERT: D 80 TYR cc_start: 0.7861 (t80) cc_final: 0.7649 (t80) REVERT: D 115 LYS cc_start: 0.8709 (ptpt) cc_final: 0.7809 (tttt) REVERT: D 343 ARG cc_start: 0.8277 (ttp80) cc_final: 0.7627 (tmt170) outliers start: 24 outliers final: 18 residues processed: 195 average time/residue: 0.1326 time to fit residues: 39.2662 Evaluate side-chains 191 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 171 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 317 TRP Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 576 GLU Chi-restraints excluded: chain C residue 602 MET Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 822 SER Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain D residue 191 CYS Chi-restraints excluded: chain D residue 218 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 133 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 78 optimal weight: 7.9990 chunk 100 optimal weight: 0.6980 chunk 77 optimal weight: 7.9990 chunk 136 optimal weight: 6.9990 chunk 157 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 181 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 975 ASN ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN B 282 GLN B 324 ASN D 53 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.139037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.112175 restraints weight = 21858.097| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.80 r_work: 0.3215 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16829 Z= 0.151 Angle : 0.601 9.423 23182 Z= 0.330 Chirality : 0.047 0.333 2531 Planarity : 0.004 0.044 2614 Dihedral : 21.815 178.104 3083 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.67 % Allowed : 10.19 % Favored : 88.14 % 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: -0.33 (0.21), residues: 1749 helix: 1.08 (0.21), residues: 570 sheet: -0.18 (0.30), residues: 321 loop : -1.13 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 237 TYR 0.018 0.001 TYR A 757 PHE 0.016 0.001 PHE B 48 TRP 0.010 0.001 TRP B 317 HIS 0.011 0.001 HIS B 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (16821) covalent geometry : angle 0.59736 / 0.33 (23178) hydrogen bonds : bond 0.04084 / 2.73 ( 723) hydrogen bonds : angle 5.31819 / 3.69 ( 2009) metal coordination : bond 0.00879 / 0.67 ( 8) metal coordination : angle 5.18076 / 2.21 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 179 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: A 568 MET cc_start: 0.8419 (mmm) cc_final: 0.8142 (mmt) REVERT: A 897 CYS cc_start: 0.8490 (t) cc_final: 0.7723 (t) REVERT: B 52 GLN cc_start: 0.7996 (tm-30) cc_final: 0.7693 (tm-30) REVERT: B 152 MET cc_start: 0.8481 (mmt) cc_final: 0.8102 (mmt) REVERT: B 317 TRP cc_start: 0.9076 (OUTLIER) cc_final: 0.8640 (p90) REVERT: C 650 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8039 (pp) REVERT: D 80 TYR cc_start: 0.7769 (t80) cc_final: 0.7554 (t80) REVERT: D 343 ARG cc_start: 0.8219 (ttp80) cc_final: 0.7439 (tmt170) outliers start: 26 outliers final: 19 residues processed: 197 average time/residue: 0.1283 time to fit residues: 38.8492 Evaluate side-chains 193 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 172 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 317 TRP Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 576 GLU Chi-restraints excluded: chain C residue 602 MET Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 822 SER Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain D residue 191 CYS Chi-restraints excluded: chain D residue 264 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 84 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 116 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 chunk 141 optimal weight: 7.9990 chunk 151 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 149 optimal weight: 0.7980 chunk 144 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 53 ASN ** 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 = 0.3680 r_free = 0.3680 target = 0.140005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.113199 restraints weight = 21709.521| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.79 r_work: 0.3224 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16829 Z= 0.139 Angle : 0.584 10.066 23182 Z= 0.321 Chirality : 0.046 0.333 2531 Planarity : 0.004 0.043 2614 Dihedral : 21.737 177.722 3083 