Starting phenix.real_space_refine on Fri Jul 3 12:07:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ea3_47825/07_2026/9ea3_47825.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ea3_47825/07_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_47825/07_2026/9ea3_47825.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ea3_47825/07_2026/9ea3_47825.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ea3_47825/07_2026/9ea3_47825.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ea3_47825/07_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-dev-6108/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: 2.30, per 1000 atoms: 0.17 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: 1.05 Conformation dependent library (CDL) restraints added in 481.3 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: 1.48 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: 2.35 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 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: 18342 1.54 - 3.07: 779 3.07 - 4.61: 89 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: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.580 Find NCS groups from input model: 0.190 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:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.900 ------------------------------------------------------------------------------- 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 : 0.710 7.681 19253 Z= 0.466 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 0.70993 / 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 : 0.527 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: 0.3286 (ppp) REVERT: A 83 MET cc_start: 0.6722 (tpp) cc_final: 0.6518 (tpp) REVERT: A 85 ASP cc_start: 0.8869 (t0) cc_final: 0.8579 (t0) REVERT: A 238 ARG cc_start: 0.8807 (mtp-110) cc_final: 0.8394 (ptm160) REVERT: A 486 MET cc_start: 0.8083 (ttp) cc_final: 0.7727 (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: 0.8335 (tpp) REVERT: A 721 HIS cc_start: 0.7683 (OUTLIER) cc_final: 0.7136 (p-80) REVERT: A 881 GLU cc_start: 0.9147 (OUTLIER) cc_final: 0.8660 (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: 0.8939 (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: 0.7510 (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: 0.7892 (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: 0.7189 (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: 0.8936 (mmm) outliers start: 63 outliers final: 32 residues processed: 270 average time/residue: 0.1194 time to fit residues: 47.3751 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 : 0.540 ------------------------------------------------------------------------------- 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 = 0.108142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.082241 restraints weight = 47464.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.084427 restraints weight = 29171.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.085505 restraints weight = 18577.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.085877 restraints weight = 17404.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.086111 restraints weight = 15353.310| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14074 Z= 0.151 Angle : 0.662 11.169 19253 Z= 0.353 Chirality : 0.047 0.296 2120 Planarity : 0.004 0.053 2287 Dihedral : 18.574 153.225 2399 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.34 % Allowed : 15.53 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.21), residues: 1574 helix: 0.83 (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 103 TYR 0.020 0.002 TYR B 39 PHE 0.022 0.001 PHE B 109 TRP 0.014 0.001 TRP A 593 HIS 0.005 0.001 HIS B 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 (14074) covalent geometry : angle 0.66219 / 0.35 (19253) hydrogen bonds : bond 0.04507 / 2.97 ( 681) hydrogen bonds : angle 5.61351 / 3.85 ( 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 248 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 189 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 TYR cc_start: 0.7438 (p90) cc_final: 0.7167 (p90) REVERT: A 30 GLU cc_start: 0.7921 (pp20) cc_final: 0.7620 (pp20) REVERT: A 37 MET cc_start: 0.4416 (ptt) cc_final: 0.3246 (ppp) REVERT: A 85 ASP cc_start: 0.8603 (t0) cc_final: 0.8186 (t70) REVERT: A 236 MET cc_start: 0.7689 (mtp) cc_final: 0.7466 (mtm) REVERT: A 238 ARG cc_start: 0.8747 (mtp-110) cc_final: 0.8379 (ptm160) REVERT: A 324 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7706 (p0) REVERT: A 486 MET cc_start: 0.8127 (ttp) cc_final: 0.7657 (tpt) REVERT: B 14 PHE cc_start: 0.8808 (m-10) cc_final: 0.8574 (m-80) REVERT: B 52 VAL cc_start: 0.8649 (OUTLIER) cc_final: 0.8442 (m) REVERT: B 78 ASP cc_start: 0.8958 (t70) cc_final: 0.8741 (p0) REVERT: B 124 GLN cc_start: 0.8939 (tm-30) cc_final: 0.8627 (tm-30) REVERT: B 128 ARG cc_start: 0.9237 (mmt90) cc_final: 0.8982 (mmm-85) REVERT: D 