Starting phenix.real_space_refine on Thu Aug 6 03:45:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j86_36061/08_2026/8j86_36061.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j86_36061/08_2026/8j86_36061.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8j86_36061/08_2026/8j86_36061.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j86_36061/08_2026/8j86_36061.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j86_36061/08_2026/8j86_36061.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j86_36061/08_2026/8j86_36061.map" } resolution = 3.22 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= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 3 9.91 5 P 35 5.49 5 S 67 5.16 5 C 8456 2.51 5 N 2225 2.21 5 O 2581 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13367 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 8132 Classifications: {'peptide': 993} Link IDs: {'PTRANS': 36, 'TRANS': 956} Chain breaks: 3 Chain: "B" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1686 Classifications: {'peptide': 209} Incomplete info: {'backbone_only': 2} Link IDs: {'PTRANS': 13, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 2830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2830 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 8, 'TRANS': 341} Chain breaks: 10 Chain: "P" Number of atoms: 291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 291 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "T" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 425 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 13 residue: pdb=" P DT P 17 " occ=0.04 ... (18 atoms not shown) pdb=" C6 DT P 17 " occ=0.04 residue: pdb=" P DT P 18 " occ=0.19 ... (18 atoms not shown) pdb=" C6 DT P 18 " occ=0.19 residue: pdb=" P DA P 19 " occ=0.49 ... (19 atoms not shown) pdb=" C4 DA P 19 " occ=0.49 residue: pdb=" P DA P 20 " occ=0.68 ... (19 atoms not shown) pdb=" C4 DA P 20 " occ=0.68 residue: pdb=" P DT T 1 " occ=0.32 ... (18 atoms not shown) pdb=" C6 DT T 1 " occ=0.32 residue: pdb=" P DT T 2 " occ=0.67 ... (18 atoms not shown) pdb=" C6 DT T 2 " occ=0.67 residue: pdb=" P DG T 3 " occ=0.68 ... (20 atoms not shown) pdb=" C4 DG T 3 " occ=0.68 residue: pdb=" P DA T 4 " occ=0.72 ... (19 atoms not shown) pdb=" C4 DA T 4 " occ=0.72 residue: pdb=" P DT T 5 " occ=0.49 ... (18 atoms not shown) pdb=" C6 DT T 5 " occ=0.49 residue: pdb=" P DC T 14 " occ=0.81 ... (17 atoms not shown) pdb=" C6 DC T 14 " occ=0.81 residue: pdb=" P DT T 15 " occ=0.33 ... (18 atoms not shown) pdb=" C6 DT T 15 " occ=0.33 residue: pdb=" P DC T 16 " occ=0.89 ... (17 atoms not shown) pdb=" C6 DC T 16 " occ=0.89 residue: pdb=" P DA T 17 " occ=0.92 ... (19 atoms not shown) pdb=" C4 DA T 17 " occ=0.92 Time building chain proxies: 2.61, per 1000 atoms: 0.20 Number of scatterers: 13367 At special positions: 0 Unit cell: (89.88, 113.4, 143.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 3 19.99 S 67 16.00 P 35 15.00 O 2581 8.00 N 2225 7.00 C 8456 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: 0.90 Conformation dependent library (CDL) restraints added in 448.2 milliseconds 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2968 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 13 sheets defined 36.1% alpha, 10.8% beta 0 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 43 through 48 removed outlier: 3.773A pdb=" N TYR A 47 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN A 48 " --> pdb=" O ASP A 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 43 through 48' Processing helix chain 'A' and resid 109 through 118 removed outlier: 3.540A pdb=" N PHE A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 220 Processing helix chain 'A' and resid 240 through 254 Processing helix chain 'A' and resid 267 through 280 Processing helix chain 'A' and resid 331 through 336 Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 380 through 390 Processing helix chain 'A' and resid 439 through 446 Processing helix chain 'A' and resid 448 through 474 Processing helix chain 'A' and resid 474 through 487 Processing helix chain 'A' and resid 497 through 502 removed outlier: 3.738A pdb=" N ILE A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 514 Processing helix chain 'A' and resid 552 through 562 Processing helix chain 'A' and resid 564 through 566 No H-bonds generated for 'chain 'A' and resid 564 through 566' Processing helix chain 'A' and resid 579 through 591 Processing helix chain 'A' and resid 592 through 594 No H-bonds generated for 'chain 'A' and resid 592 through 594' Processing helix chain 'A' and resid 621 through 639 removed outlier: 3.579A pdb=" N ARG A 628 " --> pdb=" O PRO A 624 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS A 639 " --> pdb=" O ALA A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 652 Processing helix chain 'A' and resid 655 through 665 Processing helix chain 'A' and resid 666 through 671 Processing helix chain 'A' and resid 680 through 700 Processing helix chain 'A' and resid 763 through 782 removed outlier: 3.610A pdb=" N SER A 767 " --> pdb=" O ASP A 763 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN A 779 " --> pdb=" O GLU A 775 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER A 780 " --> pdb=" O ARG A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 856 removed outlier: 3.558A pdb=" N ILE A 843 " --> pdb=" O HIS A 839 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU A 852 " --> pdb=" O THR A 848 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU A 856 " --> pdb=" O GLU A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 876 removed outlier: 4.167A pdb=" N ILE A 866 " --> pdb=" O ASN A 862 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR A 874 " --> pdb=" O ARG A 870 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASP A 875 " --> pdb=" O SER A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 881 removed outlier: 3.501A pdb=" N PHE A 880 " --> pdb=" O ARG A 877 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASP A 881 " --> pdb=" O SER A 878 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 