Starting phenix.real_space_refine on Thu Aug 6 06:53:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ea3_47825/08_2026/9ea3_47825.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ea3_47825/08_2026/9ea3_47825.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ea3_47825/08_2026/9ea3_47825.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ea3_47825/08_2026/9ea3_47825.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ea3_47825/08_2026/9ea3_47825.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ea3_47825/08_2026/9ea3_47825.map" } resolution = 3.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 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: 5 Type Number sf(0) Gaussians P 56 5.49 5 S 67 5.16 5 C 8547 2.51 5 N 2289 2.21 5 O 2720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 13679 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 898, 7284 Classifications: {'peptide': 898} Link IDs: {'PTRANS': 40, 'TRANS': 857} Chain: "B" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1749 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain: "D" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1749 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain: "E" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1749 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain: "P" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 512 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 636 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Time building chain proxies: 2.79, per 1000 atoms: 0.20 Number of scatterers: 13679 At special positions: 0 Unit cell: (105.156, 105.984, 136.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 67 16.00 P 56 15.00 O 2720 8.00 N 2289 7.00 C 8547 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 585.9 milliseconds 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2964 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 18 sheets defined 36.9% alpha, 22.9% beta 25 base pairs and 40 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 62 through 76 removed outlier: 3.516A pdb=" N ILE A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 96 removed outlier: 3.550A pdb=" N TYR A 95 " --> pdb=" O ILE A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 106 removed outlier: 3.805A pdb=" N VAL A 106 " --> pdb=" O ARG A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 166 Processing helix chain 'A' and resid 167 through 171 Processing helix chain 'A' and resid 176 through 181 removed outlier: 3.591A pdb=" N LEU A 180 " --> pdb=" O PRO A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 205 Processing helix chain 'A' and resid 218 through 232 Processing helix chain 'A' and resid 233 through 240 removed outlier: 3.513A pdb=" N PHE A 239 " --> pdb=" O SER A 235 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER A 240 " --> pdb=" O MET A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 removed outlier: 3.619A pdb=" N ALA A 278 " --> pdb=" O TYR A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 296 Processing helix chain 'A' and resid 305 through 313 removed outlier: 3.899A pdb=" N ARG A 310 " --> pdb=" O ILE A 306 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU A 311 " --> pdb=" O ASN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 336 Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 357 through 373 Processing helix chain 'A' and resid 411 through 421 Processing helix chain 'A' and resid 435 through 441 removed outlier: 3.623A pdb=" N TYR A 439 " --> pdb=" O PRO A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 503 Processing helix chain 'A' and resid 520 through 528 Processing helix chain 'A' and resid 531 through 568 removed outlier: 4.246A pdb=" N TYR A 564 " --> pdb=" O ILE A 560 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N GLY A 565 " --> pdb=" O ASN A 561 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY A 568 " --> pdb=" O TYR A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 607 Processing helix chain 'A' and resid 626 through 634 removed outlier: 3.521A pdb=" N ILE A 630 " --> pdb=" O VAL A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 655 Processing helix chain 'A' and resid 656 through 671 Processing helix chain 'A' and resid 735 through 752 Processing helix chain 'A' and resid 753 through 769 removed outlier: 3.560A pdb=" N VAL A 757 " --> pdb=" O GLY A 753 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ARG A 769 " --> pdb=" O GLU A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 771 No H-bonds generated for 'chain 'A' and resid 770 through 771' Processing helix chain 'A' and resid 772 through 776 removed outlier: 3.763A pdb=" N ILE A 776 " --> pdb=" O TYR A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 787 Processing helix chain 'A' and resid 799 through 813 Processing helix chain 'A' and resid 851 through 861 removed outlier: 3.952A pdb=" N SER A 856 " --> pdb=" O LYS A 852 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ASP A 857 " --> pdb=" O GLU A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 872 removed outlier: 3.637A pdb=" N LEU A 867 " --> pdb=" O ASP A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 883 Processing helix chain 'A' and resid 892 through 896 removed outlier: 4.425A pdb=" N PHE A 895 " --> pdb=" O SER A 892 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 16 removed outlier: 3.583A pdb=" N THR B 16 " --> pdb=" O LYS B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 67 removed outlier: 3.685A pdb=" N VAL B 67 " --> pdb=" O ILE B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 133 Processing helix chain 'B' and resid 185 through 187 No H-bonds generated for 'chain 'B' and resid 185 through 187' Processing helix chain 'D' and resid 4 through 18 Processing helix chain 'D' and resid 56 through 67 removed outlier: 3.513A pdb=" N PHE D 60 " --> pdb=" O ASP D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 131 removed outlier: 4.353A pdb=" N ARG D 131 " --> pdb=" O LEU D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 187 No H-bonds generated for 'chain 'D' and resid 185 through 187' Processing helix chain 'E' and resid 4 through 16 removed outlier: 3.501A pdb=" N THR E 16 " --> pdb=" O LYS E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 67 Processing helix chain 'E' and resid 119 through 134 Processing helix chain 'E' and resid 185 through 187 No H-bonds generated for 'chain 'E' and resid 185 through 187' Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 11 removed outlier: 6.157A pdb=" N TYR A 5 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ILE A 20 " --> pdb=" O TYR A 5 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 