87 ARG cc_start: 0.7565 (mtp180) cc_final: 0.7189 (mtp180) REVERT: D 198 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9066 (mp) REVERT: E 1 MET cc_start: 0.7406 (mmt) cc_final: 0.6929 (mmt) REVERT: E 125 GLN cc_start: 0.9143 (tm-30) cc_final: 0.8791 (tm-30) REVERT: E 184 MET cc_start: 0.9119 (mmm) cc_final: 0.8830 (mmm) outliers start: 59 outliers final: 37 residues processed: 238 average time/residue: 0.1103 time to fit residues: 39.2706 Evaluate side-chains 195 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 155 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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 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 52 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: 0.9990 chunk 60 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 chunk 152 optimal weight: 8.9990 chunk 97 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 151 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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** ** D 125 GLN ** 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 = 0.3963 r_free = 0.3963 target = 0.105500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.079866 restraints weight = 48468.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.081357 restraints weight = 29012.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.082031 restraints weight = 20334.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.082396 restraints weight = 19129.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.082631 restraints weight = 16880.582| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 14074 Z= 0.223 Angle : 0.659 9.618 19253 Z= 0.355 Chirality : 0.046 0.316 2120 Planarity : 0.004 0.048 2287 Dihedral : 18.537 163.355 2371 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.64 % Allowed : 16.85 % Favored : 78.51 % 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: -0.32 (0.21), residues: 1574 helix: 0.73 (0.22), residues: 538 sheet: -0.52 (0.25), residues: 393 loop : -0.69 (0.25), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 103 TYR 0.018 0.002 TYR B 39 PHE 0.022 0.002 PHE B 109 TRP 0.012 0.002 TRP A 593 HIS 0.004 0.001 HIS B 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.22 (14074) covalent geometry : angle 0.65917 / 0.36 (19253) hydrogen bonds : bond 0.04679 / 3.04 ( 681) hydrogen bonds : angle 5.61169 / 3.84 ( 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 230 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 167 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 TYR cc_start: 0.7374 (p90) cc_final: 0.7169 (p90) REVERT: A 37 MET cc_start: 0.4279 (ptt) cc_final: 0.3218 (ppp) REVERT: A 85 ASP cc_start: 0.8679 (t0) cc_final: 0.8414 (t70) REVERT: A 114 GLU cc_start: 0.6526 (OUTLIER) cc_final: 0.6267 (mp0) REVERT: A 236 MET cc_start: 0.7752 (mtp) cc_final: 0.7492 (mtm) REVERT: A 238 ARG cc_start: 0.8764 (mtp-110) cc_final: 0.8386 (ptm160) REVERT: A 246 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8497 (mmtt) REVERT: A 324 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.7798 (p0) REVERT: A 350 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7481 (pmm) REVERT: A 486 MET cc_start: 0.8209 (ttp) cc_final: 0.7715 (tpt) REVERT: A 665 ARG cc_start: 0.8711 (mmm160) cc_final: 0.8471 (mmm-85) REVERT: A 671 MET cc_start: 0.8147 (tpp) cc_final: 0.7830 (tpp) REVERT: A 721 HIS cc_start: 0.7863 (OUTLIER) cc_final: 0.7322 (p-80) REVERT: A 727 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7321 (mtt) REVERT: A 881 GLU cc_start: 0.9142 (OUTLIER) cc_final: 0.8591 (pp20) REVERT: D 87 ARG cc_start: 0.7541 (mtp180) cc_final: 0.7060 (mtp180) REVERT: E 125 GLN cc_start: 0.9153 (tm-30) cc_final: 0.8799 (tm-30) outliers start: 63 outliers final: 48 residues processed: 216 average time/residue: 0.1173 time to fit residues: 37.6114 Evaluate side-chains 204 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 149 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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 114 GLU 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 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 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 785 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 857 ASP 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 137 THR Chi-restraints excluded: chain B residue 140 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 88 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 52 optimal weight: 20.0000 chunk 29 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.105012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.078961 restraints weight = 48052.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.080865 restraints weight = 28621.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.081468 restraints weight = 19828.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.081729 restraints weight = 18174.