Starting phenix.real_space_refine on Sat Jul 4 04:51:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n6h_49061/07_2026/9n6h_49061.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n6h_49061/07_2026/9n6h_49061.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n6h_49061/07_2026/9n6h_49061.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n6h_49061/07_2026/9n6h_49061.map" model { file = "/net/cci-nas-00/data/ceres_data/9n6h_49061/07_2026/9n6h_49061.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n6h_49061/07_2026/9n6h_49061.cif" } resolution = 2.54 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= 0.004 sd= 0.027 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 320 5.49 5 S 37 5.16 5 C 10844 2.51 5 N 3454 2.21 5 O 4152 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 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: 18807 Number of models: 1 Model: "" Number of chains: 11 Chain: "I" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 3260 Classifications: {'DNA': 160} Link IDs: {'rna3p': 159} Chain: "J" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 3300 Classifications: {'DNA': 160} Link IDs: {'rna3p': 159} Chain: "B" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 702 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 840 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 104} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 647 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 842 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 104} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 712 Classifications: {'peptide': 92} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 89} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 6159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 781, 6159 Classifications: {'peptide': 781} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 24, 'TRANS': 756} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 245 Unresolved non-hydrogen angles: 297 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 18, 'ASP:plan': 7, 'GLN:plan1': 5, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 137 Chain: "E" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 808 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "A" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 806 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Time building chain proxies: 2.86, per 1000 atoms: 0.15 Number of scatterers: 18807 At special positions: 0 Unit cell: (127.098, 134.451, 170.165, 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 37 16.00 P 320 15.00 O 4152 8.00 N 3454 7.00 C 10844 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: 1.23 Conformation dependent library (CDL) restraints added in 447.2 milliseconds 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2930 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 14 sheets defined 60.5% alpha, 7.3% beta 158 base pairs and 296 stacking pairs defined. Time for finding SS restraints: 2.52 Creating SS restraints... Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.888A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.504A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 15 removed outlier: 3.645A pdb=" N ALA C 14 " --> pdb=" O ARG C 11 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS C 15 " --> pdb=" O ALA C 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 11 through 15' Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.389A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 122 removed outlier: 3.561A pdb=" N ALA D 107 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.878A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.541A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.433A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.506A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.529A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 143 through 147 Processing helix chain 'K' and resid 203 through 211 removed outlier: 3.876A pdb=" N GLU K 209 " --> pdb=" O ASN K 205 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR K 211 " --> pdb=" O CYS K 207 " (cutoff:3.500A) Processing helix chain 'K' and resid 229 through 234 removed outlier: 3.523A pdb=" N GLY K 234 " --> pdb=" O TYR K 230 " (cutoff:3.500A) Processing helix chain 'K' and resid 238 through 259 removed outlier: 3.560A pdb=" N LEU K 242 " --> pdb=" O GLY K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 263 through 283 Processing helix chain 'K' and resid 315 through 319 Processing helix chain 'K' and resid 324 through 331 Processing helix chain 'K' and resid 331 through 343 removed outlier: 3.868A pdb=" N VAL K 335 " --> pdb=" O ALA K 331 " (cutoff:3.500A) Processing helix chain 'K' and resid 347 through 351 Processing helix chain 'K' and resid 377 through 393 Processing helix chain 'K' and resid 406 through 421 Processing helix chain 'K' and resid 436 through 448 removed outlier: 3.740A pdb=" N THR K 443 " --> pdb=" O ALA K 439 " (cutoff:3.500A) Processing helix chain 'K' and resid 459 through 471 removed outlier: 3.923A pdb=" N PHE K 471 " --> pdb=" O ARG K 467 " (cutoff:3.500A) Processing helix chain 'K' and resid 492 through 498 Processing helix chain 'K' and resid 498 through 504 removed outlier: 4.059A pdb=" N SER K 504 " --> pdb=" O ALA K 500 " (cutoff:3.500A) Processing helix chain 'K' and