877 through 881' Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 969 through 983 removed outlier: 4.750A pdb=" N LYS A 973 " --> pdb=" O GLU A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 993 Processing helix chain 'B' and resid 19 through 38 removed outlier: 3.932A pdb=" N MET B 23 " --> pdb=" O TRP B 19 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N SER B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN B 25 " --> pdb=" O PRO B 21 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU B 28 " --> pdb=" O SER B 24 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL B 33 " --> pdb=" O PHE B 29 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER B 35 " --> pdb=" O ASN B 31 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N TRP B 36 " --> pdb=" O GLU B 32 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 54 removed outlier: 3.507A pdb=" N LEU B 53 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS B 54 " --> pdb=" O ILE B 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 50 through 54' Processing helix chain 'B' and resid 86 through 100 Processing helix chain 'B' and resid 137 through 151 removed outlier: 3.757A pdb=" N LYS B 142 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS B 147 " --> pdb=" O LEU B 143 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE B 148 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS B 151 " --> pdb=" O HIS B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 164 Processing helix chain 'B' and resid 195 through 205 removed outlier: 3.666A pdb=" N ASN B 199 " --> pdb=" O PHE B 195 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLU B 203 " --> pdb=" O ASN B 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 19 removed outlier: 3.656A pdb=" N LYS C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER C 19 " --> pdb=" O SER C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 42 removed outlier: 3.916A pdb=" N SER C 33 " --> pdb=" O GLU C 29 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER C 40 " --> pdb=" O GLU C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 108 No H-bonds generated for 'chain 'C' and resid 106 through 108' Processing helix chain 'C' and resid 109 through 114 Processing helix chain 'C' and resid 116 through 121 Processing helix chain 'C' and resid 147 through 158 removed outlier: 4.038A pdb=" N ILE C 151 " --> pdb=" O SER C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 256 Processing helix chain 'C' and resid 288 through 297 Processing helix chain 'C' and resid 315 through 324 removed outlier: 3.963A pdb=" N LEU C 319 " --> pdb=" O GLY C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 341 removed outlier: 3.537A pdb=" N SER C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 349 Processing helix chain 'C' and resid 352 through 362 Processing helix chain 'C' and resid 364 through 374 Processing helix chain 'C' and resid 392 through 396 Processing helix chain 'C' and resid 397 through 406 Processing helix chain 'C' and resid 406 through 424 removed outlier: 3.592A pdb=" N PHE C 410 " --> pdb=" O ASN C 406 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 133 through 134 removed outlier: 7.949A pdb=" N TYR A 140 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N PHE A 31 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N PHE A 17 " --> pdb=" O GLU A 10 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLU A 10 " --> pdb=" O PHE A 17 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N TYR A 19 " --> pdb=" O TRP A 8 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N TRP A 8 " --> pdb=" O TYR A 19 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LYS A 21 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N MET A 1 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLY A 123 " --> pdb=" O CYS A 5 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N CYS A 124 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE A 153 " --> pdb=" O CYS A 124 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 40 removed outlier: 3.573A pdb=" N LEU A 90 " --> pdb=" O ARG A 58 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASN A 56 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 63 through 66 Processing sheet with id=AA4, first strand: chain 'A' and resid 72 through 73 removed outlier: 3.630A pdb=" N SER A 73 " --> pdb=" O VAL A 571 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 573 " --> pdb=" O SER A 73 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE A 614 " --> pdb=" O VAL A 569 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VAL A 571 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ILE A 612 " --> pdb=" O VAL A 571 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N VAL A 573 " --> pdb=" O SER A 610 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N SER A 610 " --> pdb=" O VAL A 573 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 197 through 203 removed outlier: 3.616A pdb=" N THR A 186 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE A 164 " --> pdb=" O CYS A 189 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL A 259 " --> pdb=" O PHE A 329 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 300 through 303 Processing sheet with id=AA7, first strand: chain 'A' and resid 355 through 359 Processing sheet with id=AA8, first strand: chain 'A' and resid 705 through 706 removed outlier: 6.092A pdb=" N SER A 747 " --> pdb=" O GLU A 758 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLU A 758 " --> pdb=" O SER A 747 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR A 749 " --> pdb=" O PHE A 756 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA A 793 " --> pdb=" O ILE A 547 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASP A 549 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N PHE A 791 " --> pdb=" O ASP A 549 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS A 796 " --> pdb=" O MET A 809 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU A 798 " --> pdb=" O THR A 807 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR A 807 " --> pdb=" O LEU A 798 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 116 through 120 removed outlier: 6.267A pdb=" N VAL B 62 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N TRP B 119 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N VAL B 64 " --> pdb=" O TRP B 119 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU B 158 " --> pdb=" O CYS B 65 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU B 155 " --> pdb=" O ILE B 177 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N GLY B 179 " --> pdb=" O LEU B 155 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N CYS B 157 " --> pdb=" O GLY B 179 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 85 through 89 Processing sheet with id=AB2, first strand: chain 'C' and resid 220 through 223 removed outlier: 7.245A pdb=" N ILE C 238 " --> pdb=" O GLU C 221 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS C 243 " --> pdb=" O THR C 239 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 267 through 268 Processing sheet with id=AB4, first strand: chain 'C' and resid 301 through 303 411 hydrogen bonds defined for protein. 1173 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 2.29 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3889 1.34 - 1.45: 2293 1.45 - 1.57: 7355 1.57 - 1.69: 68 1.69 - 1.81: 102 Bond restraints: 13707 Sorted by residual: bond pdb=" C3' DA T 12 " pdb=" C2' DA T 12 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 bond pdb=" C3' DT T 9 " pdb=" C2' DT T 9 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.56e+00 bond pdb=" C3' DA P 14 " pdb=" O3' DA P 14 " ideal model delta sigma weight residual 1.435 1.472 -0.037 1.30e-02 5.92e+03 7.95e+00 bond pdb=" C1' DT T 5 " pdb=" N1 DT T 5 " ideal model delta sigma weight residual 1.468 1.507 -0.039 1.40e-02 5.10e+03 7.57e+00 bond pdb=" C3' DT T 13 " pdb=" C2' DT T 13 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.48e+00 ... (remaining 13702 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 18089 1.44 - 2.87: 469 2.87 - 4.31: 73 4.31 - 5.75: 11 5.75 - 7.19: 5 Bond angle restraints: 18647 Sorted by residual: angle pdb=" C GLU A 339 " pdb=" CA GLU A 339 " pdb=" CB GLU A 339 " ideal model delta sigma weight residual 116.34 110.36 5.98 1.40e+00 5.10e-01 1.83e+01 angle pdb=" O4' DT P 17 " pdb=" C4' DT P 17 " pdb=" C3' DT P 17 " ideal model delta sigma weight residual 106.00 103.46 2.54 6.00e-01 2.78e+00 1.79e+01 angle pdb=" N3 DT T 10 " pdb=" C4 DT T 10 " pdb=" O4 DT T 10 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 angle pdb=" N3 DT T 15 " pdb=" C4 DT T 15 " pdb=" O4 DT T 15 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT P 22 " pdb=" C4 DT P 22 " pdb=" O4 DT P 22 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.70e+01 ... (remaining 18642 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.64: 7930 35.64 - 71.29: 256 71.29 - 106.93: 14 106.93 - 142.57: 2 142.57 - 178.21: 2 Dihedral angle restraints: 8204 sinusoidal: 3616 harmonic: 4588 Sorted by residual: dihedral pdb=" CA SER C 196 " pdb=" C SER C 196 " pdb=" N ILE C 197 " pdb=" CA ILE C 197 " ideal model delta harmonic sigma weight residual 180.00 150.94 29.06 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA ASN A 109 " pdb=" C ASN A 109 " pdb=" N ILE A 110 " pdb=" CA ILE A 110 " ideal model delta harmonic sigma weight residual -180.00 -156.97 -23.03 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA SER A 184 " pdb=" C SER A 184 " pdb=" N HIS A 185 " pdb=" CA HIS A 185 " ideal model delta harmonic sigma weight residual -180.00 -158.46 -21.54 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 8201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1746 0.056 - 0.112: 295 0.112 - 0.168: 29 0.168 - 0.224: 3 0.224 - 0.280: 1 Chirality restraints: 2074 Sorted by residual: chirality pdb=" CB ILE B 112 " pdb=" CA ILE B 112 " pdb=" CG1 ILE B 112 " pdb=" CG2 ILE B 112 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CG LEU A 546 " pdb=" CB LEU A 546 " pdb=" CD1 LEU A 546 " pdb=" CD2 LEU A 546 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" C3' DA P 14 " pdb=" C4' DA P 14 " pdb=" O3' DA P 14 " pdb=" C2' DA P 14 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.35e-01 ... (remaining 2071 not shown) Planarity restraints: 2240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 45 " -0.031 5.00e-02 4.00e+02 4.77e-02 3.63e+00 pdb=" N PRO B 46 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 46 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 46 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 592 " 0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO A 593 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 593 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 593 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT P 17 " 0.021 2.00e-02 2.50e+03 1.01e-02 2.57e+00 pdb=" N1 DT P 17 " -0.021 2.00e-02 2.50e+03 pdb=" C2 DT P 17 " -0.003 2.00e-02 2.50e+03 pdb=" O2 DT P 17 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DT P 17 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DT P 17 " 0.005 2.00e-02 2.50e+03 pdb=" O4 DT P 17 " 0.006 2.00e-02 2.50e+03 pdb=" C5 DT P 17 " 0.002 2.00e-02 2.50e+03 pdb=" C7 DT P 17 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DT P 17 " -0.005 2.00e-02 2.50e+03 ... (remaining 2237 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 66 2.46 - 3.07: 8892 3.07 - 3.68: 20530 3.68 - 4.29: 29642 4.29 - 4.90: 48432 Nonbonded interactions: 107562 Sorted by model distance: nonbonded pdb="CA CA A1102 " pdb="CA CA A1103 " model vdw 1.849 1.980 nonbonded pdb=" O GLU A 879 " pdb=" OH TYR A 968 " model vdw 2.074 3.040 nonbonded pdb=" O ASN A 181 " pdb=" OH TYR A 271 " model vdw 2.123 3.040 nonbonded pdb=" OH TYR A 332 " pdb=" OE1 GLU A 926 " model vdw 2.202 3.040 nonbonded pdb=" OH TYR A 162 " pdb=" OE1 GLU A 476 " model vdw 2.259 3.040 ... (remaining 107557 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 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: 5.470 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: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 