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.081971 restraints weight = 16280.456| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 14074 Z= 0.213 Angle : 0.668 10.416 19253 Z= 0.356 Chirality : 0.046 0.336 2120 Planarity : 0.004 0.067 2287 Dihedral : 18.546 163.507 2369 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 5.37 % Allowed : 17.66 % Favored : 76.97 % 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: -0.37 (0.21), residues: 1574 helix: 0.63 (0.22), residues: 538 sheet: -0.48 (0.26), residues: 386 loop : -0.72 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 192 TYR 0.019 0.002 TYR B 39 PHE 0.024 0.002 PHE B 109 TRP 0.010 0.002 TRP A 844 HIS 0.003 0.001 HIS B 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.21 (14074) covalent geometry : angle 0.66816 / 0.36 (19253) hydrogen bonds : bond 0.04410 / 2.86 ( 681) hydrogen bonds : angle 5.59318 / 3.82 ( 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 238 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 165 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 TYR cc_start: 0.7446 (p90) cc_final: 0.7213 (p90) REVERT: A 37 MET cc_start: 0.4362 (ptt) cc_final: 0.3278 (ppp) REVERT: A 85 ASP cc_start: 0.8641 (t0) cc_final: 0.8421 (t70) REVERT: A 196 MET cc_start: 0.8689 (mpp) cc_final: 0.8323 (mpp) REVERT: A 238 ARG cc_start: 0.8756 (mtp-110) cc_final: 0.8379 (ptm160) REVERT: A 246 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8496 (mmtt) REVERT: A 324 ASP cc_start: 0.8344 (OUTLIER) cc_final: 0.7830 (p0) REVERT: A 350 MET cc_start: 0.7962 (OUTLIER) cc_final: 0.7505 (pmm) REVERT: A 486 MET cc_start: 0.8221 (ttp) cc_final: 0.7788 (tpt) REVERT: A 671 MET cc_start: 0.8224 (tpp) cc_final: 0.7886 (tpp) REVERT: A 721 HIS cc_start: 0.8078 (OUTLIER) cc_final: 0.7379 (p-80) REVERT: A 727 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.7193 (mtt) REVERT: A 881 GLU cc_start: 0.9134 (OUTLIER) cc_final: 0.8579 (pp20) REVERT: A 885 MET cc_start: 0.8279 (mmt) cc_final: 0.8010 (mmt) REVERT: D 87 ARG cc_start: 0.7518 (mtp180) cc_final: 0.6983 (mtp180) REVERT: D 128 ARG cc_start: 0.8435 (ttm110) cc_final: 0.8221 (ttp-110) REVERT: E 1 MET cc_start: 0.7361 (mmt) cc_final: 0.5585 (mmt) REVERT: E 125 GLN cc_start: 0.9178 (tm-30) cc_final: 0.8811 (tm-30) REVERT: E 187 MET cc_start: 0.9311 (mpp) cc_final: 0.8866 (mpp) outliers start: 73 outliers final: 52 residues processed: 226 average time/residue: 0.1017 time to fit residues: 34.4143 Evaluate side-chains 213 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 155 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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 114 GLU 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 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 622 VAL 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 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 131 ARG 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 12 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 141 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 152 optimal weight: 0.8980 chunk 138 optimal weight: 9.9990 chunk 88 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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** B 186 ASN ** 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 = 0.4003 r_free = 0.4003 target = 0.107875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.080474 restraints weight = 47664.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.083162 restraints weight = 27591.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.084980 restraints weight = 19206.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.086179 restraints weight = 15057.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.086903 restraints weight = 12759.954| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14074 Z= 0.131 Angle : 0.648 13.196 19253 Z= 0.338 Chirality : 0.045 0.264 2120 Planarity : 0.004 0.047 2287 Dihedral : 18.414 159.464 2369 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.34 % Allowed : 18.62 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.21), residues: 1574 helix: 0.69 (0.22), residues: 546 sheet: -0.34 (0.26), residues: 396 loop : -0.68 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 128 TYR 0.017 0.001 TYR B 39 PHE 0.022 0.001 PHE A 651 TRP 0.020 0.002 TRP B 92 HIS 0.003 0.001 HIS A 801 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (14074) covalent geometry : angle 0.64805 / 0.34 (19253) hydrogen bonds : bond 0.03838 / 2.48 ( 681) hydrogen bonds : angle 5.33933 / 3.66 ( 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 237 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 178 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.4252 (ptt) cc_final: 0.3251 (ppp) REVERT: A 85 ASP cc_start: 0.8558 (t0) cc_final: 0.8278 (t70) REVERT: A 226 ARG cc_start: 0.9234 (OUTLIER) cc_final: 0.8474 (tpp80) REVERT: A 236 MET cc_start: 0.7533 (mtm) cc_final: 0.6894 (mpp) REVERT: A 238 ARG cc_start: 0.8631 (mtp-110) cc_final: 0.8250 (ptm160) REVERT: A 246 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8383 (mmtt) REVERT: A 272 ASP cc_start: 0.8503 (p0) cc_final: 0.8222 (p0) REVERT: A 324 ASP cc_start: 0.8300 (OUTLIER) cc_final: 0.7821 (p0) REVERT: A 350 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7482 (pmm) REVERT: A 486 MET cc_start: 0.8249 (ttp) cc_final: 0.7563 (mmm) REVERT: A 671 MET cc_start: 0.8174 (tpp) cc_final: 0.7935 (tpp) REVERT: A 721 HIS cc_start: 0.7890 (OUTLIER) cc_final: 0.7105 (p-80) REVERT: A 722 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8066 (tt) REVERT: A 727 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7373 (mtm) REVERT: A 829 LEU cc_start: 0.7379 (mt) cc_final: 0.7148 (mp) REVERT: A 881 GLU cc_start: 0.9053 (OUTLIER) cc_final: 0.8461 (pp20) REVERT: A 885 MET cc_start: 0.8174 (mmt) cc_final: 0.7932 (mmt) REVERT: D 116 THR cc_start: 0.8440 (t) cc_final: 0.8157 (m) REVERT: D 181 ILE cc_start: 0.9127 (mm) cc_final: 0.8805 (mp) REVERT: E 125 GLN cc_start: 0.9127 (tm-30) cc_final: 0.8750 (tm-30) REVERT: E 187 MET cc_start: 0.9164 (mpp) cc_final: 0.8722 (mpp) outliers start: 59 outliers final: 38 residues processed: 225 average time/residue: 0.0921 time to fit residues: 31.1068 Evaluate side-chains 205 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 159 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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 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 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 433 VAL Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 614 ILE 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 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 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 34 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 138 ILE 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: 9.9990 chunk 152 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 127 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 18 optimal weight: 0.3980 chunk 34 optimal weight: 8.9990 chunk 90 optimal weight: 9.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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** E 13 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.107328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.081813 restraints weight = 47560.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.083700 restraints weight = 28043.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.084285 restraints weight = 20254.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.084839 restraints weight = 17473.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.085284 restraints weight = 15737.478| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14074 Z= 0.147 Angle : 0.660 11.356 19253 Z= 0.344 Chirality : 0.045 0.295 2120 Planarity : 0.004 0.046 2287 Dihedral : 18.355 157.658 2362 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 5.15 % Allowed : 19.35 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.21), residues: 1574 helix: 0.63 (0.22), residues: 552 sheet: -0.40 (0.25), residues: 396 loop : -0.70 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 128 TYR 0.017 0.002 TYR B 39 PHE 0.018 0.001 PHE A 651 TRP 0.017 0.001 TRP A 593 HIS 0.003 0.001 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (14074) covalent geometry : angle 0.66030 / 0.34 (19253) hydrogen bonds : bond 0.03868 / 2.50 ( 681) hydrogen bonds : angle 5.30370 / 3.64 ( 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 239 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 169 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.4179 (ptt) cc_final: 0.3080 (ppp) REVERT: A 85 ASP cc_start: 0.8593 (t0) cc_final: 0.8263 (t70) REVERT: A 196 MET cc_start: 0.8749 (mpp) cc_final: 0.8497 (mpp) REVERT: A 236 MET cc_start: 0.7803 (mtm) cc_final: 0.7212 (mpp) REVERT: A 238 ARG cc_start: 0.8689 (mtp-110) cc_final: 0.8333 (ptm160) REVERT: A 246 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8430 (mmtt) REVERT: A 272 ASP cc_start: 0.8459 (p0) cc_final: 0.8193 (p0) REVERT: A 324 ASP cc_start: 0.8328 (OUTLIER) cc_final: 0.7862 (p0) REVERT: A 350 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.7502 (pmm) REVERT: A 486 MET cc_start: 0.8149 (ttp) cc_final: 0.7571 (mmm) REVERT: A 671 MET cc_start: 0.8335 (tpp) cc_final: 0.8018 (tpp) REVERT: A 721 HIS cc_start: 0.7923 (OUTLIER) cc_final: 0.7129 (p-80) REVERT: A 722 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8090 (tt) REVERT: A 727 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7578 (mtt) REVERT: A 881 GLU cc_start: 0.9098 (OUTLIER) cc_final: 0.8524 (pp20) REVERT: A 885 MET cc_start: 0.8240 (mmt) cc_final: 0.7951 (mmt) REVERT: B 30 MET cc_start: 0.8149 (mmm) cc_final: 0.7809 (mmm) REVERT: B 32 ARG cc_start: 0.8292 (tpt170) cc_final: 0.7366 (tpp-160) REVERT: D 87 ARG