55 through 59 removed outlier: 3.733A pdb=" N PHE A 38 " --> pdb=" O LEU A 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 183 through 185 removed outlier: 5.451A pdb=" N ALA A 109 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE A 210 " --> pdb=" O SER A 266 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 150 through 151 Processing sheet with id=AA5, first strand: chain 'A' and resid 245 through 247 Processing sheet with id=AA6, first strand: chain 'A' and resid 614 through 618 removed outlier: 5.415A pdb=" N ILE A 614 " --> pdb=" O CYS A 625 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N CYS A 625 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ILE A 404 " --> pdb=" O ILE A 685 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ILE A 685 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N SER A 406 " --> pdb=" O GLU A 683 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N GLU A 683 " --> pdb=" O MET A 712 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N MET A 712 " --> pdb=" O GLU A 683 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE A 685 " --> pdb=" O TYR A 710 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ARG A 704 " --> pdb=" O LYS A 700 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 614 through 618 removed outlier: 5.415A pdb=" N ILE A 614 " --> pdb=" O CYS A 625 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N CYS A 625 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ILE A 404 " --> pdb=" O ILE A 685 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ILE A 685 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N SER A 406 " --> pdb=" O GLU A 683 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N GLU A 683 " --> pdb=" O MET A 712 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N MET A 712 " --> pdb=" O GLU A 683 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE A 685 " --> pdb=" O TYR A 710 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU A 707 " --> pdb=" O LYS A 723 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ASP A 711 " --> pdb=" O GLU A 719 " (cutoff:3.500A) removed outlier: 11.525A pdb=" N GLU A 719 " --> pdb=" O ASP A 711 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 427 through 430 Processing sheet with id=AA9, first strand: chain 'A' and resid 789 through 790 removed outlier: 3.695A pdb=" N ASP A 790 " --> pdb=" O TRP A 793 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 826 through 830 Processing sheet with id=AB2, first strand: chain 'B' and resid 21 through 23 Processing sheet with id=AB3, first strand: chain 'B' and resid 26 through 32 removed outlier: 5.527A pdb=" N GLN B 27 " --> pdb=" O ILE B 44 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 72 through 75 removed outlier: 6.622A pdb=" N ILE E 147 " --> pdb=" O LEU E 169 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL E 142 " --> pdb=" O PHE E 178 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N PHE E 178 " --> pdb=" O VAL E 142 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 225 through 227 removed outlier: 6.250A pdb=" N PHE B 178 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL B 142 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE B 147 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR B 165 " --> pdb=" O GLY B 151 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 21 through 23 Processing sheet with id=AB7, first strand: chain 'D' and resid 26 through 32 removed outlier: 5.964A pdb=" N PHE D 28 " --> pdb=" O ASP D 46 " (cutoff:3.500A) removed outlier: 10.338A pdb=" N ASP D 46 " --> pdb=" O PHE D 28 " (cutoff:3.500A) removed outlier: 10.978A pdb=" N MET D 30 " --> pdb=" O ILE D 44 " (cutoff:3.500A) removed outlier: 11.275A pdb=" N ILE D 44 " --> pdb=" O MET D 30 " (cutoff:3.500A) removed outlier: 11.553A pdb=" N ARG D 32 " --> pdb=" O ALA D 42 " (cutoff:3.500A) removed outlier: 11.958A pdb=" N ALA D 42 " --> pdb=" O ARG D 32 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 225 through 227 removed outlier: 6.535A pdb=" N PHE D 178 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL D 142 " --> pdb=" O PHE D 178 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ILE D 147 " --> pdb=" O LEU D 169 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR D 165 " --> pdb=" O GLY D 151 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 26 through 32 removed outlier: 5.155A pdb=" N GLN E 27 " --> pdb=" O ILE E 44 " (cutoff:3.500A) 633 hydrogen bonds defined for protein. 1743 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 60 hydrogen bonds 120 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 40 stacking parallelities Total time for adding SS restraints: 2.37 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3715 1.33 - 1.45: 2633 1.45 - 1.57: 7496 1.57 - 1.69: 110 1.69 - 1.81: 120 Bond restraints: 14074 Sorted by residual: bond pdb=" C3' DT P 16 " pdb=" C2' DT P 16 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.48e+01 bond pdb=" C3' DC P 10 " pdb=" C2' DC P 10 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.28e+01 bond pdb=" C3' DA P 14 " pdb=" C2' DA P 14 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.20e+01 bond pdb=" C3' DA T 12 " pdb=" C2' DA T 12 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" N ILE D 182 " pdb=" CA ILE D 182 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.19e-02 7.06e+03 1.01e+01 ... (remaining 14069 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 18339 1.54 - 3.07: 781 3.07 - 4.61: 90 4.61 - 6.15: 31 6.15 - 7.68: 12 Bond angle restraints: 19253 Sorted by residual: angle pdb=" N3 DT P 16 " pdb=" C4 DT P 16 " pdb=" O4 DT P 16 " 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 31 " pdb=" C4 DT T 31 " pdb=" O4 DT T 31 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.66e+01 angle pdb=" N3 DT P 6 " pdb=" C4 DT P 6 " pdb=" O4 DT P 6 " ideal model delta sigma weight residual 119.90 122.33 -2.43 6.00e-01 2.78e+00 1.65e+01 angle pdb=" N3 DT P 4 " pdb=" C4 DT P 4 " pdb=" O4 DT P 4 " ideal model delta sigma weight residual 119.90 122.32 -2.42 6.00e-01 2.78e+00 1.63e+01 angle pdb=" N3 DT P 23 " pdb=" C4 DT P 23 " pdb=" O4 DT P 23 " ideal model delta sigma weight residual 119.90 122.31 -2.41 6.00e-01 2.78e+00 1.61e+01 ... (remaining 19248 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.19: 7548 22.19 - 44.39: 613 44.39 - 66.58: 201 66.58 - 88.77: 7 88.77 - 110.97: 1 Dihedral angle restraints: 8370 sinusoidal: 3763 harmonic: 4607 Sorted by residual: dihedral pdb=" CA PRO A 455 " pdb=" C PRO A 455 " pdb=" N ASN A 456 " pdb=" CA ASN A 456 " ideal model delta harmonic sigma weight residual 180.00 162.14 17.86 