resid 515 through 520 removed outlier: 4.394A pdb=" N ASN K 520 " --> pdb=" O ARG K 517 " (cutoff:3.500A) Processing helix chain 'K' and resid 523 through 531 removed outlier: 3.532A pdb=" N SER K 531 " --> pdb=" O GLU K 527 " (cutoff:3.500A) Processing helix chain 'K' and resid 548 through 560 removed outlier: 4.093A pdb=" N LEU K 552 " --> pdb=" O ASN K 548 " (cutoff:3.500A) Processing helix chain 'K' and resid 576 through 590 Processing helix chain 'K' and resid 619 through 631 Processing helix chain 'K' and resid 633 through 639 Processing helix chain 'K' and resid 650 through 661 Processing helix chain 'K' and resid 662 through 665 Processing helix chain 'K' and resid 668 through 676 removed outlier: 3.644A pdb=" N VAL K 672 " --> pdb=" O ALA K 668 " (cutoff:3.500A) Processing helix chain 'K' and resid 684 through 694 removed outlier: 3.630A pdb=" N ARG K 688 " --> pdb=" O GLU K 684 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N SER K 694 " --> pdb=" O LEU K 690 " (cutoff:3.500A) Processing helix chain 'K' and resid 694 through 710 removed outlier: 3.884A pdb=" N VAL K 698 " --> pdb=" O SER K 694 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU K 699 " --> pdb=" O GLY K 695 " (cutoff:3.500A) Processing helix chain 'K' and resid 720 through 735 Processing helix chain 'K' and resid 746 through 758 Processing helix chain 'K' and resid 794 through 804 removed outlier: 3.799A pdb=" N ASP K 798 " --> pdb=" O ASN K 794 " (cutoff:3.500A) Processing helix chain 'K' and resid 825 through 844 Processing helix chain 'K' and resid 845 through 848 removed outlier: 4.177A pdb=" N VAL K 848 " --> pdb=" O SER K 845 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 845 through 848' Processing helix chain 'K' and resid 857 through 873 removed outlier: 3.752A pdb=" N ALA K 862 " --> pdb=" O ASN K 858 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLY K 863 " --> pdb=" O GLU K 859 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER K 866 " --> pdb=" O ALA K 862 " (cutoff:3.500A) Processing helix chain 'K' and resid 913 through 917 Processing helix chain 'K' and resid 937 through 954 Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.534A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.528A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.500A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 45 through 46 removed outlier: 7.418A pdb=" N ARG B 45 " --> pdb=" O ILE A 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.414A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.003A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'F' and resid 45 through 46 removed outlier: 7.486A pdb=" N ARG F 45 " --> pdb=" O ILE E 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'F' and resid 80 through 81 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.068A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 179 through 186 removed outlier: 5.314A pdb=" N VAL K 182 " --> pdb=" O LYS K 216 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LYS K 216 " --> pdb=" O VAL K 182 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN K 184 " --> pdb=" O LEU K 214 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 287 through 296 removed outlier: 6.529A pdb=" N LEU K 308 " --> pdb=" O ILE K 291 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N SER K 293 " --> pdb=" O GLN K 306 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLN K 306 " --> pdb=" O SER K 293 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ARG K 295 " --> pdb=" O GLN K 304 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N GLN K 304 " --> pdb=" O ARG K 295 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 453 through 456 removed outlier: 6.484A pdb=" N ILE K 454 " --> pdb=" O LEU K 489 " (cutoff:3.500A) removed outlier: 8.837A pdb=" N THR K 491 " --> pdb=" O ILE K 454 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N TYR K 456 " --> pdb=" O THR K 491 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLN K 508 " --> pdb=" O ASN K 536 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N MET K 538 " --> pdb=" O GLN K 508 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N MET K 510 " --> pdb=" O MET K 538 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ILE K 540 " --> pdb=" O MET K 510 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL K 512 " --> pdb=" O ILE K 540 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY K 397 " --> pdb=" O ARG K 537 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE K 398 " --> pdb=" O LEU K 595 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 738 through 741 removed outlier: 6.638A pdb=" N GLN K 739 " --> pdb=" O LEU K 768 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N SER K 770 " --> pdb=" O GLN K 739 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LEU K 741 " --> pdb=" O SER K 770 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL K 714 " --> pdb=" O PHE K 767 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N LEU K 769 " --> pdb=" O VAL K 714 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ILE K 716 " --> pdb=" O LEU K 769 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU K 715 " --> pdb=" O VAL K 787 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N THR K 610 " --> pdb=" O VAL K 816 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ARG K 818 " --> pdb=" O THR K 610 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ARG K 612 " --> pdb=" O ARG K 818 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N VAL K 820 " --> pdb=" O ARG K 612 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU K 614 " --> pdb=" O VAL K 820 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N THR K 924 " --> pdb=" O GLU K 611 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE K 613 " --> pdb=" O THR K 924 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N TYR K 926 " --> pdb=" O ILE K 613 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ARG K 615 " --> pdb=" O TYR K 926 " (cutoff:3.500A) 662 hydrogen bonds defined for protein. 