cc_start: 0.7458 (mmm160) cc_final: 0.7008 (mtp180) REVERT: D 116 THR cc_start: 0.8412 (t) cc_final: 0.8151 (m) REVERT: E 125 GLN cc_start: 0.9134 (tm-30) cc_final: 0.8772 (tm-30) REVERT: E 187 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8322 (pmm) outliers start: 70 outliers final: 48 residues processed: 222 average time/residue: 0.0923 time to fit residues: 30.7953 Evaluate side-chains 218 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 162 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 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 567 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 681 ASP 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 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 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 131 ARG Chi-restraints excluded: chain D residue 158 SER 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 187 MET 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: 6.9990 chunk 108 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 chunk 95 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 106 optimal weight: 20.0000 chunk 18 optimal weight: 4.9990 chunk 159 optimal weight: 30.0000 chunk 63 optimal weight: 9.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.106515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.080958 restraints weight = 47956.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.082899 restraints weight = 28143.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.083680 restraints weight = 19403.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.083933 restraints weight = 17203.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.084157 restraints weight = 15677.787| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14074 Z= 0.171 Angle : 0.665 12.384 19253 Z= 0.347 Chirality : 0.046 0.273 2120 Planarity : 0.004 0.044 2287 Dihedral : 18.353 156.595 2362 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.86 % Allowed : 20.38 % Favored : 74.76 % 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: -0.34 (0.21), residues: 1574 helix: 0.64 (0.22), residues: 551 sheet: -0.39 (0.26), residues: 392 loop : -0.76 (0.26), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 128 TYR 0.017 0.002 TYR B 39 PHE 0.016 0.002 PHE B 28 TRP 0.018 0.002 TRP B 92 HIS 0.003 0.001 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (14074) covalent geometry : angle 0.66520 / 0.35 (19253) hydrogen bonds : bond 0.03980 / 2.58 ( 681) hydrogen bonds : angle 5.28993 / 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 233 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 167 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 TYR cc_start: 0.7323 (p90) cc_final: 0.7087 (p90) REVERT: A 37 MET cc_start: 0.4082 (ptt) cc_final: 0.3046 (ppp) REVERT: A 85 ASP cc_start: 0.8632 (t0) cc_final: 0.8373 (t70) REVERT: A 196 MET cc_start: 0.8738 (mpp) cc_final: 0.8420 (mpp) REVERT: A 236 MET cc_start: 0.7872 (mtm) cc_final: 0.7251 (mpp) REVERT: A 238 ARG cc_start: 0.8723 (mtp-110) cc_final: 0.8324 (ptm160) REVERT: A 246 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8428 (mmtt) REVERT: A 324 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.7902 (p0) REVERT: A 350 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7506 (pmm) REVERT: A 486 MET cc_start: 0.8162 (ttp) cc_final: 0.7570 (mmm) REVERT: A 671 MET cc_start: 0.8316 (tpp) cc_final: 0.8019 (tpp) REVERT: A 721 HIS cc_start: 0.8013 (OUTLIER) cc_final: 0.7159 (p-80) REVERT: A 722 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8218 (tt) REVERT: A 727 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7558 (mtt) REVERT: A 881 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.8491 (pp20) REVERT: A 885 MET cc_start: 0.8310 (mmt) cc_final: 0.8005 (mmt) REVERT: B 32 ARG cc_start: 0.8307 (tpt170) cc_final: 0.7635 (tpp-160) REVERT: B 50 PHE cc_start: 0.6706 (p90) cc_final: 0.6259 (p90) REVERT: D 87 ARG cc_start: 0.7502 (mmm160) cc_final: 0.7155 (mmm160) REVERT: D 116 THR cc_start: 0.8415 (t) cc_final: 0.8188 (m) REVERT: E 1 MET cc_start: 0.7292 (mmt) cc_final: 0.6794 (mmt) REVERT: E 125 GLN cc_start: 0.9129 (tm-30) cc_final: 0.8853 (tm-30) REVERT: E 184 MET cc_start: 0.9167 (mmm) cc_final: 0.8935 (mmm) REVERT: E 187 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8484 (pmm) outliers start: 66 outliers final: 49 residues processed: 217 average time/residue: 0.0987 time to fit residues: 32.2457 Evaluate side-chains 217 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 160 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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 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 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 775 VAL Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 806 LEU 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 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 131 ARG Chi-restraints excluded: chain D residue 158 SER 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 187 MET 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: 7.9990 chunk 22 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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** ** B 75 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 = 0.3991 r_free = 0.3991 target = 0.106966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.081537 restraints weight = 48502.