12.550 Find NCS groups from input model: 0.060 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: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6191 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 : 0.003 0.039 13707 Z= 0.195 Angle : 0.553 7.185 18647 Z= 0.367 Chirality : 0.042 0.280 2074 Planarity : 0.004 0.048 2240 Dihedral : 16.998 178.214 5236 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: -1.41 (0.22), residues: 1518 helix: 1.07 (0.24), residues: 488 sheet: -0.52 (0.38), residues: 219 loop : -2.46 (0.21), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 33 TYR 0.010 0.001 TYR A 658 PHE 0.020 0.001 PHE A 673 TRP 0.007 0.001 TRP B 212 HIS 0.001 0.000 HIS A 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.20 (13707) covalent geometry : angle 0.55344 / 0.37 (18647) hydrogen bonds : bond 0.15743 / 10.45 ( 411) hydrogen bonds : angle 5.87247 / 4.11 ( 1173) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 SER cc_start: 0.8437 (m) cc_final: 0.8079 (m) REVERT: A 215 GLU cc_start: 0.7397 (tm-30) cc_final: 0.7183 (tm-30) REVERT: A 374 ASP cc_start: 0.7372 (m-30) cc_final: 0.7165 (t0) REVERT: A 435 LYS cc_start: 0.7945 (ptpp) cc_final: 0.7192 (tptt) REVERT: A 525 LYS cc_start: 0.5422 (tptp) cc_final: 0.5174 (tptp) REVERT: A 539 LYS cc_start: 0.6881 (ttmt) cc_final: 0.6623 (ttmt) REVERT: A 668 TYR cc_start: 0.7115 (t80) cc_final: 0.6847 (t80) REVERT: A 844 LYS cc_start: 0.6512 (mtmt) cc_final: 0.5656 (ttmm) REVERT: A 909 TYR cc_start: 0.6059 (m-80) cc_final: 0.5778 (m-80) REVERT: A 993 PHE cc_start: 0.7632 (m-80) cc_final: 0.7387 (m-80) REVERT: C 243 LYS cc_start: 0.7844 (mttm) cc_final: 0.7487 (ttpp) REVERT: C 288 GLU cc_start: 0.4867 (pm20) cc_final: 0.4562 (pm20) REVERT: C 297 ILE cc_start: 0.6932 (mm) cc_final: 0.6707 (mp) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.1180 time to fit residues: 47.1930 Evaluate side-chains 172 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.0020 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.0020 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 3.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 322 ASN ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 897 HIS A 994 GLN B 120 ASN ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4901 r_free = 0.4901 target = 0.231969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.193105 restraints weight = 16116.601| |-----------------------------------------------------------------------------| r_work (start): 0.4562 rms_B_bonded: 2.54 r_work: 0.4322 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.4322 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4320 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4320 r_free = 0.4320 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4320 r_free = 0.4320 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 9 (10 function evaluations) r_final: 0.4320 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6439 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13707 Z= 0.145 Angle : 0.631 8.040 18647 Z= 0.333 Chirality : 0.045 0.339 2074 Planarity : 0.005 0.060 2240 Dihedral : 16.498 179.650 2088 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.21 % Favored : 89.79 % Rotamer: Outliers : 1.12 % Allowed : 9.07 % Favored : 89.81 % 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: -1.72 (0.22), residues: 1518 helix: 0.67 (0.24), residues: 503 sheet: -0.72 (0.37), residues: 222 loop : -2.61 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 519 TYR 0.036 0.002 TYR A 486 PHE 0.017 0.002 PHE C 188 TRP 0.008 0.001 TRP B 212 HIS 0.007 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 (13707) covalent geometry : angle 0.63055 / 0.33 (18647) hydrogen bonds : bond 0.04630 / 3.15 ( 411) hydrogen bonds : angle 5.27230 / 3.72 ( 1173) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 191 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.3978 (mpp) cc_final: 0.3682 (mpp) REVERT: A 374 ASP cc_start: 0.7334 (m-30) cc_final: 0.7101 (t0) REVERT: A 435 LYS cc_start: 0.7929 (ptpp) cc_final: 0.7220 (tptt) REVERT: A 525 LYS cc_start: 0.5604 (tptp) cc_final: 0.5190 (tptp) REVERT: A 620 GLU cc_start: 0.7475 (mp0) cc_final: 0.6979 (tt0) REVERT: A 668 TYR cc_start: 0.7073 (t80) cc_final: 0.6751 (t80) REVERT: A 741 TYR cc_start: 0.5772 (m-80) cc_final: 0.5463 (m-80) REVERT: A 844 LYS cc_start: 0.6509 (mtmt) cc_final: 0.5538 (ttmm) REVERT: A 891 MET cc_start: 0.6393 (mmm) cc_final: 0.5362 (mmm) REVERT: A 899 ASN cc_start: 0.6366 (OUTLIER) cc_final: 0.6107 (p0) REVERT: A 908 MET cc_start: 0.5186 (tpt) cc_final: 0.4889 (tpt) REVERT: A 909 TYR cc_start: 0.6211 (m-80) cc_final: 0.5848 (m-80) REVERT: C 243 LYS cc_start: 0.8346 (mttm) cc_final: 0.7473 (ttpp) REVERT: C 251 ASP cc_start: 0.6920 (p0) cc_final: 0.6614 (m-30) outliers start: 16 outliers final: 6 residues processed: 205 average time/residue: 0.1024 time to fit residues: 31.5180 Evaluate side-chains 174 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 167 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 899 ASN Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 392 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 86 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 126 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 19 optimal weight: 0.0020 chunk 45 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 442 GLN ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4883 r_free = 0.4883 target = 0.229547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.190856 restraints weight = 16418.673| |-----------------------------------------------------------------------------| r_work (start): 0.4518 rms_B_bonded: 2.71 r_work: 0.4258 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4258 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4254 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4254 r_free = 0.4254 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4254 r_free = 0.4254 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.4254 