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.41 % Allowed : 11.35 % Favored : 87.24 % 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: -0.19 (0.21), residues: 1749 helix: 1.26 (0.22), residues: 568 sheet: -0.11 (0.30), residues: 334 loop : -1.09 (0.22), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 237 TYR 0.020 0.001 TYR C 928 PHE 0.021 0.001 PHE B 187 TRP 0.011 0.001 TRP B 317 HIS 0.009 0.001 HIS B 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 (16821) covalent geometry : angle 0.58033 / 0.32 (23178) hydrogen bonds : bond 0.03909 / 2.62 ( 723) hydrogen bonds : angle 5.11286 / 3.54 ( 2009) metal coordination : bond 0.00819 / 0.63 ( 8) metal coordination : angle 5.14851 / 2.20 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: A 568 MET cc_start: 0.8429 (mmm) cc_final: 0.8174 (mmt) REVERT: A 897 CYS cc_start: 0.8452 (t) cc_final: 0.7719 (t) REVERT: A 928 TYR cc_start: 0.8432 (m-80) cc_final: 0.8231 (m-80) REVERT: B 52 GLN cc_start: 0.8010 (tm-30) cc_final: 0.7706 (tm-30) REVERT: B 152 MET cc_start: 0.8478 (mmt) cc_final: 0.8075 (mmt) REVERT: B 317 TRP cc_start: 0.9080 (OUTLIER) cc_final: 0.8594 (p90) REVERT: C 650 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8051 (pp) REVERT: D 343 ARG cc_start: 0.8210 (ttp80) cc_final: 0.7501 (tmt170) outliers start: 22 outliers final: 18 residues processed: 196 average time/residue: 0.1237 time to fit residues: 37.1449 Evaluate side-chains 192 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 317 TRP Chi-restraints excluded: chain C residue 576 GLU Chi-restraints excluded: chain C residue 602 MET Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 822 SER Chi-restraints excluded: chain C residue 910 SER Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain D residue 191 CYS Chi-restraints excluded: chain D residue 264 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 97 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 59 optimal weight: 0.0870 chunk 162 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 overall best weight: 1.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.138986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.112114 restraints weight = 21734.810| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.79 r_work: 0.3216 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16829 Z= 0.164 Angle : 0.596 9.019 23182 Z= 0.326 Chirality : 0.047 0.335 2531 Planarity : 0.004 0.055 2614 Dihedral : 21.777 178.088 3083 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.73 % Allowed : 12.24 % Favored : 86.03 % 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: -0.18 (0.21), residues: 1749 helix: 1.25 (0.22), residues: 569 sheet: -0.15 (0.30), residues: 340 loop : -1.06 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 237 TYR 0.020 0.001 TYR C 928 PHE 0.020 0.001 PHE B 187 TRP 0.012 0.001 TRP B 317 HIS 0.009 0.001 HIS B 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (16821) covalent geometry : angle 0.59200 / 0.33 (23178) hydrogen bonds : bond 0.04049 / 2.71 ( 723) hydrogen bonds : angle 5.06683 / 3.51 ( 2009) metal coordination : bond 0.01052 / 0.81 ( 8) metal coordination : angle 5.24531 / 2.24 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 188 time to evaluate : 0.632 Fit side-chains revert: symmetry clash REVERT: A 568 MET cc_start: 0.8407 (mmm) cc_final: 0.8172 (mmt) REVERT: A 584 ASP cc_start: 0.8681 (p0) cc_final: 0.8266 (p0) REVERT: A 897 CYS cc_start: 0.8487 (t) cc_final: 0.7684 (t) REVERT: B 52 GLN cc_start: 0.8072 (tm-30) cc_final: 0.7764 (tm-30) REVERT: B 152 MET cc_start: 0.8462 (mmt) cc_final: 0.8090 (mmt) REVERT: B 317 TRP cc_start: 0.9115 (OUTLIER) cc_final: 0.8579 (p90) REVERT: C 650 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8031 (pp) REVERT: C 661 ASP cc_start: 0.8227 (t70) cc_final: 0.7921 (t70) REVERT: D 343 ARG cc_start: 0.8207 (ttp80) cc_final: 0.7442 (tmt170) outliers start: 27 outliers final: 22 residues processed: 208 average time/residue: 0.1259 time to fit residues: 40.2530 Evaluate side-chains 208 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 184 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 317 TRP Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 576 GLU Chi-restraints excluded: chain C residue 602 MET Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 822 SER Chi-restraints excluded: chain C residue 910 SER Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain D residue 191 CYS Chi-restraints excluded: chain D residue 264 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 151 optimal weight: 7.9990 chunk 142 optimal weight: 0.0020 chunk 42 optimal weight: 1.9990 chunk 173 optimal weight: 4.9990 chunk 99 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 174 optimal weight: 20.0000 chunk 152 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 overall best weight: 1.