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.083010 restraints weight = 28456.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.083767 restraints weight = 20237.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.084220 restraints weight = 18579.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.084364 restraints weight = 16256.711| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14074 Z= 0.160 Angle : 0.690 14.744 19253 Z= 0.352 Chirality : 0.046 0.271 2120 Planarity : 0.004 0.044 2287 Dihedral : 18.324 156.692 2362 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.71 % Allowed : 20.46 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.21), residues: 1574 helix: 0.62 (0.22), residues: 551 sheet: -0.35 (0.26), residues: 391 loop : -0.77 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 128 TYR 0.020 0.002 TYR B 39 PHE 0.018 0.001 PHE A 651 TRP 0.019 0.002 TRP B 92 HIS 0.003 0.001 HIS A 721 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (14074) covalent geometry : angle 0.68993 / 0.35 (19253) hydrogen bonds : bond 0.03865 / 2.50 ( 681) hydrogen bonds : angle 5.23962 / 3.59 ( 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 232 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 168 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 TYR cc_start: 0.7374 (p90) cc_final: 0.7149 (p90) REVERT: A 37 MET cc_start: 0.4117 (ptt) cc_final: 0.3124 (ppp) REVERT: A 70 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.7959 (mpp) REVERT: A 85 ASP cc_start: 0.8606 (t0) cc_final: 0.8404 (t70) REVERT: A 196 MET cc_start: 0.8774 (mpp) cc_final: 0.8500 (mpp) REVERT: A 236 MET cc_start: 0.7806 (mtm) cc_final: 0.7221 (mpp) REVERT: A 238 ARG cc_start: 0.8701 (mtp-110) cc_final: 0.8300 (ptm160) REVERT: A 246 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8184 (mtmm) REVERT: A 324 ASP cc_start: 0.8380 (OUTLIER) cc_final: 0.7923 (p0) REVERT: A 350 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.7515 (pmm) REVERT: A 486 MET cc_start: 0.8146 (ttp) cc_final: 0.7574 (mmm) REVERT: A 501 MET cc_start: 0.7865 (ppp) cc_final: 0.7450 (ppp) REVERT: A 671 MET cc_start: 0.8321 (tpp) cc_final: 0.8023 (tpp) REVERT: A 721 HIS cc_start: 0.7995 (OUTLIER) cc_final: 0.7145 (p-80) REVERT: A 722 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8249 (tt) REVERT: A 727 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7547 (mtt) REVERT: A 881 GLU cc_start: 0.9093 (OUTLIER) cc_final: 0.8501 (pp20) REVERT: A 885 MET cc_start: 0.8336 (mmt) cc_final: 0.8063 (mmt) REVERT: B 30 MET cc_start: 0.8102 (mmm) cc_final: 0.7880 (mmm) REVERT: B 32 ARG cc_start: 0.8263 (tpt170) cc_final: 0.7552 (tpp-160) REVERT: B 50 PHE cc_start: 0.6880 (p90) cc_final: 0.6056 (p90) REVERT: D 87 ARG cc_start: 0.7525 (mmm160) cc_final: 0.7171 (mmm160) REVERT: D 116 THR cc_start: 0.8417 (t) cc_final: 0.8201 (m) REVERT: E 1 MET cc_start: 0.7304 (mmt) cc_final: 0.6763 (mmt) REVERT: E 125 GLN cc_start: 0.9145 (tm-30) cc_final: 0.8851 (tm-30) outliers start: 64 outliers final: 50 residues processed: 217 average time/residue: 0.1013 time to fit residues: 33.0405 Evaluate side-chains 220 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 162 time to evaluate : 0.422 ------------------------------------------------------------------------------- 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 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 377 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 775 VAL Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 806 LEU 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 131 ARG Chi-restraints excluded: chain D residue 158 SER 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 187 MET 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: 3.9990 chunk 155 optimal weight: 40.0000 chunk 103 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 143 optimal weight: 0.3980 chunk 16 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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** B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.108634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.083132 restraints weight = 48541.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.085052 restraints weight = 28691.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.085663 restraints weight = 19507.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.086082 restraints weight = 17893.