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA PRO A 851 " pdb=" C PRO A 851 " pdb=" N LYS A 852 " pdb=" CA LYS A 852 " ideal model delta harmonic sigma weight residual 180.00 -163.00 -17.00 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA ILE D 21 " pdb=" C ILE D 21 " pdb=" N MET D 22 " pdb=" CA MET D 22 " ideal model delta harmonic sigma weight residual 180.00 163.61 16.39 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 8367 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 2058 0.117 - 0.233: 49 0.233 - 0.350: 0 0.350 - 0.467: 0 0.467 - 0.584: 13 Chirality restraints: 2120 Sorted by residual: chirality pdb=" P DG P 24 " pdb=" OP1 DG P 24 " pdb=" OP2 DG P 24 " pdb=" O5' DG P 24 " both_signs ideal model delta sigma weight residual True 2.34 -2.92 -0.58 2.00e-01 2.50e+01 8.52e+00 chirality pdb=" P DT P 22 " pdb=" OP1 DT P 22 " pdb=" OP2 DT P 22 " pdb=" O5' DT P 22 " both_signs ideal model delta sigma weight residual True 2.34 -2.88 -0.55 2.00e-01 2.50e+01 7.53e+00 chirality pdb=" P DA P 21 " pdb=" OP1 DA P 21 " pdb=" OP2 DA P 21 " pdb=" O5' DA P 21 " both_signs ideal model delta sigma weight residual True 2.34 -2.88 -0.55 2.00e-01 2.50e+01 7.48e+00 ... (remaining 2117 not shown) Planarity restraints: 2287 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 468 " -0.027 5.00e-02 4.00e+02 4.15e-02 2.75e+00 pdb=" N PRO A 469 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 469 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 469 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG T 30 " 0.019 2.00e-02 2.50e+03 8.40e-03 2.12e+00 pdb=" N9 DG T 30 " -0.021 2.00e-02 2.50e+03 pdb=" C8 DG T 30 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DG T 30 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DG T 30 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DG T 30 " 0.003 2.00e-02 2.50e+03 pdb=" O6 DG T 30 " 0.003 2.00e-02 2.50e+03 pdb=" N1 DG T 30 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DG T 30 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG T 30 " 0.000 2.00e-02 2.50e+03 pdb=" N3 DG T 30 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DG T 30 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP E 96 " -0.022 5.00e-02 4.00e+02 3.34e-02 1.78e+00 pdb=" N PRO E 97 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO E 97 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 97 " -0.019 5.00e-02 4.00e+02 ... (remaining 2284 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1260 2.74 - 3.28: 14952 3.28 - 3.82: 24959 3.82 - 4.36: 28538 4.36 - 4.90: 45567 Nonbonded interactions: 115276 Sorted by model distance: nonbonded pdb=" O PRO A 845 " pdb=" OG1 THR A 848 " model vdw 2.196 3.040 nonbonded pdb=" OG SER A 345 " pdb=" O MET A 350 " model vdw 2.201 3.040 nonbonded pdb=" O ASN D 13 " pdb=" OG1 THR D 16 " model vdw 2.204 3.040 nonbonded pdb=" O ASP A 160 " pdb=" NE2 GLN A 315 " model vdw 2.216 3.120 nonbonded pdb=" O LYS D 5 " pdb=" OG1 THR D 8 " model vdw 2.220 3.040 ... (remaining 115271 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.310 Find NCS groups from input model: 0.120 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:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14074 Z= 0.350 Angle : 0.712 7.681 19253 Z= 0.468 Chirality : 0.063 0.584 2120 Planarity : 0.004 0.041 2287 Dihedral : 16.765 110.966 5406 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.07 % Favored : 95.87 % Rotamer: Outliers : 4.64 % Allowed : 11.26 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.21), residues: 1574 helix: 0.97 (0.23), residues: 533 sheet: -0.52 (0.26), residues: 348 loop : -0.83 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 27 TYR 0.018 0.001 TYR B 39 PHE 0.012 0.001 PHE A 698 TRP 0.010 0.001 TRP A 593 HIS 0.005 0.001 HIS D 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.35 (14074) covalent geometry : angle 0.71185 / 0.47 (19253) hydrogen bonds : bond 0.13171 / 8.54 ( 681) hydrogen bonds : angle 6.54558 / 4.52 ( 1863) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 220 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.4425 (ptt) cc_final: 0.3288 (ppp) REVERT: A 83 MET cc_start: 0.6722 (tpp) cc_final: 0.6515 (tpp) REVERT: A 85 ASP cc_start: 0.8869 (t0) cc_final: 0.8576 (t0) REVERT: A 238 ARG cc_start: 0.8807 (mtp-110) cc_final: 0.8395 (ptm160) REVERT: A 486 MET cc_start: 0.8083 (ttp) cc_final: 0.7723 (tpt) REVERT: A 667 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8757 (mp) REVERT: A 671 MET cc_start: 0.8583 (tpp) cc_final: 0.8334 (tpp) REVERT: A 721 HIS cc_start: 0.7683 (OUTLIER) cc_final: 0.7140 (p-80) REVERT: A 881 GLU cc_start: 0.9147 (OUTLIER) cc_final: 0.8661 (pp20) REVERT: B 14 PHE cc_start: 0.8800 (m-10) cc_final: 0.8509 (m-80) REVERT: B 32 ARG cc_start: 0.8244 (tpp-160) cc_final: 0.8029 (tpp-160) REVERT: B 128 ARG cc_start: 0.9208 (mmt90) cc_final: 0.8940 (mmm-85) REVERT: B 215 ASN cc_start: 0.8001 (m-40) cc_final: 0.7724 (m-40) REVERT: D 30 MET cc_start: 0.8102 (ptm) cc_final: 0.7512 (ptp) REVERT: D 55 TYR cc_start: 0.8120 (t80) cc_final: 0.7864 (t80) REVERT: D 58 ASN cc_start: 0.8656 (OUTLIER) cc_final: 0.8411 (m-40) REVERT: D 70 ASP cc_start: 0.7597 (t70) cc_final: 0.7332 (t70) REVERT: D 128 ARG cc_start: 0.8265 (tpp80) cc_final: 0.7891 (ttm170) REVERT: D 198 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9048 (mp) REVERT: E 1 MET cc_start: 0.7607 (mmt) cc_final: 0.7190 (mmt) REVERT: E 125 GLN cc_start: 0.9114 (tm-30) cc_final: 0.8763 (tm-30) REVERT: E 180 PHE cc_start: 0.8338 (m-10) cc_final: 0.7446 (m-10) REVERT: E 187 MET cc_start: 0.9181 (mmm) cc_final: 0.8935 (mmm) outliers start: 63 outliers final: 32 residues processed: 270 average time/residue: 0.1023 time to fit residues: 40.8455 Evaluate side-chains 204 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 167 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 676 HIS Chi-restraints excluded: chain A residue 721 HIS Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 869 GLN Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 881 GLU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain E residue 6 ASP Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 195 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 0.0670 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.1980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 125 GLN D 13 ASN ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.108083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.082129 restraints weight = 47967.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.084317 restraints weight = 29329.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.085282 restraints weight = 19289.