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.137913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.111004 restraints weight = 21633.378| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.78 r_work: 0.3191 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16829 Z= 0.189 Angle : 0.624 9.450 23182 Z= 0.339 Chirality : 0.048 0.336 2531 Planarity : 0.004 0.051 2614 Dihedral : 21.841 178.548 3083 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.73 % Allowed : 13.14 % Favored : 85.13 % 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: -0.21 (0.21), residues: 1749 helix: 1.22 (0.21), residues: 568 sheet: -0.18 (0.29), residues: 340 loop : -1.06 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 237 TYR 0.021 0.001 TYR C 928 PHE 0.018 0.002 PHE B 187 TRP 0.012 0.001 TRP B 317 HIS 0.011 0.001 HIS B 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.19 (16821) covalent geometry : angle 0.62020 / 0.34 (23178) hydrogen bonds : bond 0.04182 / 2.81 ( 723) hydrogen bonds : angle 5.07224 / 3.52 ( 2009) metal coordination : bond 0.01214 / 0.93 ( 8) metal coordination : angle 5.42708 / 2.29 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 180 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: A 568 MET cc_start: 0.8376 (mmm) cc_final: 0.8164 (mmt) REVERT: A 584 ASP cc_start: 0.8661 (p0) cc_final: 0.8334 (p0) REVERT: A 897 CYS cc_start: 0.8527 (t) cc_final: 0.7711 (t) REVERT: B 52 GLN cc_start: 0.8104 (tm-30) cc_final: 0.7772 (tm-30) REVERT: B 152 MET cc_start: 0.8483 (mmt) cc_final: 0.8052 (mmt) REVERT: B 317 TRP cc_start: 0.9142 (OUTLIER) cc_final: 0.8615 (p90) REVERT: C 650 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8058 (pp) REVERT: D 303 GLU cc_start: 0.8156 (pm20) cc_final: 0.7785 (tp30) REVERT: D 343 ARG cc_start: 0.8188 (ttp80) cc_final: 0.7456 (tmt170) outliers start: 27 outliers final: 24 residues processed: 198 average time/residue: 0.1277 time to fit residues: 38.7510 Evaluate side-chains 206 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 180 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 317 TRP Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 576 GLU Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 602 MET Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 822 SER Chi-restraints excluded: chain C residue 827 LYS Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain D residue 191 CYS Chi-restraints excluded: chain D residue 264 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 146 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 71 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 53 ASN B 324 ASN D 265 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.139447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.112537 restraints weight = 21638.841| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.78 r_work: 0.3213 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 16829 Z= 0.147 Angle : 0.597 8.822 23182 Z= 0.325 Chirality : 0.046 0.335 2531 Planarity : 0.004 0.047 2614 Dihedral : 21.798 177.920 3083 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.92 % Allowed : 13.33 % Favored : 84.74 % 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: -0.10 (0.21), residues: 1749 helix: 1.33 (0.22), residues: 568 sheet: -0.15 (0.29), residues: 340 loop : -1.00 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 237 TYR 0.018 0.001 TYR C 928 PHE 0.022 0.001 PHE B 187 TRP 0.011 0.001 TRP B 317 HIS 0.010 0.001 HIS B 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 (16821) covalent geometry : angle 0.59282 / 0.32 (23178) hydrogen bonds : bond 0.03896 / 2.61 ( 723) hydrogen bonds : angle 4.98656 / 3.46 ( 2009) metal coordination : bond 0.00851 / 0.65 ( 8) metal coordination : angle 5.40695 / 2.29 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 184 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: A 568 MET