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.086236 restraints weight = 15951.738| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14074 Z= 0.127 Angle : 0.685 13.903 19253 Z= 0.347 Chirality : 0.046 0.231 2120 Planarity : 0.004 0.044 2287 Dihedral : 18.263 154.797 2362 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.19 % Allowed : 21.19 % Favored : 74.61 % 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: -0.36 (0.21), residues: 1574 helix: 0.61 (0.22), residues: 551 sheet: -0.41 (0.26), residues: 355 loop : -0.74 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 128 TYR 0.020 0.001 TYR A 460 PHE 0.023 0.001 PHE A 651 TRP 0.031 0.002 TRP B 92 HIS 0.003 0.001 HIS A 801 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (14074) covalent geometry : angle 0.68477 / 0.35 (19253) hydrogen bonds : bond 0.03621 / 2.35 ( 681) hydrogen bonds : angle 5.12732 / 3.52 ( 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 234 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 177 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 TYR cc_start: 0.7432 (p90) cc_final: 0.7204 (p90) REVERT: A 37 MET cc_start: 0.4080 (ptt) cc_final: 0.3045 (ppp) REVERT: A 63 MET cc_start: 0.8502 (mmt) cc_final: 0.8246 (mmp) REVERT: A 70 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.7981 (mpp) REVERT: A 136 TYR cc_start: 0.7284 (t80) cc_final: 0.6917 (t80) REVERT: A 194 MET cc_start: 0.7875 (tpt) cc_final: 0.7583 (tpp) REVERT: A 196 MET cc_start: 0.8737 (mpp) cc_final: 0.8521 (mpp) REVERT: A 229 MET cc_start: 0.8732 (ppp) cc_final: 0.8030 (ptp) REVERT: A 236 MET cc_start: 0.7774 (mtm) cc_final: 0.7245 (mpp) REVERT: A 238 ARG cc_start: 0.8692 (mtp-110) cc_final: 0.8296 (ptm160) REVERT: A 245 VAL cc_start: 0.7721 (OUTLIER) cc_final: 0.6620 (t) REVERT: A 246 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8332 (mmtt) REVERT: A 324 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.7902 (p0) REVERT: A 350 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7447 (pmm) REVERT: A 486 MET cc_start: 0.8092 (ttp) cc_final: 0.7558 (mmm) REVERT: A 501 MET cc_start: 0.7889 (ppp) cc_final: 0.7508 (ppp) REVERT: A 671 MET cc_start: 0.8387 (tpp) cc_final: 0.8125 (tpp) REVERT: A 721 HIS cc_start: 0.7823 (OUTLIER) cc_final: 0.7062 (p-80) REVERT: A 722 LEU cc_start: 0.8556 (tt) cc_final: 0.8186 (tt) REVERT: A 727 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7484 (mtm) REVERT: A 881 GLU cc_start: 0.9067 (OUTLIER) cc_final: 0.8462 (pp20) REVERT: A 885 MET cc_start: 0.8227 (mmt) cc_final: 0.8009 (mmt) REVERT: B 30 MET cc_start: 0.8073 (mmm) cc_final: 0.7850 (mmm) REVERT: B 32 ARG cc_start: 0.8263 (tpt170) cc_final: 0.7372 (tpp-160) REVERT: B 50 PHE cc_start: 0.6680 (p90) cc_final: 0.6315 (p90) REVERT: D 87 ARG cc_start: 0.7530 (mmm160) cc_final: 0.7220 (mmm160) REVERT: D 116 THR cc_start: 0.8403 (t) cc_final: 0.8134 (m) REVERT: E 1 MET cc_start: 0.7404 (mmt) cc_final: 0.6999 (mmt) REVERT: E 125 GLN cc_start: 0.9109 (tm-30) cc_final: 0.8820 (tm-30) outliers start: 57 outliers final: 46 residues processed: 219 average time/residue: 0.1021 time to fit residues: 33.3885 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 : 0.467 ------------------------------------------------------------------------------- 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 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 377 ILE 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 727 MET Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 790 ASP 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 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 129 VAL Chi-restraints excluded: chain D residue 131 ARG 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 Chi-restraints excluded: chain E residue 217 VAL 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: 20.0000 chunk 88 optimal weight: 0.0570 chunk 116 optimal weight: 9.9990 chunk 140 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 34 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 90 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 overall best weight: 5.2106 ------------------------------------------------------------------------------- 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** E 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.104122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.078957 restraints weight = 48465.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.079724 restraints weight = 29488.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.080564 restraints weight = 21876.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.080852 restraints weight = 19435.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.081011 restraints weight = 17468.913| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 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 : 0.006 0.079 14074 Z= 0.292 Angle : 0.776 11.835 19253 Z= 0.402 Chirality : 0.048 0.339 2120 Planarity : 0.004 0.043 2287 Dihedral : 18.447 157.206 2362 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 20.