1929 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 406 hydrogen bonds 812 hydrogen bond angles 0 basepair planarities 158 basepair parallelities 296 stacking parallelities Total time for adding SS restraints: 5.17 Time building geometry restraints manager: 1.61 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: 3891 1.33 - 1.45: 5862 1.45 - 1.57: 9346 1.57 - 1.70: 638 1.70 - 1.82: 66 Bond restraints: 19803 Sorted by residual: bond pdb=" C3' DG I 52 " pdb=" O3' DG I 52 " ideal model delta sigma weight residual 1.435 1.486 -0.051 1.30e-02 5.92e+03 1.52e+01 bond pdb=" C3' DG I 52 " pdb=" C2' DG I 52 " 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 I 23 " pdb=" C2' DA I 23 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.80e+00 bond pdb=" C5' DA I -5 " pdb=" C4' DA I -5 " ideal model delta sigma weight residual 1.512 1.534 -0.022 7.00e-03 2.04e+04 9.77e+00 bond pdb=" C3' DC I 22 " pdb=" C2' DC I 22 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.31e+00 ... (remaining 19798 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 27550 2.44 - 4.89: 550 4.89 - 7.33: 29 7.33 - 9.77: 11 9.77 - 12.22: 2 Bond angle restraints: 28142 Sorted by residual: angle pdb=" O4' DC I -21 " pdb=" C4' DC I -21 " pdb=" C3' DC I -21 " ideal model delta sigma weight residual 106.00 102.46 3.54 6.00e-01 2.78e+00 3.47e+01 angle pdb=" N3 DT I 30 " pdb=" C4 DT I 30 " pdb=" O4 DT I 30 " ideal model delta sigma weight residual 119.90 122.73 -2.83 6.00e-01 2.78e+00 2.23e+01 angle pdb=" N3 DT J 9 " pdb=" C4 DT J 9 " pdb=" O4 DT J 9 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" N3 DT I 43 " pdb=" C4 DT I 43 " pdb=" O4 DT I 43 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" N3 DT I 38 " pdb=" C4 DT I 38 " pdb=" O4 DT I 38 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.90e+01 ... (remaining 28137 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.34: 8770 25.34 - 50.68: 1863 50.68 - 76.03: 429 76.03 - 101.37: 13 101.37 - 126.71: 1 Dihedral angle restraints: 11076 sinusoidal: 6550 harmonic: 4526 Sorted by residual: dihedral pdb=" CA THR K 631 " pdb=" C THR K 631 " pdb=" N LYS K 632 " pdb=" CA LYS K 632 " ideal model delta harmonic sigma weight residual -180.00 -148.08 -31.92 0 5.00e+00 4.00e-02 4.08e+01 dihedral pdb=" CA LEU K 769 " pdb=" C LEU K 769 " pdb=" N SER K 770 " pdb=" CA SER K 770 " ideal model delta harmonic sigma weight residual 180.00 151.22 28.78 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CD ARG B 92 " pdb=" NE ARG B 92 " pdb=" CZ ARG B 92 " pdb=" NH1 ARG B 92 " ideal model delta sinusoidal sigma weight residual 0.00 -44.17 44.17 1 1.00e+01 1.00e-02 2.71e+01 ... (remaining 11073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2659 0.065 - 0.131: 482 0.131 - 0.196: 36 0.196 - 0.261: 3 0.261 - 0.327: 1 Chirality restraints: 3181 Sorted by residual: chirality pdb=" CG LEU K 769 " pdb=" CB LEU K 769 " pdb=" CD1 LEU K 769 " pdb=" CD2 LEU K 769 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CB VAL K 602 " pdb=" CA VAL K 602 " pdb=" CG1 VAL K 602 " pdb=" CG2 VAL K 602 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB ILE K 429 " pdb=" CA ILE K 429 " pdb=" CG1 ILE K 429 " pdb=" CG2 ILE K 429 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 3178 not shown) Planarity restraints: 2486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 92 " -0.774 9.50e-02 1.11e+02 3.47e-01 7.32e+01 pdb=" NE ARG B 92 " 0.044 2.00e-02 2.50e+03 pdb=" CZ ARG B 92 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 92 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 92 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.047 5.00e-02 4.00e+02 7.05e-02 7.95e+00 pdb=" N PRO G 80 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 767 " 0.018 2.00e-02 2.50e+03 2.13e-02 7.91e+00 pdb=" CG PHE K 767 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE K 767 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE K 767 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE K 767 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE K 767 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE K 767 " 0.001 2.00e-02 2.50e+03 ... (remaining 2483 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4183 2.80 - 3.33: 15456 3.33 - 3.85: 36067 3.85 - 4.38: 42696 4.38 - 4.90: 62671 Nonbonded interactions: 161073 Sorted by model distance: nonbonded pdb=" O GLY K 689 " pdb=" OG SER K 693 " model vdw 2.275 3.040 nonbonded pdb=" OG1 THR D 87 " pdb=" OE1 GLU D 90 " model vdw 2.324 3.040 nonbonded pdb=" OD2 ASP K 742 " pdb=" OG1 THR K 744 " model vdw 2.324 3.040 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.332 3.040 nonbonded pdb=" OP1 DT I 30 " pdb=" OG1 THR D 29 " model vdw 2.334 3.040 ... (remaining 161068 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and ((resid 38 and (name N or name CA or name C or name O or name CB \ )) or resid 39 through 135)) } ncs_group { reference = (chain 'B' and resid 21 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and ((resid 10 through 12 and (name N or name CA or name C or name O \ or name CB )) or resid 13 through 119)) selection = (chain 'G' and (resid 10 through 117 or (resid 118 through 119 and (name N or na \ me CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'D' and ((resid 30 and (name N or name CA or name C or name O or name CB \ )) or resid 31 through 120 or (resid 121 and (name N or name CA or name C or nam \ e O )))) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.020 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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:7.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 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 : 0.006 0.055 19803 Z= 0.492 Angle : 0.843 12.215 28142 Z= 0.656 Chirality : 0.049 0.327 3181 Planarity : 0.009 0.347 2486 Dihedral : 24.590 126.711 8146 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.18), residues: 1527 helix: -0.75 (0.15), residues: 879 sheet: -0.17 (0.50), residues: 89 loop : -1.29 (0.23), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 597 TYR 0.034 0.002 TYR C 50 PHE 0.049 0.002 PHE K 767 TRP 0.011 0.001 TRP K 932 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.49 (19803) covalent geometry : angle 0.84258 / 0.66 (28142) hydrogen bonds : bond 0.12941 / 14.34 ( 1068) hydrogen bonds : angle 5.04650 / 6.48 ( 2741) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.607 Fit side-chains REVERT: B 85 ASP cc_start: 0.8709 (m-30) cc_final: 0.8486 (m-30) REVERT: B 93 GLN cc_start: 0.8719 (mt0) cc_final: 0.8501 (mm-40) REVERT: C 15 LYS cc_start: 0.8397 (ttpt) cc_final: 0.8019 (ttmt) REVERT: C 75 LYS cc_start: 0.9055 (mmtm) cc_final: 0.8748 (mmtt) REVERT: D 53 CYS cc_start: 0.8456 (m) cc_final: 0.7974 (t) REVERT: H 90 GLU cc_start: 0.8728 (mp0) cc_final: 0.8103 (mp0) REVERT: K 378 ASP cc_start: 0.8462 (p0) cc_final: 0.8247 (p0) REVERT: K 389 PHE cc_start: 0.8724 (t80) cc_final: 0.8476 (t80) REVERT: K 483 MET cc_start: 0.9070 (mmm) cc_final: 0.8753 (mmm) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.8705 time to fit residues: 222.0356 Evaluate side-chains 183 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN C 104 GLN K 129 ASN K 235 GLN ** K 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.124866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.088406 restraints weight = 33680.124| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.85 r_work: 0.3338 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19803 Z= 0.157 Angle : 0.598 7.912 28142 Z= 0.352 Chirality : 0.044 0.228 3181 Planarity : 0.004 0.049 2486 Dihedral : 28.268 117.575 5199 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.95 % Allowed : 10.66 % Favored : 88.39 % 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: 0.17 (0.21), residues: 1527 helix: 0.83 (0.17), residues: 891 sheet: 0.24 (0.50), residues: 96 loop : -1.05 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 83 TYR 0.011 0.001 TYR K 494 PHE 0.010 0.001 PHE E 67 TRP 0.007 0.001 TRP K 932 HIS 0.003 0.001 HIS K 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.16 (19803) covalent geometry : angle 0.59772 / 0.35 (28142) hydrogen bonds : bond 0.04343 / 4.70 ( 1068) hydrogen bonds : angle 3.59255 / 4.66 ( 2741) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 192 time to evaluate : 0.583 Fit side-chains REVERT: C 15 LYS cc_start: 0.8494 (ttpt) cc_final: 0.8275 (ttmt) REVERT: C 75 LYS cc_start: 0.8972 (mmtm) cc_final: 0.8751 (mmtt) REVERT: D 53 CYS cc_start: 0.8702 (m) cc_final: 0.8296 (t) REVERT: D 83 ARG cc_start: 0.8858 (mmt-90) cc_final: 0.8593 (mmt90) REVERT: D 110 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8263 (mp0) REVERT: H 44 GLN cc_start: 0.8928 (mt0) cc_final: 0.8700 (mt0) REVERT: H 90 GLU cc_start: 0.8710 (mp0) cc_final: 0.8167 (mp0) REVERT: K 692 MET cc_start: 0.8653 (mpt) cc_final: 0.8438 (mpt) outliers start: 12 outliers final: 2 residues processed: 195 average time/residue: 0.8666 time to fit residues: 183.8538 Evaluate side-chains 184 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 181 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain K residue 345 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 99 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 75 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 14 optimal weight: 50.0000 chunk 152 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 95 optimal weight: 8.9990 chunk 159 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN K 222 HIS ** K 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 76 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.122855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.084862 restraints weight = 33568.993| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.03 r_work: 0.3283 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19803 Z= 0.172 Angle : 0.571 7.831 28142 Z= 0.333 Chirality : 0.043 0.241 3181 Planarity : 0.004 0.042 2486 Dihedral : 28.568 105.113 5199 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.34 % Allowed : 12.56 % Favored : 86.10 % 