cc_start: 0.8445 (mmm) cc_final: 0.8208 (mmt) REVERT: A 584 ASP cc_start: 0.8671 (p0) cc_final: 0.8263 (p0) REVERT: A 897 CYS cc_start: 0.8481 (t) cc_final: 0.7728 (t) REVERT: B 52 GLN cc_start: 0.8106 (tm-30) cc_final: 0.7781 (tm-30) REVERT: B 110 MET cc_start: 0.8640 (mmt) cc_final: 0.7963 (mmt) REVERT: B 152 MET cc_start: 0.8482 (mmt) cc_final: 0.8155 (mmt) REVERT: B 317 TRP cc_start: 0.9136 (OUTLIER) cc_final: 0.8615 (p90) REVERT: C 473 ASN cc_start: 0.8965 (OUTLIER) cc_final: 0.8531 (m-40) REVERT: C 650 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8032 (pp) REVERT: D 4 GLN cc_start: 0.8934 (mt0) cc_final: 0.8582 (tt0) REVERT: D 98 THR cc_start: 0.8770 (OUTLIER) cc_final: 0.8466 (p) REVERT: D 303 GLU cc_start: 0.8166 (pm20) cc_final: 0.7854 (tp30) REVERT: D 343 ARG cc_start: 0.8197 (ttp80) cc_final: 0.7603 (tmt170) outliers start: 30 outliers final: 23 residues processed: 205 average time/residue: 0.1271 time to fit residues: 40.1213 Evaluate side-chains 209 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 182 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 317 TRP Chi-restraints excluded: chain C residue 473 ASN Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 576 GLU Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 602 MET Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 822 SER Chi-restraints excluded: chain C residue 910 SER Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 191 CYS Chi-restraints excluded: chain D residue 264 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 158 optimal weight: 4.9990 chunk 66 optimal weight: 0.0000 chunk 144 optimal weight: 0.7980 chunk 171 optimal weight: 0.3980 chunk 59 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 159 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 324 ASN D 265 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.139100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.112260 restraints weight = 21685.523| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.79 r_work: 0.3218 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 16829 Z= 0.158 Angle : 0.609 10.113 23182 Z= 0.330 Chirality : 0.047 0.335 2531 Planarity : 0.004 0.047 2614 Dihedral : 21.791 177.973 3083 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.92 % Allowed : 13.53 % Favored : 84.55 % 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: -0.10 (0.21), residues: 1749 helix: 1.34 (0.22), residues: 568 sheet: -0.16 (0.29), residues: 340 loop : -0.99 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 237 TYR 0.018 0.001 TYR C 928 PHE 0.021 0.001 PHE B 187 TRP 0.012 0.001 TRP B 317 HIS 0.010 0.001 HIS B 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 (16821) covalent geometry : angle 0.60430 / 0.33 (23178) hydrogen bonds : bond 0.03933 / 2.64 ( 723) hydrogen bonds : angle 4.96665 / 3.45 ( 2009) metal coordination : bond 0.01046 / 0.81 ( 8) metal coordination : angle 5.53184 / 2.33 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 189 time to evaluate : 0.594 Fit side-chains revert: symmetry clash REVERT: A 568 MET cc_start: 0.8422 (mmm) cc_final: 0.8196 (mmt) REVERT: A 584 ASP cc_start: 0.8686 (p0) cc_final: 0.8126 (p0) REVERT: A 897 CYS cc_start: 0.8492 (t) cc_final: 0.7705 (t) REVERT: B 52 GLN cc_start: 0.8116 (tm-30) cc_final: 0.7892 (tm-30) REVERT: B 110 MET cc_start: 0.8627 (mmt) cc_final: 0.7897 (mmt) REVERT: B 152 MET cc_start: 0.8447 (mmt) cc_final: 0.8106 (mmt) REVERT: B 317 TRP cc_start: 0.9140 (OUTLIER) cc_final: 0.8625 (p90) REVERT: C 650 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.8049 (pp) REVERT: C 661 ASP cc_start: 0.8181 (t70) cc_final: 0.7874 (t70) REVERT: D 98 THR cc_start: 0.8761 (OUTLIER) cc_final: 0.8450 (p) REVERT: D 343 ARG cc_start: 0.8158 (ttp80) cc_final: 0.7532 (tmt170) outliers start: 30 outliers final: 25 residues processed: 208 average time/residue: 0.1282 time to fit residues: 41.1539 Evaluate side-chains 211 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 183 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 929 GLU Chi-restraints excluded: chain B residue 4 GLN Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 317 TRP Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 576 GLU Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 602 MET Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 822 