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6568 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13707 Z= 0.162 Angle : 0.624 7.565 18647 Z= 0.330 Chirality : 0.044 0.340 2074 Planarity : 0.005 0.058 2240 Dihedral : 16.552 179.254 2088 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % Rotamer: Outliers : 1.47 % Allowed : 12.70 % Favored : 85.83 % 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: -1.80 (0.22), residues: 1518 helix: 0.54 (0.23), residues: 497 sheet: -0.66 (0.38), residues: 213 loop : -2.61 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 146 TYR 0.025 0.002 TYR C 82 PHE 0.024 0.002 PHE C 188 TRP 0.008 0.001 TRP A 8 HIS 0.006 0.001 HIS C 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (13707) covalent geometry : angle 0.62352 / 0.33 (18647) hydrogen bonds : bond 0.04298 / 2.92 ( 411) hydrogen bonds : angle 5.26200 / 3.70 ( 1173) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 177 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 ASP cc_start: 0.7328 (m-30) cc_final: 0.7098 (t0) REVERT: A 435 LYS cc_start: 0.8029 (ptpp) cc_final: 0.7342 (tptt) REVERT: A 525 LYS cc_start: 0.5839 (tptp) cc_final: 0.5396 (tptp) REVERT: A 620 GLU cc_start: 0.7563 (mp0) cc_final: 0.7133 (tt0) REVERT: A 668 TYR cc_start: 0.7117 (t80) cc_final: 0.6867 (t80) REVERT: A 711 MET cc_start: 0.5559 (mmm) cc_final: 0.5237 (mmt) REVERT: A 741 TYR cc_start: 0.5884 (m-80) cc_final: 0.5085 (m-80) REVERT: A 844 LYS cc_start: 0.6643 (mtmt) cc_final: 0.5639 (ttmm) REVERT: A 908 MET cc_start: 0.5199 (tpt) cc_final: 0.4871 (tpt) REVERT: A 909 TYR cc_start: 0.6242 (m-80) cc_final: 0.5825 (m-80) REVERT: C 219 TYR cc_start: 0.6951 (t80) cc_final: 0.6377 (t80) REVERT: C 243 LYS cc_start: 0.8367 (mttm) cc_final: 0.7486 (ttpp) REVERT: C 297 ILE cc_start: 0.6824 (mm) cc_final: 0.6583 (mp) outliers start: 21 outliers final: 13 residues processed: 195 average time/residue: 0.0994 time to fit residues: 28.7237 Evaluate side-chains 170 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 725 ASP Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 972 PHE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 392 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 33 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 152 optimal weight: 0.7980 chunk 98 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 GLN A 181 ASN A 322 ASN A 825 ASN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 HIS C 409 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4845 r_free = 0.4845 target = 0.225437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.187354 restraints weight = 16288.962| |-----------------------------------------------------------------------------| r_work (start): 0.4490 rms_B_bonded: 2.54 r_work: 0.4220 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.4220 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4214 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4214 r_free = 0.4214 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4213 r_free = 0.4213 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.4213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13707 Z= 0.191 Angle : 0.663 9.733 18647 Z= 0.351 Chirality : 0.046 0.334 2074 Planarity : 0.005 0.059 2240 Dihedral : 16.651 179.230 2088 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.99 % Favored : 88.01 % Rotamer: Outliers : 2.30 % Allowed : 15.00 % Favored : 82.69 % 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: -2.13 (0.21), residues: 1518 helix: 0.24 (0.23), residues: 500 sheet: -0.96 (0.37), residues: 216 loop : -2.76 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 146 TYR 0.025 0.002 TYR A 928 PHE 0.024 0.002 PHE A 328 TRP 0.009 0.001 TRP A 8 HIS 0.007 0.001 HIS B 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 (13707) covalent geometry : angle 0.66257 / 0.35 (18647) hydrogen bonds : bond 0.04428 / 3.02 ( 411) hydrogen bonds : angle 5.47505 / 3.84 ( 1173) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 174 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 106 GLU cc_start: 0.5796 (OUTLIER) cc_final: 0.5058 (pm20) REVERT: A 374 ASP cc_start: 0.7368 (m-30) cc_final: 0.7056 (t0) REVERT: A 525 LYS cc_start: 0.5917 (tptp) cc_final: 0.5464 (tptp) REVERT: A 620 GLU cc_start: 0.7609 (mp0) cc_final: 0.7114 (tt0) REVERT: A 668 TYR cc_start: 0.7206 (t80) cc_final: 0.6946 (t80) REVERT: A 741 TYR cc_start: 0.5969 (m-80) cc_final: 0.5229 (m-80) REVERT: A 908 MET cc_start: 0.5175 (tpt) cc_final: 0.4857 (tpt) REVERT: A 909 TYR cc_start: 0.6226 (m-80) cc_final: 0.5760 (m-80) REVERT: C 219 TYR cc_start: 0.7022 (t80) cc_final: 0.6444 (t80) REVERT: C 243 LYS cc_start: 0.8371 (mttm) cc_final: 0.7522 (ttpp) REVERT: C 297 ILE cc_start: 0.6751 (mm) cc_final: 0.6500 (mp) outliers start: 33 outliers final: 22 residues processed: 200 average time/residue: 0.0944 time to fit residues: 28.4589 Evaluate side-chains 180 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 157 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 424 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 40 optimal weight: 0.0270 chunk 63 optimal weight: 0.0060 chunk 150 optimal weight: 4.9990 chunk 118 optimal weight: 0.2980 chunk 84 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 136 optimal weight: 10.0000 chunk 101 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.3854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 322 ASN A 336 GLN B 120 ASN C 115 ASN C 252 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4876 r_free = 0.4876 target = 0.228655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.190864 restraints weight = 16309.363| |-----------------------------------------------------------------------------| r_work (start): 0.4525 rms_B_bonded: 2.52 r_work: 0.4267 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4267 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4265 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4265 r_free = 0.4265 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4265 r_free = 0.4265 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.4265 