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: 0.81 (0.21), residues: 1527 helix: 1.42 (0.17), residues: 904 sheet: 0.50 (0.50), residues: 97 loop : -0.97 (0.25), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 83 TYR 0.012 0.001 TYR K 494 PHE 0.016 0.002 PHE K 389 TRP 0.008 0.001 TRP K 932 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.17 (19803) covalent geometry : angle 0.57075 / 0.33 (28142) hydrogen bonds : bond 0.04570 / 5.01 ( 1068) hydrogen bonds : angle 3.27787 / 4.18 ( 2741) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 190 time to evaluate : 0.479 Fit side-chains REVERT: C 75 LYS cc_start: 0.9035 (mmtm) cc_final: 0.8806 (mmtt) REVERT: D 83 ARG cc_start: 0.8850 (mmt-90) cc_final: 0.8614 (mmt90) REVERT: H 44 GLN cc_start: 0.8877 (mt0) cc_final: 0.8636 (mt0) REVERT: H 90 GLU cc_start: 0.8714 (mp0) cc_final: 0.8203 (mp0) REVERT: K 483 MET cc_start: 0.8930 (mmm) cc_final: 0.8560 (mmm) REVERT: A 120 MET cc_start: 0.8726 (mtt) cc_final: 0.8329 (mtt) outliers start: 17 outliers final: 5 residues processed: 200 average time/residue: 0.7789 time to fit residues: 169.6704 Evaluate side-chains 183 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 178 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain K residue 204 LEU Chi-restraints excluded: chain K residue 560 MET Chi-restraints excluded: chain K residue 766 VAL Chi-restraints excluded: chain E residue 45 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 134 optimal weight: 5.9990 chunk 182 optimal weight: 0.0470 chunk 178 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 15 optimal weight: 50.0000 chunk 147 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 127 optimal weight: 4.9990 chunk 107 optimal weight: 0.5980 chunk 1 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 overall best weight: 1.7284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN K 235 GLN ** K 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.121194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.084201 restraints weight = 33337.364| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.00 r_work: 0.3242 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19803 Z= 0.204 Angle : 0.597 7.145 28142 Z= 0.340 Chirality : 0.044 0.235 3181 Planarity : 0.004 0.051 2486 Dihedral : 28.780 100.277 5199 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.18 % Allowed : 13.90 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.21), residues: 1527 helix: 1.52 (0.17), residues: 912 sheet: 0.38 (0.51), residues: 99 loop : -0.94 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 83 TYR 0.016 0.002 TYR K 494 PHE 0.012 0.002 PHE E 67 TRP 0.009 0.001 TRP K 932 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.20 (19803) covalent geometry : angle 0.59717 / 0.34 (28142) hydrogen bonds : bond 0.04808 / 5.30 ( 1068) hydrogen bonds : angle 3.25241 / 4.10 ( 2741) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 183 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: C 92 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7924 (mt-10) REVERT: D 73 GLU cc_start: 0.8480 (tp30) cc_final: 0.8278 (tp30) REVERT: D 83 ARG cc_start: 0.8889 (mmt-90) cc_final: 0.8599 (mmt90) REVERT: H 90 GLU cc_start: 0.8771 (mp0) cc_final: 0.8228 (mp0) REVERT: K 483 MET cc_start: 0.8962 (mmm) cc_final: 0.8516 (mmm) REVERT: A 120 MET cc_start: 0.8820 (mtt) cc_final: 0.8441 (mtt) outliers start: 15 outliers final: 7 residues processed: 194 average time/residue: 0.8357 time to fit residues: 175.7150 Evaluate side-chains 183 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 175 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain K residue 204 LEU Chi-restraints excluded: chain K residue 560 MET Chi-restraints excluded: chain K residue 766 VAL Chi-restraints excluded: chain K residue 828 GLU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 57 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 175 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 chunk 148 optimal weight: 2.9990 chunk 15 optimal weight: 50.0000 chunk 23 optimal weight: 8.9990 chunk 5 optimal weight: 8.9990 chunk 123 optimal weight: 2.9990 chunk 13 optimal weight: 50.0000 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN ** K 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 800 GLN A 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.120836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.083826 restraints weight = 33434.355| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.03 r_work: 0.3249 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 19803 Z= 0.194 Angle : 0.583 7.766 28142 Z= 0.334 Chirality : 0.043 0.226 3181 Planarity : 0.004 0.055 2486 Dihedral : 28.803 97.473 5199 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.34 % Allowed : 14.69 % Favored : 83.97 % 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: 1.08 (0.21), residues: 1527 helix: 1.67 (0.17), residues: 909 sheet: 0.33 (0.52), residues: 99 loop : -0.91 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 30 TYR 0.017 0.002 TYR K 494 PHE 0.012 0.001 PHE E 67 TRP 0.009 0.001 TRP K 932 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.19 (19803) covalent geometry : angle 0.58287 / 0.33 (28142) hydrogen bonds : bond 0.04451 / 4.88 ( 1068) hydrogen bonds : angle 3.21230 / 4.03 ( 2741) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 180 