SER Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 264 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 25 optimal weight: 6.9990 chunk 27 optimal weight: 0.0060 chunk 128 optimal weight: 0.6980 chunk 157 optimal weight: 2.9990 chunk 46 optimal weight: 0.0970 chunk 176 optimal weight: 20.0000 chunk 71 optimal weight: 5.9990 chunk 182 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 324 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.141900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.115467 restraints weight = 21515.446| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.73 r_work: 0.3264 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16829 Z= 0.122 Angle : 0.587 9.817 23182 Z= 0.320 Chirality : 0.045 0.333 2531 Planarity : 0.004 0.047 2614 Dihedral : 21.696 176.937 3083 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.60 % Allowed : 13.78 % Favored : 84.62 % 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: 0.07 (0.21), residues: 1749 helix: 1.48 (0.22), residues: 569 sheet: -0.04 (0.30), residues: 339 loop : -0.91 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 237 TYR 0.016 0.001 TYR A 805 PHE 0.016 0.001 PHE B 48 TRP 0.012 0.001 TRP A 893 HIS 0.008 0.001 HIS B 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 (16821) covalent geometry : angle 0.58294 / 0.32 (23178) hydrogen bonds : bond 0.03621 / 2.42 ( 723) hydrogen bonds : angle 4.84556 / 3.36 ( 2009) metal coordination : bond 0.00611 / 0.47 ( 8) metal coordination : angle 5.57248 / 2.30 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 195 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: A 568 MET cc_start: 0.8449 (mmm) cc_final: 0.8182 (mmt) REVERT: A 584 ASP cc_start: 0.8658 (p0) cc_final: 0.8311 (p0) REVERT: A 897 CYS cc_start: 0.8375 (t) cc_final: 0.7729 (t) REVERT: B 152 MET cc_start: 0.8456 (mmt) cc_final: 0.8155 (mmt) REVERT: C 473 ASN cc_start: 0.8959 (OUTLIER) cc_final: 0.8511 (m-40) REVERT: C 650 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.8017 (pp) REVERT: C 661 ASP cc_start: 0.8125 (t70) cc_final: 0.7849 (t70) REVERT: D 4 GLN cc_start: 0.8883 (mt0) cc_final: 0.8609 (tt0) REVERT: D 343 ARG cc_start: 0.8187 (ttp80) cc_final: 0.7736 (tmt170) outliers start: 25 outliers final: 20 residues processed: 209 average time/residue: 0.1267 time to fit residues: 40.6176 Evaluate side-chains 209 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 187 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain C residue 473 ASN Chi-restraints excluded: chain C residue 576 GLU Chi-restraints excluded: chain C residue 602 MET Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 822 SER Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 264 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 174 optimal weight: 20.0000 chunk 39 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 68 optimal weight: 9.9990 chunk 162 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 178 optimal weight: 20.0000 chunk 122 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 495 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.144910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.118857 restraints weight = 21580.137| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.56 r_work: 0.3308 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 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 : 0.003 0.112 16829 Z= 0.158 Angle : 0.630 14.103 23182 Z= 0.341 Chirality : 0.046 0.334 2531 Planarity : 0.004 0.045 2614 Dihedral : 21.728 177.693 3083 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.79 % Allowed : 13.59 % Favored : 84.62 % 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: 0.03 (0.21), residues: 1749 helix: 1.43 (0.22), residues: 569 sheet: -0.07 (0.29), residues: 349 loop : -0.93 (0.23), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 237 TYR 0.020 0.001 TYR C 928 PHE 0.035 0.001 PHE B 187 TRP 0.012 0.001 TRP B 317 HIS 0.010 0.001 HIS B 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (16821) covalent geometry : angle 0.62561 / 0.34 (23178) hydrogen bonds : bond 0.03846 / 2.59 ( 723) hydrogen bonds : angle 4.86226 / 3.37 ( 2009) metal coordination : bond 0.00995 / 0.76 ( 8) metal coordination : angle 5.45594 / 2.30 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3845.06 seconds wall clock time: 66 minutes 46.32 seconds (4006.32 seconds total)