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13707 Z= 0.128 Angle : 0.613 8.533 18647 Z= 0.322 Chirality : 0.044 0.406 2074 Planarity : 0.004 0.060 2240 Dihedral : 16.546 178.933 2088 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.94 % Favored : 89.06 % Rotamer: Outliers : 2.37 % Allowed : 16.75 % Favored : 80.88 % 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: -1.94 (0.21), residues: 1518 helix: 0.47 (0.23), residues: 495 sheet: -0.95 (0.38), residues: 207 loop : -2.64 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 146 TYR 0.016 0.001 TYR A 811 PHE 0.015 0.001 PHE A 328 TRP 0.012 0.001 TRP A 89 HIS 0.007 0.001 HIS C 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (13707) covalent geometry : angle 0.61260 / 0.32 (18647) hydrogen bonds : bond 0.03788 / 2.60 ( 411) hydrogen bonds : angle 5.25948 / 3.70 ( 1173) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.3945 (mpp) cc_final: 0.3713 (mpp) REVERT: A 374 ASP cc_start: 0.7416 (m-30) cc_final: 0.7103 (t0) REVERT: A 525 LYS cc_start: 0.5902 (tptp) cc_final: 0.5369 (tptp) REVERT: A 620 GLU cc_start: 0.7539 (mp0) cc_final: 0.7040 (tt0) REVERT: A 668 TYR cc_start: 0.7091 (t80) cc_final: 0.6852 (t80) REVERT: A 741 TYR cc_start: 0.5940 (m-80) cc_final: 0.5191 (m-80) REVERT: A 908 MET cc_start: 0.5189 (tpt) cc_final: 0.4863 (tpt) REVERT: A 909 TYR cc_start: 0.6232 (m-80) cc_final: 0.5773 (m-80) REVERT: C 48 GLN cc_start: 0.7822 (mp10) cc_final: 0.7518 (mp10) REVERT: C 100 SER cc_start: 0.7206 (m) cc_final: 0.6993 (t) REVERT: C 243 LYS cc_start: 0.8392 (mttm) cc_final: 0.7613 (ttpp) outliers start: 34 outliers final: 24 residues processed: 197 average time/residue: 0.1021 time to fit residues: 30.5633 Evaluate side-chains 183 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 972 PHE Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 301 TYR Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 424 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 25 optimal weight: 1.9990 chunk 82 optimal weight: 0.0040 chunk 72 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 129 optimal weight: 7.9990 chunk 78 optimal weight: 0.5980 chunk 109 optimal weight: 0.7980 chunk 116 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 322 ASN B 120 ASN C 164 ASN C 252 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4869 r_free = 0.4869 target = 0.228141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.190393 restraints weight = 16314.417| |-----------------------------------------------------------------------------| r_work (start): 0.4520 rms_B_bonded: 2.52 r_work: 0.4259 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4259 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4253 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4253 r_free = 0.4253 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4253 r_free = 0.4253 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.4253 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6571 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13707 Z= 0.135 Angle : 0.611 10.323 18647 Z= 0.322 Chirality : 0.043 0.325 2074 Planarity : 0.005 0.060 2240 Dihedral : 16.514 179.052 2088 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.26 % Favored : 88.74 % Rotamer: Outliers : 2.58 % Allowed : 17.86 % Favored : 79.55 % 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: -1.97 (0.21), residues: 1518 helix: 0.37 (0.23), residues: 502 sheet: -0.87 (0.38), residues: 204 loop : -2.65 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 849 TYR 0.020 0.001 TYR C 219 PHE 0.016 0.001 PHE A 328 TRP 0.007 0.001 TRP A 470 HIS 0.007 0.001 HIS C 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (13707) covalent geometry : angle 0.61139 / 0.32 (18647) hydrogen bonds : bond 0.03792 / 2.60 ( 411) hydrogen bonds : angle 5.28214 / 3.74 ( 1173) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 162 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.4062 (mpp) cc_final: 0.3482 (mpp) REVERT: A 106 GLU cc_start: 0.5705 (OUTLIER) cc_final: 0.4749 (pm20) REVERT: A 374 ASP cc_start: 0.7388 (m-30) cc_final: 0.7074 (t0) REVERT: A 525 LYS cc_start: 0.5693 (tptp) cc_final: 0.5231 (tptp) REVERT: A 620 GLU cc_start: 0.7562 (mp0) cc_final: 0.7051 (tt0) REVERT: A 668 TYR cc_start: 0.7128 (t80) cc_final: 0.6890 (t80) REVERT: C 95 MET cc_start: 0.5456 (OUTLIER) cc_final: 0.4760 (pmm) REVERT: C 100 SER cc_start: 0.7187 (m) cc_final: 0.6977 (t) REVERT: C 243 LYS cc_start: 0.8435 (mttm) cc_final: 0.7644 (ttpp) REVERT: C 297 ILE cc_start: 0.6825 (mm) cc_final: 0.6579 (mp) outliers start: 37 outliers final: 27 residues processed: 192 average time/residue: 0.1029 time to fit residues: 30.2347 Evaluate side-chains 188 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 601 CYS Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 424 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 39 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 70 optimal weight: 8.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 322 ASN A 352 ASN B 120 ASN B 133 HIS ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN C 252 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4834 r_free = 0.4834 target = 0.224087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.186040 restraints weight = 16272.251| |-----------------------------------------------------------------------------| r_work (start): 0.4471 rms_B_bonded: 2.47 r_work: 0.4204 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4195 r_free = 0.4195 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4195 r_free = 0.4195 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.4195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6678 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13707 Z= 0.195 Angle : 0.664 7.958 18647 Z= 0.353 Chirality : 0.046 0.322 2074 Planarity : 0.005 0.061 2240 Dihedral : 16.587 179.459 2088 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.19 % Favored : 87.81 % Rotamer: Outliers : 3.21 % Allowed : 18.35 % Favored : 78.44 % 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: -2.27 (0.21), residues: 1518 helix: 0.05 (0.23), residues: 507 sheet: -0.98 (0.38), residues: 204 loop : -2.81 (0.20), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 849 TYR 0.021 0.002 TYR A 909 PHE 0.037 0.002 PHE A 113 TRP 0.009 0.002 TRP B 212 HIS 0.007 0.001 HIS C 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 (13707) covalent geometry : angle 0.66420 / 0.35 (18647) hydrogen bonds : bond 0.04474 / 3.06 ( 411) hydrogen bonds : angle 5.55664 / 3.92 ( 1173) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 164 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.4124 (mpp) cc_final: 0.3626 (mpp) REVERT: A 106 GLU cc_start: 0.5859 (OUTLIER) cc_final: 0.4998 (pm20) REVERT: A 374 ASP cc_start: 0.7413 (m-30) cc_final: 0.7036 (t0) REVERT: A 525 LYS cc_start: 0.5969 (tptp) cc_final: 0.5454 (tptp) REVERT: A 620 GLU cc_start: 0.7601 (mp0) cc_final: 0.7091 (tt0) REVERT: A 668 TYR cc_start: 0.7205 (t80) cc_final: 0.6978 (t80) REVERT: A 833 ARG cc_start: 0.7243 (tpm170) cc_final: 0.6815 (tpm170) REVERT: C 100 SER cc_start: 0.7132 (m) cc_final: 0.6931 (t) REVERT: C 243 LYS cc_start: 0.8402 (mttm) cc_final: 0.7850 (ttpp) outliers start: 46 outliers final: 29 residues processed: 201 average time/residue: 0.0951 time to fit residues: 29.3241 Evaluate side-chains 184 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 301 TYR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 424 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 142 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 106 optimal weight: 0.0030 chunk 35 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 120 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 141 optimal weight: 10.0000 chunk 27 optimal weight: 0.5980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 322 ASN A 336 GLN B 120 ASN C 164 ASN C 252 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4855 r_free = 0.4855 target = 0.226350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.188671 restraints weight = 16172.060| |-----------------------------------------------------------------------------| r_work (start): 0.4505 rms_B_bonded: 2.50 r_work: 0.4256 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.4256 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4250 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4250 r_free = 0.4250 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4250 r_free = 0.4250 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.4250 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13707 Z= 0.139 Angle : 0.634 9.844 18647 Z= 0.333 Chirality : 0.044 0.323 2074 Planarity : 0.005 0.061 2240 Dihedral : 16.535 179.482 2088 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.87 % Favored : 89.13 % Rotamer: Outliers : 2.37 % Allowed : 19.89 % Favored : 77.74 % 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: -2.10 (0.21), residues: 1518 helix: 0.27 (0.23), residues: 496 sheet: -0.97 (0.40), residues: 192 loop : -2.69 (0.20), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 849 TYR 0.025 0.001 TYR A 909 PHE 0.031 0.001 PHE A 113 TRP 0.017 0.001 TRP C 136 HIS 0.008 0.001 HIS C 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (13707) covalent geometry : angle 0.63407 / 0.33 (18647) hydrogen bonds : bond 0.03861 / 2.64 ( 411) hydrogen bonds : angle 5.37941 / 3.81 ( 1173) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.4131 (mpp) cc_final: 0.3634 (mpp) REVERT: A 106 GLU cc_start: 0.5810 (OUTLIER) cc_final: 0.4821 (pm20) REVERT: A 250 GLN cc_start: 0.7022 (tt0) cc_final: 0.5947 (mm-40) REVERT: A 374 ASP cc_start: 0.7423 (m-30) cc_final: 0.7073 (t0) REVERT: A 525 LYS cc_start: 0.5696 (tptp) cc_final: 0.5218 (tptp) REVERT: A 620 GLU cc_start: 0.7549 (mp0) cc_final: 0.7044 (tt0) REVERT: C 100 SER cc_start: 0.7178 (m) cc_final: 0.6963 (t) REVERT: C 164 ASN cc_start: 0.2990 (OUTLIER) cc_final: 0.2403 (m-40) REVERT: C 243 LYS cc_start: 0.8389 (mttm) cc_final: 0.7875 (ttpp) outliers start: 34 outliers final: 24 residues processed: 185 average time/residue: 0.1048 time to fit residues: 29.5671 Evaluate side-chains 180 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 972 PHE Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 301 TYR Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 424 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 87 optimal weight: 0.8980 chunk 121 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 129 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 134 optimal weight: 9.9990 chunk 151 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 336 GLN B 120 ASN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4856 r_free = 0.4856 target = 0.226336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.188701 restraints weight = 16370.344| |-----------------------------------------------------------------------------| r_work (start): 0.4496 rms_B_bonded: 2.49 r_work: 0.4235 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.4235 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4229 r_free = 0.4229 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4229 r_free = 0.4229 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.4229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6608 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13707 Z= 0.156 Angle : 0.643 8.238 18647 Z= 0.339 Chirality : 0.044 0.322 2074 Planarity : 0.005 0.062 2240 Dihedral : 16.558 179.634 2088 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.66 % Favored : 88.27 % Rotamer: Outliers : 2.09 % Allowed : 19.54 % Favored : 78.37 % 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: -2.14 (0.21), residues: 1518 helix: 0.13 (0.23), residues: 500 sheet: -0.90 (0.39), residues: 191 loop : -2.68 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 849 TYR 0.016 0.002 TYR A 668 PHE 0.044 0.002 PHE A 113 TRP 0.024 0.001 TRP C 136 HIS 0.008 0.001 HIS C 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (13707) covalent geometry : angle 0.64277 / 0.34 (18647) hydrogen bonds : bond 0.03933 / 2.72 ( 411) hydrogen bonds : angle 5.43576 / 3.86 ( 