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: D 53 CYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8493 (t) REVERT: D 73 GLU cc_start: 0.8433 (tp30) cc_final: 0.8178 (tp30) REVERT: D 83 ARG cc_start: 0.8882 (mmt-90) cc_final: 0.8620 (mmt90) REVERT: H 90 GLU cc_start: 0.8732 (mp0) cc_final: 0.8229 (mp0) REVERT: K 229 THR cc_start: 0.8435 (OUTLIER) cc_final: 0.8211 (p) REVERT: K 272 MET cc_start: 0.8246 (ppp) cc_final: 0.7948 (tmm) REVERT: K 276 ARG cc_start: 0.8206 (ttm170) cc_final: 0.7976 (ttm170) REVERT: K 483 MET cc_start: 0.8959 (mmm) cc_final: 0.8520 (mmm) REVERT: K 827 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8363 (mm-30) outliers start: 17 outliers final: 7 residues processed: 192 average time/residue: 0.8361 time to fit residues: 173.9780 Evaluate side-chains 183 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 173 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain K residue 229 THR Chi-restraints excluded: chain K residue 470 GLU Chi-restraints excluded: chain K residue 560 MET Chi-restraints excluded: chain K residue 766 VAL Chi-restraints excluded: chain K residue 827 GLU Chi-restraints excluded: chain K residue 828 GLU Chi-restraints excluded: chain E residue 45 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 57 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 40 optimal weight: 0.0970 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 16 optimal weight: 60.0000 chunk 70 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN K 486 ASN ** K 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 800 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.121353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.083506 restraints weight = 33164.399| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.09 r_work: 0.3254 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19803 Z= 0.159 Angle : 0.567 7.666 28142 Z= 0.327 Chirality : 0.042 0.224 3181 Planarity : 0.004 0.046 2486 Dihedral : 28.800 97.075 5199 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.50 % Allowed : 14.85 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.22), residues: 1527 helix: 1.78 (0.17), residues: 907 sheet: 0.40 (0.53), residues: 99 loop : -0.84 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 30 TYR 0.015 0.001 TYR K 494 PHE 0.012 0.001 PHE E 67 TRP 0.009 0.001 TRP K 311 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.16 (19803) covalent geometry : angle 0.56745 / 0.33 (28142) hydrogen bonds : bond 0.04143 / 4.54 ( 1068) hydrogen bonds : angle 3.18411 / 3.99 ( 2741) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: D 53 CYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8480 (t) REVERT: D 73 GLU cc_start: 0.8384 (tp30) cc_final: 0.8135 (tp30) REVERT: D 83 ARG cc_start: 0.8889 (mmt-90) cc_final: 0.8608 (mmt90) REVERT: H 90 GLU cc_start: 0.8731 (mp0) cc_final: 0.8226 (mp0) REVERT: K 229 THR cc_start: 0.8452 (OUTLIER) cc_final: 0.8207 (p) REVERT: K 483 MET cc_start: 0.8965 (mmm) cc_final: 0.8541 (mmm) REVERT: E 59 GLU cc_start: 0.8765 (pm20) cc_final: 0.8399 (pm20) outliers start: 19 outliers final: 8 residues processed: 188 average time/residue: 0.8323 time to fit residues: 170.3155 Evaluate side-chains 181 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 171 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain K residue 204 LEU Chi-restraints excluded: chain K residue 229 THR Chi-restraints excluded: chain K residue 470 GLU Chi-restraints excluded: chain K residue 560 MET Chi-restraints excluded: chain K residue 766 VAL Chi-restraints excluded: chain K residue 828 GLU Chi-restraints excluded: chain E residue 45 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 114 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 162 optimal weight: 0.8980 chunk 131 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 130 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 163 optimal weight: 10.0000 chunk 103 optimal weight: 20.0000 chunk 68 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN K 486 ASN ** K 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.120873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.083074 restraints weight = 33345.854| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.02 r_work: 0.3227 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19803 Z= 0.183 Angle : 0.574 7.362 28142 Z= 0.329 Chirality : 0.043 0.227 3181 Planarity : 0.004 0.049 2486 Dihedral : 28.794 97.597 5199 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.50 % Allowed : 15.17 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.22), residues: 1527 helix: 1.78 (0.17), residues: 912 sheet: 0.47 (0.53), residues: 99 loop : -0.88 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 30 TYR 0.017 0.001 TYR K 494 PHE 0.013 0.001 PHE E 67 TRP 0.009 0.001 TRP K 311 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.18 (19803) covalent geometry : angle 0.57416 / 0.33 (28142) hydrogen bonds : bond 0.04400 / 4.83 ( 1068) hydrogen bonds : angle 3.16243 / 3.95 ( 2741) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 0.569 Fit side-chains revert: symmetry clash REVERT: D 53 CYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8421 (t) REVERT: D 83 ARG cc_start: 0.8911 (mmt-90) cc_final: 0.8596 (mmt90) REVERT: D 102 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7887 (tp30) REVERT: H 90 GLU cc_start: 