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.97 % Allowed : 22.00 % Favored : 74.03 % 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: -0.59 (0.21), residues: 1574 helix: 0.39 (0.22), residues: 549 sheet: -0.45 (0.26), residues: 369 loop : -0.92 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 162 TYR 0.023 0.002 TYR D 165 PHE 0.015 0.002 PHE A 868 TRP 0.015 0.002 TRP A 844 HIS 0.007 0.001 HIS D 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00633 / 0.29 (14074) covalent geometry : angle 0.77569 / 0.40 (19253) hydrogen bonds : bond 0.04829 / 3.19 ( 681) hydrogen bonds : angle 5.47679 / 3.74 ( 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 210 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 156 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.4346 (ptt) cc_final: 0.3201 (ppp) REVERT: A 70 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.7952 (mpp) REVERT: A 73 MET cc_start: 0.6852 (tpp) cc_final: 0.6489 (tpp) REVERT: A 194 MET cc_start: 0.8053 (tpt) cc_final: 0.7797 (tpp) REVERT: A 196 MET cc_start: 0.8813 (mpp) cc_final: 0.8515 (mpp) REVERT: A 236 MET cc_start: 0.7978 (mtm) cc_final: 0.7371 (mpp) REVERT: A 238 ARG cc_start: 0.8766 (mtp-110) cc_final: 0.8368 (ptm160) REVERT: A 246 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8230 (mtmm) REVERT: A 350 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.7563 (pmm) REVERT: A 486 MET cc_start: 0.8136 (ttp) cc_final: 0.7567 (mmm) REVERT: A 501 MET cc_start: 0.7929 (ppp) cc_final: 0.7552 (ppp) REVERT: A 671 MET cc_start: 0.8417 (tpp) cc_final: 0.8128 (tpp) REVERT: A 721 HIS cc_start: 0.8131 (OUTLIER) cc_final: 0.7530 (p-80) REVERT: A 727 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7295 (mtt) REVERT: A 881 GLU cc_start: 0.9131 (OUTLIER) cc_final: 0.8574 (pp20) REVERT: A 885 MET cc_start: 0.8413 (mmt) cc_final: 0.8016 (mmt) REVERT: B 30 MET cc_start: 0.8011 (mmm) cc_final: 0.7749 (mmm) REVERT: B 32 ARG cc_start: 0.8232 (tpt170) cc_final: 0.7374 (tpp-160) REVERT: B 50 PHE cc_start: 0.6908 (p90) cc_final: 0.6378 (p90) REVERT: B 128 ARG cc_start: 0.9194 (mmt90) cc_final: 0.8959 (mmm-85) REVERT: D 87 ARG cc_start: 0.7499 (mmm160) cc_final: 0.7032 (mtp180) REVERT: E 1 MET cc_start: 0.7342 (mmt) cc_final: 0.6760 (mmt) REVERT: E 125 GLN cc_start: 0.9114 (tm-30) cc_final: 0.8731 (tm-30) outliers start: 54 outliers final: 46 residues processed: 196 average time/residue: 0.1012 time to fit residues: 29.3854 Evaluate side-chains 206 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 154 time to evaluate : 0.315 ------------------------------------------------------------------------------- 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 245 VAL Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 285 PHE 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 377 ILE 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 727 MET Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 806 LEU 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 81 ILE Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 129 VAL 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 Chi-restraints excluded: chain E residue 217 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 103 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 147 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 81 optimal weight: 0.0070 chunk 57 optimal weight: 2.9990 overall best weight: 1.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.107453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.081968 restraints weight = 48793.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.083591 restraints weight = 28355.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.084140 restraints weight = 19979.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.084537 restraints weight = 18401.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.084772 restraints weight = 16388.433| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14074 Z= 0.140 Angle : 0.732 14.959 19253 Z= 0.370 Chirality : 0.047 0.277 2120 Planarity : 0.004 0.047 2287 Dihedral : 18.355 158.206 2361 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.83 % Allowed : 22.08 % Favored : 74.10 % 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: -0.49 (0.21), residues: 1574 helix: 0.49 (0.22), residues: 551 sheet: -0.42 (0.25), residues: 379 loop : -0.85 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG E 162 TYR 0.023 0.002 TYR A 460 PHE 0.023 0.001 PHE A 651 TRP 0.017 0.002 TRP B 92 HIS 0.003 0.001 HIS A 721 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (14074) covalent geometry : angle 0.73152 / 0.37 (19253) hydrogen bonds : bond 0.03794 / 2.47 ( 681) hydrogen bonds : angle 5.24124 / 3.59 ( 1863) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2092.83 seconds wall clock time: 37 minutes 16.45 seconds (2236.45 seconds total)