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.085627 restraints weight = 17737.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.085824 restraints weight = 15908.336| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14074 Z= 0.148 Angle : 0.661 11.093 19253 Z= 0.352 Chirality : 0.046 0.281 2120 Planarity : 0.004 0.052 2287 Dihedral : 18.461 105.215 2399 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.19 % Allowed : 16.04 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.21), residues: 1574 helix: 0.85 (0.22), residues: 542 sheet: -0.48 (0.25), residues: 393 loop : -0.60 (0.26), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 704 TYR 0.020 0.002 TYR B 39 PHE 0.021 0.001 PHE B 109 TRP 0.013 0.001 TRP A 593 HIS 0.005 0.001 HIS B 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 (14074) covalent geometry : angle 0.66140 / 0.35 (19253) hydrogen bonds : bond 0.04673 / 3.07 ( 681) hydrogen bonds : angle 5.63815 / 3.87 ( 1863) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 188 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.4427 (ptt) cc_final: 0.3252 (ppp) REVERT: A 85 ASP cc_start: 0.8641 (t0) cc_final: 0.8230 (t70) REVERT: A 236 MET cc_start: 0.7620 (mtp) cc_final: 0.7413 (mtm) REVERT: A 238 ARG cc_start: 0.8749 (mtp-110) cc_final: 0.8363 (ptm160) REVERT: A 324 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7711 (p0) REVERT: A 486 MET cc_start: 0.8136 (ttp) cc_final: 0.7664 (tpt) REVERT: A 727 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7367 (mtm) REVERT: B 14 PHE cc_start: 0.8800 (m-10) cc_final: 0.8563 (m-80) REVERT: B 78 ASP cc_start: 0.8991 (t70) cc_final: 0.8710 (p0) REVERT: B 215 ASN cc_start: 0.7807 (m-40) cc_final: 0.7506 (m-40) REVERT: D 198 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9029 (mp) REVERT: E 1 MET cc_start: 0.7426 (mmt) cc_final: 0.6947 (mmt) REVERT: E 125 GLN cc_start: 0.9131 (tm-30) cc_final: 0.8778 (tm-30) outliers start: 57 outliers final: 37 residues processed: 235 average time/residue: 0.0927 time to fit residues: 33.2289 Evaluate side-chains 193 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 153 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 676 HIS Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 869 GLN Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 195 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 21 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 39 optimal weight: 0.8980 chunk 98 optimal weight: 10.0000 chunk 115 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 152 optimal weight: 20.0000 chunk 97 optimal weight: 7.9990 chunk 77 optimal weight: 0.5980 chunk 151 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 ASN ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.108275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.081051 restraints weight = 48052.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.083657 restraints weight = 27804.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.085459 restraints weight = 19369.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.086673 restraints weight = 15209.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.087539 restraints weight = 12885.110| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14074 Z= 0.137 Angle : 0.625 11.101 19253 Z= 0.334 Chirality : 0.045 0.223 2120 Planarity : 0.004 0.050 2287 Dihedral : 18.366 143.999 2371 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.97 % Allowed : 16.11 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.21), residues: 1574 helix: 0.76 (0.22), residues: 542 sheet: -0.42 (0.25), residues: 393 loop : -0.60 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 131 TYR 0.018 0.001 TYR B 39 PHE 0.027 0.001 PHE B 109 TRP 0.013 0.001 TRP A 593 HIS 0.003 0.001 HIS B 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 (14074) covalent geometry : angle 0.62510 / 0.33 (19253) hydrogen bonds : bond 0.04121 / 2.68 ( 681) hydrogen bonds : angle 5.47853 / 3.75 ( 1863) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 182 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 TYR cc_start: 0.7394 (p90) cc_final: 0.7146 (p90) REVERT: A 37 MET cc_start: 0.4117 (ptt) cc_final: 0.3161 (ppp) REVERT: A 85 ASP cc_start: 0.8495 (t0) cc_final: 0.8207 (t70) REVERT: A 236 MET cc_start: 0.7526 (mtp) cc_final: 0.7326 (mtm) REVERT: A 238 ARG cc_start: 0.8653 (mtp-110) cc_final: 0.8283 (ptm160) REVERT: A 246 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8366 (mmtt) REVERT: A 324 ASP cc_start: 0.8237 (OUTLIER) cc_final: 0.7769 (p0) REVERT: A 350 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7360 (pmm) REVERT: A 486 MET cc_start: 0.8203 (ttp) cc_final: 0.7745 (tpt) REVERT: A 671 MET cc_start: 0.7969 (tpp) cc_final: 0.7741 (tpp) REVERT: A 721 HIS cc_start: 0.7531 (OUTLIER) cc_final: 0.6969 (p-80) REVERT: A 727 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7695 (mtm) REVERT: B 14 PHE cc_start: 0.8802 (m-10) cc_final: 0.8553 (m-80) REVERT: D 87 ARG cc_start: 0.7517 (mtp180) cc_final: 0.7239 (mtp180) REVERT: D 124 GLN cc_start: 0.8620 (tp-100) cc_final: 0.7923 (tp-100) REVERT: D 198 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9149 (mp) REVERT: E 1 MET cc_start: 0.7154 (mmt) cc_final: 0.5297 (mmt) REVERT: E 125 GLN cc_start: 0.9109 (tm-30) cc_final: 0.8745 (tm-30) outliers start: 54 outliers final: 37 residues processed: 225 average time/residue: 0.0964 time to fit residues: 32.7917 Evaluate side-chains 201 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 158 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 676 HIS Chi-restraints excluded: chain A residue 721 HIS Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 869 GLN Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 195 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 88 optimal weight: 5.9990 chunk 120 optimal weight: 0.0170 chunk 123 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 105 optimal weight: 7.9990 chunk 93 optimal weight: 20.0000 chunk 147 optimal weight: 0.9990 chunk 52 optimal weight: 0.0470 chunk 29 optimal weight: 6.9990 chunk 71 optimal weight: 0.0470 overall best weight: 1.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 ASN ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.108588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.083017 restraints weight = 48886.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.084333 restraints weight = 30366.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.085282 restraints weight = 21855.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.086506 restraints weight = 18783.