0.8812 (mp0) cc_final: 0.8230 (mp0) REVERT: K 229 THR cc_start: 0.8416 (OUTLIER) cc_final: 0.8151 (p) REVERT: K 483 MET cc_start: 0.8985 (mmm) cc_final: 0.8494 (mmm) REVERT: K 827 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8391 (mm-30) outliers start: 19 outliers final: 7 residues processed: 187 average time/residue: 0.8925 time to fit residues: 180.7138 Evaluate side-chains 184 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 173 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain K residue 204 LEU Chi-restraints excluded: chain K residue 229 THR Chi-restraints excluded: chain K residue 470 GLU Chi-restraints excluded: chain K residue 560 MET Chi-restraints excluded: chain K residue 827 GLU Chi-restraints excluded: chain E residue 45 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 68 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 141 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 131 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 154 optimal weight: 4.9990 chunk 12 optimal weight: 9.9990 chunk 98 optimal weight: 7.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN K 486 ASN ** K 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.120808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.084328 restraints weight = 33456.896| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.89 r_work: 0.3241 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19803 Z= 0.171 Angle : 0.572 7.150 28142 Z= 0.328 Chirality : 0.042 0.226 3181 Planarity : 0.004 0.048 2486 Dihedral : 28.797 97.551 5199 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.18 % Allowed : 16.11 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.22), residues: 1527 helix: 1.84 (0.17), residues: 907 sheet: 0.53 (0.54), residues: 99 loop : -0.87 (0.25), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 30 TYR 0.016 0.001 TYR K 494 PHE 0.011 0.001 PHE E 67 TRP 0.009 0.001 TRP K 311 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.17 (19803) covalent geometry : angle 0.57237 / 0.33 (28142) hydrogen bonds : bond 0.04142 / 4.54 ( 1068) hydrogen bonds : angle 3.15518 / 3.94 ( 2741) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 176 time to evaluate : 0.560 Fit side-chains revert: symmetry clash REVERT: C 92 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.7846 (mt-10) REVERT: D 53 CYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8359 (t) REVERT: D 83 ARG cc_start: 0.8934 (mmt-90) cc_final: 0.8560 (mmt90) REVERT: D 102 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8063 (tp30) REVERT: H 90 GLU cc_start: 0.8802 (mp0) cc_final: 0.8236 (mp0) REVERT: K 229 THR cc_start: 0.8411 (OUTLIER) cc_final: 0.8151 (p) REVERT: K 483 MET cc_start: 0.8960 (mmm) cc_final: 0.8454 (mmm) REVERT: K 692 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8296 (mpt) outliers start: 15 outliers final: 7 residues processed: 185 average time/residue: 0.8271 time to fit residues: 166.1527 Evaluate side-chains 187 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 175 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain K residue 204 LEU Chi-restraints excluded: chain K residue 229 THR Chi-restraints excluded: chain K residue 470 GLU Chi-restraints excluded: chain K residue 560 MET Chi-restraints excluded: chain K residue 692 MET Chi-restraints excluded: chain K residue 766 VAL Chi-restraints excluded: chain E residue 45 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 20 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 132 optimal weight: 0.5980 chunk 167 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 43 optimal weight: 0.0870 chunk 9 optimal weight: 8.9990 chunk 131 optimal weight: 5.9990 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN K 486 ASN ** K 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.121104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.084103 restraints weight = 33107.646| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.01 r_work: 0.3239 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19803 Z= 0.157 Angle : 0.569 6.964 28142 Z= 0.326 Chirality : 0.042 0.225 3181 Planarity : 0.004 0.052 2486 Dihedral : 28.795 97.605 5199 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.58 % Allowed : 15.72 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.22), residues: 1527 helix: 1.87 (0.17), residues: 907 sheet: 0.53 (0.54), residues: 99 loop : -0.86 (0.25), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 30 TYR 0.016 0.001 TYR K 494 PHE 0.011 0.001 PHE E 67 TRP 0.010 0.001 TRP K 311 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.16 (19803) covalent geometry : angle 0.56866 / 0.33 (28142) hydrogen bonds : bond 0.04063 / 4.46 ( 1068) hydrogen bonds : angle 3.15553 / 3.94 ( 2741) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 177 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: C 92 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7837 (mt-10) REVERT: D 53 CYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8418 (t) REVERT: D 83 ARG cc_start: 0.8909 (mmt-90) cc_final: 0.8591 (mmt90) REVERT: D 102 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7927 (tp30) REVERT: H 90 GLU cc_start: 0.8809 (mp0) cc_final: 0.8280 (mp0) REVERT: K 229 THR cc_start: 0.8372 (OUTLIER) cc_final: 0.8107 (p) REVERT: K 483 MET cc_start: 0.8976 (mmm) cc_final: 0.8451 (mmm) REVERT: K 692 