1173) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 156 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.4220 (mpp) cc_final: 0.3692 (mpp) REVERT: A 106 GLU cc_start: 0.5831 (OUTLIER) cc_final: 0.4879 (pm20) REVERT: A 113 PHE cc_start: 0.6598 (t80) cc_final: 0.6343 (t80) REVERT: A 250 GLN cc_start: 0.7134 (tt0) cc_final: 0.5963 (mm-40) REVERT: A 374 ASP cc_start: 0.7424 (m-30) cc_final: 0.7081 (t0) REVERT: A 525 LYS cc_start: 0.5641 (tptp) cc_final: 0.5154 (tptp) REVERT: A 620 GLU cc_start: 0.7576 (mp0) cc_final: 0.7045 (tt0) REVERT: C 100 SER cc_start: 0.7198 (m) cc_final: 0.6985 (t) REVERT: C 243 LYS cc_start: 0.8421 (mttm) cc_final: 0.7846 (ttpp) outliers start: 30 outliers final: 24 residues processed: 180 average time/residue: 0.1048 time to fit residues: 28.8736 Evaluate side-chains 175 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 972 PHE Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 301 TYR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 424 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 5 optimal weight: 0.1980 chunk 118 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 90 optimal weight: 8.9990 chunk 89 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 1 optimal weight: 0.1980 chunk 12 optimal weight: 0.0670 chunk 136 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 154 optimal weight: 20.0000 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 322 ASN A 336 GLN B 120 ASN B 187 HIS C 164 ASN C 252 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4875 r_free = 0.4875 target = 0.228528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.190591 restraints weight = 16342.213| |-----------------------------------------------------------------------------| r_work (start): 0.4513 rms_B_bonded: 2.58 r_work: 0.4267 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.4267 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4261 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4261 r_free = 0.4261 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4260 r_free = 0.4260 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.4260 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13707 Z= 0.134 Angle : 0.638 9.793 18647 Z= 0.335 Chirality : 0.044 0.320 2074 Planarity : 0.005 0.062 2240 Dihedral : 16.533 179.556 2088 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer: Outliers : 2.16 % Allowed : 19.89 % Favored : 77.95 % 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: -2.01 (0.21), residues: 1518 helix: 0.34 (0.24), residues: 492 sheet: -0.85 (0.40), residues: 191 loop : -2.64 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 849 TYR 0.014 0.001 TYR C 199 PHE 0.034 0.001 PHE A 113 TRP 0.031 0.001 TRP C 136 HIS 0.008 0.001 HIS C 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (13707) covalent geometry : angle 0.63812 / 0.34 (18647) hydrogen bonds : bond 0.03707 / 2.58 ( 411) hydrogen bonds : angle 5.36156 / 3.84 ( 1173) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 160 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.4221 (mpp) cc_final: 0.3684 (mpp) REVERT: A 106 GLU cc_start: 0.5701 (OUTLIER) cc_final: 0.4724 (pm20) REVERT: A 250 GLN cc_start: 0.7113 (tt0) cc_final: 0.5889 (mm-40) REVERT: A 374 ASP cc_start: 0.7428 (m-30) cc_final: 0.7085 (t0) REVERT: A 471 GLU cc_start: 0.5892 (mt-10) cc_final: 0.5349 (mt-10) REVERT: A 525 LYS cc_start: 0.5562 (tptp) cc_final: 0.5046 (tptp) REVERT: A 620 GLU cc_start: 0.7542 (mp0) cc_final: 0.7037 (tt0) REVERT: A 685 LYS cc_start: 0.6383 (mttm) cc_final: 0.6182 (ttpt) REVERT: B 156 TYR cc_start: 0.6008 (t80) cc_final: 0.5719 (t80) REVERT: C 100 SER cc_start: 0.7263 (m) cc_final: 0.7029 (t) REVERT: C 200 ILE cc_start: 0.4436 (mp) cc_final: 0.4156 (mt) REVERT: C 243 LYS cc_start: 0.8418 (mttm) cc_final: 0.7848 (ttpp) outliers start: 31 outliers final: 23 residues processed: 183 average time/residue: 0.0933 time to fit residues: 26.0979 Evaluate side-chains 176 residues out of total 1435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 972 PHE Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 301 TYR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 424 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 41 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 77 optimal weight: 0.0570 chunk 67 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 99 optimal weight: 9.9990 chunk 130 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 336 GLN B 120 ASN B 187 HIS ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4853 r_free = 0.4853 target = 0.226114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.188276 restraints weight = 16537.084| |-----------------------------------------------------------------------------| r_work (start): 0.4497 rms_B_bonded: 2.46 r_work: 0.4250 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.4250 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4246 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4246 r_free = 0.4246 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4246 r_free = 0.4246 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.4246 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13707 Z= 0.160 Angle : 0.662 8.733 18647 Z= 0.349 Chirality : 0.045 0.318 2074 Planarity : 0.005 0.063 2240 Dihedral : 16.576 179.696 2088 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.53 % Favored : 88.41 % Rotamer: Outliers : 2.02 % Allowed : 20.31 % Favored : 77.67 % 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: -2.11 (0.21), residues: 1518 helix: 0.15 (0.23), residues: 499 sheet: -0.95 (0.39), residues: 196 loop : -2.63 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 849 TYR 0.058 0.002 TYR A 668 PHE 0.041 0.002 PHE A 113 TRP 0.028 0.002 TRP C 136 HIS 0.018 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (13707) covalent geometry : angle 0.66220 / 0.35 (18647) hydrogen bonds : bond 0.03984 / 2.78 ( 411) hydrogen bonds : angle 5.46805 / 3.91 ( 1173) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3833.50 seconds wall clock time: 66 minutes 26.42 seconds (3986.42 seconds total)