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.086491 restraints weight = 16590.485| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14074 Z= 0.142 Angle : 0.634 11.014 19253 Z= 0.335 Chirality : 0.045 0.244 2120 Planarity : 0.004 0.048 2287 Dihedral : 18.361 156.146 2370 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.56 % Allowed : 16.41 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.21), residues: 1574 helix: 0.72 (0.22), residues: 539 sheet: -0.45 (0.25), residues: 403 loop : -0.59 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 128 TYR 0.019 0.001 TYR B 39 PHE 0.032 0.001 PHE B 109 TRP 0.012 0.001 TRP A 844 HIS 0.003 0.001 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (14074) covalent geometry : angle 0.63372 / 0.33 (19253) hydrogen bonds : bond 0.03966 / 2.57 ( 681) hydrogen bonds : angle 5.40748 / 3.70 ( 1863) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 177 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.4253 (ptt) cc_final: 0.3230 (ppp) REVERT: A 85 ASP cc_start: 0.8600 (t0) cc_final: 0.8332 (t70) REVERT: A 196 MET cc_start: 0.8616 (mpp) cc_final: 0.8198 (mpp) REVERT: A 236 MET cc_start: 0.7659 (mtp) cc_final: 0.7177 (mpp) REVERT: A 238 ARG cc_start: 0.8670 (mtp-110) cc_final: 0.8310 (ptm160) REVERT: A 246 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8410 (mmtt) REVERT: A 324 ASP cc_start: 0.8292 (OUTLIER) cc_final: 0.7793 (p0) REVERT: A 350 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.7371 (pmm) REVERT: A 486 MET cc_start: 0.8121 (ttp) cc_final: 0.7764 (tpt) REVERT: A 671 MET cc_start: 0.8195 (tpp) cc_final: 0.7868 (tpp) REVERT: A 721 HIS cc_start: 0.7576 (OUTLIER) cc_final: 0.7003 (p-80) REVERT: A 727 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7691 (mtm) REVERT: A 829 LEU cc_start: 0.7289 (mt) cc_final: 0.7007 (mp) REVERT: A 885 MET cc_start: 0.8001 (mmt) cc_final: 0.7679 (mmt) REVERT: B 14 PHE cc_start: 0.8805 (m-10) cc_final: 0.8594 (m-80) REVERT: B 32 ARG cc_start: 0.8375 (tpt170) cc_final: 0.7975 (tpp-160) REVERT: D 87 ARG cc_start: 0.7550 (mtp180) cc_final: 0.7048 (mtp180) REVERT: E 125 GLN cc_start: 0.9166 (tm-30) cc_final: 0.8778 (tm-30) REVERT: E 187 MET cc_start: 0.9148 (mmt) cc_final: 0.8593 (mmt) REVERT: E 189 MET cc_start: 0.8985 (mpp) cc_final: 0.8674 (mpp) outliers start: 62 outliers final: 48 residues processed: 226 average time/residue: 0.0999 time to fit residues: 34.2216 Evaluate side-chains 213 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 160 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 721 HIS Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 869 GLN Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 194 TYR Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 195 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 12 optimal weight: 10.0000 chunk 124 optimal weight: 0.3980 chunk 29 optimal weight: 6.9990 chunk 141 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 152 optimal weight: 8.9990 chunk 138 optimal weight: 9.9990 chunk 88 optimal weight: 0.2980 chunk 93 optimal weight: 20.0000 chunk 111 optimal weight: 0.6980 chunk 125 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 ASN ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.108333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.082688 restraints weight = 48689.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.084485 restraints weight = 28587.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.085357 restraints weight = 19725.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.085745 restraints weight = 18251.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.085821 restraints weight = 16103.536| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14074 Z= 0.142 Angle : 0.622 11.346 19253 Z= 0.329 Chirality : 0.044 0.262 2120 Planarity : 0.004 0.047 2287 Dihedral : 18.318 157.112 2368 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.86 % Allowed : 17.37 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.21), residues: 1574 helix: 0.79 (0.22), residues: 540 sheet: -0.34 (0.25), residues: 407 loop : -0.63 (0.26), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 32 TYR 0.019 0.001 TYR B 39 PHE 0.031 0.001 PHE B 109 TRP 0.015 0.001 TRP B 92 HIS 0.003 0.001 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (14074) covalent geometry : angle 0.62151 / 0.33 (19253) hydrogen bonds : bond 0.03844 / 2.50 ( 681) hydrogen bonds : angle 5.28406 / 3.62 ( 1863) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 173 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.4270 (ptt) cc_final: 0.3230 (ppp) REVERT: A 85 ASP cc_start: 0.8656 (t0) cc_final: 0.8333 (t70) REVERT: A 236 MET cc_start: 0.7735 (mtp) cc_final: 0.7225 (mpp) REVERT: A 238 ARG cc_start: 0.8704 (mtp-110) cc_final: 0.8324 (ptm160) REVERT: A 246 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8410 (mmtt) REVERT: A 324 ASP cc_start: 0.8317 (OUTLIER) cc_final: 0.7791 (p0) REVERT: A 350 MET cc_start: 0.7788 (OUTLIER) cc_final: 0.7395 (pmm) REVERT: A 486 MET cc_start: 0.8116 (ttp) cc_final: 0.7565 (mmm) REVERT: A 671 MET cc_start: 0.8257 (tpp) cc_final: 0.7937 (tpp) REVERT: A 721 HIS cc_start: 0.7669 (OUTLIER) cc_final: 0.7027 (p-80) REVERT: A 727 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7688 (mtm) REVERT: A 881 GLU cc_start: 0.9062 (OUTLIER) cc_final: 0.8449 (pp20) REVERT: A 885 MET cc_start: 0.8181 (mmt) cc_final: 0.7827 (mmt) REVERT: B 14 PHE cc_start: 0.8798 (m-10) cc_final: 0.8583 (m-80) REVERT: D 87 ARG cc_start: 0.7536 (mtp180) cc_final: 0.7021 (mtp180) REVERT: D 181 ILE cc_start: 0.9086 (mm) cc_final: 0.8761 (mp) REVERT: E 1 MET cc_start: 0.7596 (mmt) cc_final: 0.7108 (mmt) REVERT: E 125 GLN cc_start: 0.9138 (tm-30) cc_final: 0.8770 (tm-30) REVERT: E 187 MET cc_start: 0.9145 (mmt) cc_final: 0.8427 (mmt) REVERT: E 189 MET cc_start: 0.8996 (mpp) cc_final: 0.8598 (mpp) outliers start: 66 outliers final: 48 residues processed: 224 average time/residue: 0.1030 time to fit residues: 34.9331 Evaluate side-chains 216 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 162 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 721 HIS Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 869 GLN Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 881 GLU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 195 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 63 optimal weight: 8.9990 chunk 148 optimal weight: 10.0000 chunk 152 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 110 optimal weight: 8.9990 chunk 127 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 90 optimal weight: 8.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.104521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.078640 restraints weight = 48184.