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8290 (mpt) REVERT: K 827 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8352 (mm-30) outliers start: 20 outliers final: 10 residues processed: 191 average time/residue: 0.7988 time to fit residues: 165.6464 Evaluate side-chains 192 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 176 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain K residue 204 LEU Chi-restraints excluded: chain K residue 229 THR Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain K residue 470 GLU Chi-restraints excluded: chain K residue 560 MET Chi-restraints excluded: chain K residue 692 MET Chi-restraints excluded: chain K residue 766 VAL Chi-restraints excluded: chain K residue 827 GLU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 71 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 100 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 93 optimal weight: 30.0000 chunk 71 optimal weight: 0.3980 chunk 102 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 92 optimal weight: 8.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 18 HIS C 104 GLN K 339 GLN K 486 ASN ** K 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 667 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.120461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.082903 restraints weight = 33349.251| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.99 r_work: 0.3223 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19803 Z= 0.181 Angle : 0.578 7.423 28142 Z= 0.331 Chirality : 0.043 0.228 3181 Planarity : 0.004 0.048 2486 Dihedral : 28.807 99.307 5199 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.34 % Allowed : 16.03 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.22), residues: 1527 helix: 1.81 (0.17), residues: 912 sheet: 0.57 (0.53), residues: 99 loop : -0.91 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 30 TYR 0.017 0.001 TYR K 494 PHE 0.012 0.001 PHE E 67 TRP 0.010 0.001 TRP K 932 HIS 0.005 0.001 HIS K 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.18 (19803) covalent geometry : angle 0.57801 / 0.33 (28142) hydrogen bonds : bond 0.04405 / 4.83 ( 1068) hydrogen bonds : angle 3.16304 / 3.92 ( 2741) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3054 Ramachandran restraints generated. 1527 Oldfield, 0 Emsley, 1527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 175 time to evaluate : 0.587 Fit side-chains revert: symmetry clash REVERT: C 92 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7870 (mt-10) REVERT: D 53 CYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8386 (t) REVERT: D 83 ARG cc_start: 0.8909 (mmt-90) cc_final: 0.8573 (mmt90) REVERT: D 102 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.8032 (tp30) REVERT: H 90 GLU cc_start: 0.8777 (mp0) cc_final: 0.8251 (mp0) REVERT: K 229 THR cc_start: 0.8285 (OUTLIER) cc_final: 0.8052 (p) REVERT: K 483 MET cc_start: 0.8961 (mmm) cc_final: 0.8452 (mmm) REVERT: K 692 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8301 (mpt) REVERT: K 827 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8418 (mm-30) outliers start: 17 outliers final: 7 residues processed: 187 average time/residue: 0.9143 time to fit residues: 185.6345 Evaluate side-chains 186 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 173 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain K residue 204 LEU Chi-restraints excluded: chain K residue 229 THR Chi-restraints excluded: chain K residue 470 GLU Chi-restraints excluded: chain K residue 560 MET Chi-restraints excluded: chain K residue 692 MET Chi-restraints excluded: chain K residue 766 VAL Chi-restraints excluded: chain K residue 827 GLU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 71 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 172 optimal weight: 0.6980 chunk 92 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 75 optimal weight: 0.9980 chunk 0 optimal weight: 50.0000 chunk 1 optimal weight: 20.0000 chunk 82 optimal weight: 2.9990 chunk 16 optimal weight: 60.0000 chunk 37 optimal weight: 0.8980 chunk 24 optimal weight: 10.0000 overall best weight: 3.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN K 339 GLN K 486 ASN ** K 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.118094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.081223 restraints weight = 33249.198| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.96 r_work: 0.3175 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 19803 Z= 0.332 Angle : 0.687 8.234 28142 Z= 0.379 Chirality : 0.049 0.256 3181 Planarity : 0.005 0.050 2486 Dihedral : 29.041 103.689 5199 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.34 % Allowed : 16.11 % Favored : 82.54 % 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: 0.85 (0.21), residues: 1527 helix: 1.47 (0.17), residues: 919 sheet: 0.47 (0.52), residues: 97 loop : -1.08 (0.25), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 30 TYR 0.018 0.002 TYR E 41 PHE 0.015 0.002 PHE K 765 TRP 0.015 0.002 TRP K 932 HIS 0.007 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00726 / 0.33 (19803) covalent geometry : angle 0.68724 / 0.38 (28142) hydrogen bonds : bond 0.06904 / 7.71 ( 1068) hydrogen bonds : angle 3.38221 / 4.20 ( 2741) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8911.32 seconds wall clock time: 151 minutes 34.00 seconds (9094.00 seconds total)