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.080410 restraints weight = 28377.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.080947 restraints weight = 20163.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.081290 restraints weight = 18214.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.081538 restraints weight = 16323.127| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 14074 Z= 0.268 Angle : 0.707 12.339 19253 Z= 0.375 Chirality : 0.047 0.364 2120 Planarity : 0.004 0.044 2287 Dihedral : 18.427 162.442 2367 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 18.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 5.15 % Allowed : 18.25 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.21), residues: 1574 helix: 0.65 (0.23), residues: 542 sheet: -0.57 (0.25), residues: 407 loop : -0.77 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 192 TYR 0.021 0.002 TYR D 165 PHE 0.025 0.002 PHE B 109 TRP 0.014 0.002 TRP B 92 HIS 0.004 0.001 HIS D 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00579 / 0.27 (14074) covalent geometry : angle 0.70650 / 0.38 (19253) hydrogen bonds : bond 0.04681 / 3.05 ( 681) hydrogen bonds : angle 5.54219 / 3.78 ( 1863) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 163 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.4266 (ptt) cc_final: 0.3102 (ppp) REVERT: A 85 ASP cc_start: 0.8725 (t0) cc_final: 0.8510 (t70) REVERT: A 196 MET cc_start: 0.8847 (mpp) cc_final: 0.8545 (mpp) REVERT: A 236 MET cc_start: 0.7889 (mtp) cc_final: 0.7342 (mpp) REVERT: A 238 ARG cc_start: 0.8779 (mtp-110) cc_final: 0.8422 (ptm160) REVERT: A 246 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8432 (mmtt) REVERT: A 272 ASP cc_start: 0.8516 (p0) cc_final: 0.8276 (p0) REVERT: A 350 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7548 (pmm) REVERT: A 486 MET cc_start: 0.8215 (ttp) cc_final: 0.7606 (mmm) REVERT: A 671 MET cc_start: 0.8363 (tpp) cc_final: 0.8046 (tpp) REVERT: A 721 HIS cc_start: 0.8249 (OUTLIER) cc_final: 0.7536 (p-80) REVERT: A 727 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7483 (mtm) REVERT: A 881 GLU cc_start: 0.9132 (OUTLIER) cc_final: 0.8538 (pp20) REVERT: A 885 MET cc_start: 0.8495 (mmt) cc_final: 0.8086 (mmt) REVERT: D 87 ARG cc_start: 0.7506 (mtp180) cc_final: 0.7299 (mmm160) REVERT: E 125 GLN cc_start: 0.9184 (tm-30) cc_final: 0.8891 (tm-30) REVERT: E 187 MET cc_start: 0.9207 (mmt) cc_final: 0.8654 (mmm) REVERT: E 189 MET cc_start: 0.9102 (mpp) cc_final: 0.8720 (mpp) outliers start: 70 outliers final: 53 residues processed: 217 average time/residue: 0.1132 time to fit residues: 37.1305 Evaluate side-chains 212 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 154 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 676 HIS Chi-restraints excluded: chain A residue 721 HIS Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 869 GLN Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 881 GLU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 195 LYS Chi-restraints excluded: chain E residue 217 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 49 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 111 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 106 optimal weight: 8.9990 chunk 18 optimal weight: 0.5980 chunk 159 optimal weight: 30.0000 chunk 63 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 ASN A 603 ASN ** A 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.108293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.080809 restraints weight = 48385.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.083455 restraints weight = 28504.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.085288 restraints weight = 20021.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.086483 restraints weight = 15713.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.087209 restraints weight = 13358.225| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14074 Z= 0.132 Angle : 0.678 16.103 19253 Z= 0.347 Chirality : 0.046 0.278 2120 Planarity : 0.004 0.045 2287 Dihedral : 18.296 159.254 2367 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.34 % Allowed : 19.57 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.21), residues: 1574 helix: 0.61 (0.22), residues: 548 sheet: -0.43 (0.25), residues: 406 loop : -0.64 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 665 TYR 0.019 0.002 TYR B 39 PHE 0.019 0.001 PHE B 109 TRP 0.020 0.002 TRP B 92 HIS 0.004 0.001 HIS A 801 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (14074) covalent geometry : angle 0.67797 / 0.35 (19253) hydrogen bonds : bond 0.03723 / 2.40 ( 681) hydrogen bonds : angle 5.31251 / 3.63 ( 1863) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 180 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.4018 (ptt) cc_final: 0.3135 (ppp) REVERT: A 70 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.7972 (mpp) REVERT: A 85 ASP cc_start: 0.8495 (t0) cc_final: 0.8234 (t70) REVERT: A 194 MET cc_start: 0.8034 (tpt) cc_final: 0.7721 (tpp) REVERT: A 196 MET cc_start: 0.8732 (mpp) cc_final: 0.8351 (mpp) REVERT: A 226 ARG cc_start: 0.9205 (OUTLIER) cc_final: 0.8529 (tpp80) REVERT: A 236 MET cc_start: 0.7640 (mtp) cc_final: 0.7181 (mpp) REVERT: A 238 ARG cc_start: 0.8617 (mtp-110) cc_final: 0.8270 (ptm160) REVERT: A 246 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8329 (mmtt) REVERT: A 288 GLU cc_start: 0.8016 (mp0) cc_final: 0.7619 (mp0) REVERT: A 324 ASP cc_start: 0.8329 (OUTLIER) cc_final: 0.7875 (p0) REVERT: A 350 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.7329 (pmm) REVERT: A 486 MET cc_start: 0.8235 (ttp) cc_final: 0.7556 (mmm) REVERT: A 603 ASN cc_start: 0.8345 (OUTLIER) cc_final: 0.8128 (m-40) REVERT: A 671 MET cc_start: 0.8220 (tpp) cc_final: 0.7961 (tpp) REVERT: A 721 HIS cc_start: 0.8065 (OUTLIER) cc_final: 0.7172 (p-80) REVERT: A 881 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8449 (pp20) REVERT: A 885 MET cc_start: 0.8262 (mmt) cc_final: 0.8049 (mmt) REVERT: B 30 MET cc_start: 0.8201 (mmm) cc_final: 0.7979 (mmm) REVERT: B 32 ARG cc_start: 0.8256 (tpt170) cc_final: 0.7324 (tpp-160) REVERT: B 50 PHE cc_start: 0.6720 (p90) cc_final: 0.5881 (p90) REVERT: D 116 THR cc_start: 0.8389 (t) cc_final: 0.8116 (m) REVERT: D 181 ILE cc_start: 0.9003 (mm) cc_final: 0.8642 (mp) REVERT: E 1 MET cc_start: 0.7390 (mmt) cc_final: 0.6924 (mmt) REVERT: E 125 GLN cc_start: 0.9124 (tm-30) cc_final: 0.8757 (tm-30) outliers start: 59 outliers final: 41 residues processed: 228 average time/residue: 0.1119 time to fit residues: 38.2835 Evaluate side-chains 210 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 161 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 676 HIS Chi-restraints excluded: chain A residue 721 HIS Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 869 GLN Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 881 GLU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 195 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 133 optimal weight: 10.0000 chunk 148 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 142 optimal weight: 0.3980 chunk 154 optimal weight: 6.9990 chunk 54 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 45 optimal weight: 8.9990 chunk 46 optimal weight: 0.8980 chunk 35 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.108706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.083204 restraints weight = 48369.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.085409 restraints weight = 28570.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.086141 restraints weight = 18998.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.086390 restraints weight = 17620.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.086643 restraints weight = 15595.582| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14074 Z= 0.133 Angle : 0.699 14.148 19253 Z= 0.355 Chirality : 0.046 0.252 2120 Planarity : 0.004 0.041 2287 Dihedral : 18.229 156.629 2362 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.97 % Allowed : 20.38 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.21), residues: 1574 helix: 0.64 (0.22), residues: 548 sheet: -0.45 (0.25), residues: 406 loop : -0.60 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 665 TYR 0.020 0.002 TYR B 194 PHE 0.023 0.001 PHE B 109 TRP 0.031 0.002 TRP B 92 HIS 0.003 0.001 HIS A 721 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (14074) covalent geometry : angle 0.69874 / 0.36 (19253) hydrogen bonds : bond 0.03640 / 2.36 ( 681) hydrogen bonds : angle 5.23426 / 3.58 ( 1863) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 166 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.4021 (ptt) cc_final: 0.3052 (ppp) REVERT: A 70 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.7930 (mpp) REVERT: A 85 ASP cc_start: 0.8560 (t0) cc_final: 0.8346 (t70) REVERT: A 196 MET cc_start: 0.8768 (mpp) cc_final: 0.8500 (mpp) REVERT: A 226 ARG cc_start: 0.9195 (OUTLIER) cc_final: 0.8557 (tpp80) REVERT: A 236 MET cc_start: 0.7716 (mtp) cc_final: 0.7194 (mpp) REVERT: A 238 ARG cc_start: 0.8697 (mtp-110) cc_final: 0.8301 (ptm160) REVERT: A 246 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8368 (mmtt) REVERT: A 288 GLU cc_start: 0.8057 (mp0) cc_final: 0.7672 (mp0) REVERT: A 324 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.7891 (p0) REVERT: A 350 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.7378 (pmm) REVERT: A 486 MET cc_start: 0.8095 (ttp) cc_final: 0.7562 (mmm) REVERT: A 501 MET cc_start: 0.7786 (ppp) cc_final: 0.7351 (ppp) REVERT: A 671 MET cc_start: 0.8327 (tpp) cc_final: 0.8039 (tpp) REVERT: A 693 LYS cc_start: 0.8451 (ptmm) cc_final: 0.8239 (ttpp) REVERT: A 721 HIS cc_start: 0.8013 (OUTLIER) cc_final: 0.7179 (p-80) REVERT: A 881 GLU cc_start: 0.9054 (OUTLIER) cc_final: 0.8422 (pp20) REVERT: A 885 MET cc_start: 0.8229 (mmt) cc_final: 0.7996 (mmt) REVERT: B 32 ARG cc_start: 0.8295 (tpt170) cc_final: 0.7394 (tpp-160) REVERT: B 50 PHE cc_start: 0.6677 (p90) cc_final: 0.6017 (p90) REVERT: D 116 THR cc_start: 0.8334 (t) cc_final: 0.8073 (m) REVERT: D 181 ILE cc_start: 0.8908 (mm) cc_final: 0.8543 (mp) REVERT: E 1 MET cc_start: 0.7452 (mmt) cc_final: 0.7008 (mmt) REVERT: E 125 GLN cc_start: 0.9116 (tm-30) cc_final: 0.8818 (tm-30) REVERT: E 189 MET cc_start: 0.8856 (mpp) cc_final: 0.8087 (mpp) outliers start: 54 outliers final: 44 residues processed: 208 average time/residue: 0.1000 time to fit residues: 31.0506 Evaluate side-chains 210 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 159 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 676 HIS Chi-restraints excluded: chain A residue 721 HIS Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 869 GLN Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 881 GLU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 195 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 124 optimal weight: 0.6980 chunk 155 optimal weight: 40.0000 chunk 103 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 79 optimal weight: 0.2980 chunk 101 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 143 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.107945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.080747 restraints weight = 47967.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.083441 restraints weight = 27808.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.085306 restraints weight = 19298.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.086541 restraints weight = 14999.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.087322 restraints weight = 12668.851| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14074 Z= 0.138 Angle : 0.689 12.636 19253 Z= 0.348 Chirality : 0.046 0.254 2120 Planarity : 0.004 0.040 2287 Dihedral : 18.230 155.821 2362 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.90 % Allowed : 20.75 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.21), residues: 1574 helix: 0.68 (0.22), residues: 548 sheet: -0.50 (0.25), residues: 385 loop : -0.66 (0.26), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG E 162 TYR 0.022 0.002 TYR A 460 PHE 0.020 0.001 PHE B 28 TRP 0.024 0.002 TRP B 92 HIS 0.003 0.001 HIS A 676 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (14074) covalent geometry : angle 0.68882 / 0.35 (19253) hydrogen bonds : bond 0.03615 / 2.36 ( 681) hydrogen bonds : angle 5.17697 / 3.54 ( 1863) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 169 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.4083 (ptt) cc_final: 0.3092 (ppp) REVERT: A 70 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.7962 (mpp) REVERT: A 136 TYR cc_start: 0.7273 (t80) cc_final: 0.6876 (t80) REVERT: A 226 ARG cc_start: 0.9193 (OUTLIER) cc_final: 0.8566 (tpp80) REVERT: A 236 MET cc_start: 0.7656 (mtp) cc_final: 0.7244 (mpp) REVERT: A 238 ARG cc_start: 0.8661 (mtp-110) cc_final: 0.8263 (ptm160) REVERT: A 246 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8087 (mtmm) REVERT: A 272 ASP cc_start: 0.8360 (p0) cc_final: 0.8135 (p0) REVERT: A 288 GLU cc_start: 0.8073 (mp0) cc_final: 0.7666 (mp0) REVERT: A 350 MET cc_start: 0.7712 (OUTLIER) cc_final: 0.7310 (pmm) REVERT: A 486 MET cc_start: 0.8171 (ttp) cc_final: 0.7564 (mmm) REVERT: A 501 MET cc_start: 0.7844 (ppp) cc_final: 0.7456 (ppp) REVERT: A 671 MET cc_start: 0.8332 (tpp) cc_final: 0.8068 (tpp) REVERT: A 721 HIS cc_start: 0.7935 (OUTLIER) cc_final: 0.7144 (p-80) REVERT: A 881 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.8441 (pp20) REVERT: B 30 MET cc_start: 0.8185 (mmm) cc_final: 0.7925 (mmm) REVERT: B 32 ARG cc_start: 0.8204 (tpt170) cc_final: 0.7291 (tpp-160) REVERT: B 50 PHE cc_start: 0.6476 (p90) cc_final: 0.6056 (p90) REVERT: D 116 THR cc_start: 0.8425 (t) cc_final: 0.8186 (m) REVERT: D 181 ILE cc_start: 0.8955 (mm) cc_final: 0.8576 (mp) REVERT: E 1 MET cc_start: 0.7301 (mmt) cc_final: 0.6856 (mmt) REVERT: E 125 GLN cc_start: 0.9105 (tm-30) cc_final: 0.8801 (tm-30) outliers start: 53 outliers final: 43 residues processed: 209 average time/residue: 0.1214 time to fit residues: 37.7712 Evaluate side-chains 208 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 159 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 421 ASN Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 676 HIS Chi-restraints excluded: chain A residue 721 HIS Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 869 GLN Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 881 GLU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 195 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 8 optimal weight: 20.0000 chunk 52 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 116 optimal weight: 6.9990 chunk 140 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 90 optimal weight: 10.0000 chunk 48 optimal weight: 0.0020 overall best weight: 1.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.108125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.082582 restraints weight = 48484.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.084763 restraints weight = 28611.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.085345 restraints weight = 19022.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.085783 restraints weight = 17987.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.085955 restraints weight = 15798.647| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.208 14074 Z= 0.206 Angle : 0.902 59.200 19253 Z= 0.503 Chirality : 0.048 0.421 2120 Planarity : 0.004 0.040 2287 Dihedral : 18.236 155.788 2361 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.13 % Favored : 95.81 % Rotamer: Outliers : 3.75 % Allowed : 21.34 % Favored : 74.91 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.21), residues: 1574 helix: 0.68 (0.22), residues: 548 sheet: -0.49 (0.25), residues: 385 loop : -0.67 (0.26), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG E 162 TYR 0.018 0.002 TYR B 39 PHE 0.015 0.001 PHE A 367 TRP 0.023 0.002 TRP B 92 HIS 0.003 0.001 HIS A 676 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.21 (14074) covalent geometry : angle 0.90162 / 0.50 (19253) hydrogen bonds : bond 0.03659 / 2.40 ( 681) hydrogen bonds : angle 5.19072 / 3.54 ( 1863) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 160 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.4142 (ptt) cc_final: 0.3119 (ppp) REVERT: A 70 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.7957 (mpp) REVERT: A 226 ARG cc_start: 0.9189 (OUTLIER) cc_final: 0.8571 (tpp80) REVERT: A 236 MET cc_start: 0.7815 (mtp) cc_final: 0.7282 (mpp) REVERT: A 238 ARG cc_start: 0.8719 (mtp-110) cc_final: 0.8319 (ptm160) REVERT: A 246 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8157 (mtmm) REVERT: A 272 ASP cc_start: 0.8315 (p0) cc_final: 0.8054 (p0) REVERT: A 288 GLU cc_start: 0.8080 (mp0) cc_final: 0.7686 (mp0) REVERT: A 350 MET cc_start: 0.7719 (OUTLIER) cc_final: 0.7308 (pmm) REVERT: A 486 MET cc_start: 0.8082 (ttp) cc_final: 0.7570 (mmm) REVERT: A 501 MET cc_start: 0.7896 (ppp) cc_final: 0.7511 (ppp) REVERT: A 671 MET cc_start: 0.8397 (tpp) cc_final: 0.8099 (tpp) REVERT: A 721 HIS cc_start: 0.7927 (OUTLIER) cc_final: 0.7107 (p-80) REVERT: A 881 GLU cc_start: 0.9061 (OUTLIER) cc_final: 0.8465 (pp20) REVERT: B 30 MET cc_start: 0.8219 (mmm) cc_final: 0.7954 (mmm) REVERT: B 32 ARG cc_start: 0.8257 (tpt170) cc_final: 0.7342 (tpp-160) REVERT: B 50 PHE cc_start: 0.6860 (p90) cc_final: 0.6218 (p90) REVERT: D 116 THR cc_start: 0.8385 (t) cc_final: 0.8137 (m) REVERT: D 181 ILE cc_start: 0.8894 (mm) cc_final: 0.8532 (mp) REVERT: E 1 MET cc_start: 0.7409 (mmt) cc_final: 0.6955 (mmt) REVERT: E 125 GLN cc_start: 0.9107 (tm-30) cc_final: 0.8808 (tm-30) outliers start: 51 outliers final: 42 residues processed: 199 average time/residue: 0.1090 time to fit residues: 32.6168 Evaluate side-chains 209 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 161 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 676 HIS Chi-restraints excluded: chain A residue 721 HIS Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 869 GLN Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 881 GLU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 195 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 103 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 33 optimal weight: 7.9990 chunk 147 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 42 optimal weight: 20.0000 chunk 55 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 57 optimal weight: 7.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.108146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.082645 restraints weight = 48894.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.084790 restraints weight = 28655.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.085340 restraints weight = 19244.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.085873 restraints weight = 18028.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.086007 restraints weight = 15822.455| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.208 14074 Z= 0.206 Angle : 0.902 59.200 19253 Z= 0.503 Chirality : 0.048 0.421 2120 Planarity : 0.004 0.040 2287 Dihedral : 18.235 155.788 2360 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 18.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.13 % Favored : 95.81 % Rotamer: Outliers : 3.53 % Allowed : 21.49 % Favored : 74.98 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.21), residues: 1574 helix: 0.68 (0.22), residues: 548 sheet: -0.49 (0.25), residues: 385 loop : -0.67 (0.26), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG E 162 TYR 0.018 0.002 TYR B 39 PHE 0.015 0.001 PHE A 367 TRP 0.023 0.002 TRP B 92 HIS 0.003 0.001 HIS A 676 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.21 (14074) covalent geometry : angle 0.90163 / 0.50 (19253) hydrogen bonds : bond 0.03659 / 2.40 ( 681) hydrogen bonds : angle 5.19072 / 3.54 ( 1863) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2285.40 seconds wall clock time: 40 minutes 25.48 seconds (2425.48 seconds total)