Starting phenix.real_space_refine on Sun Aug 24 08:39:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n6h_49061/08_2025/9n6h_49061.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n6h_49061/08_2025/9n6h_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 { model { file = "/net/cci-nas-00/data/ceres_data/9n6h_49061/08_2025/9n6h_49061.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n6h_49061/08_2025/9n6h_49061.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n6h_49061/08_2025/9n6h_49061.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n6h_49061/08_2025/9n6h_49061.map" } 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-2.0-5787/lib/python3.9/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: 4.09, per 1000 atoms: 0.22 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: 1.18 Conformation dependent library (CDL) restraints added in 579.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 2.98 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: 5.99 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=" CA ALA B 89 " pdb=" CB ALA B 89 " ideal model delta sigma weight residual 1.528 1.487 0.041 1.59e-02 3.96e+03 6.61e+00 bond pdb=" N LEU K 598 " pdb=" CA LEU K 598 " ideal model delta sigma weight residual 1.454 1.482 -0.028 1.19e-02 7.06e+03 5.38e+00 bond pdb=" N ARG K 597 " pdb=" CA ARG K 597 " ideal model delta sigma weight residual 1.454 1.481 -0.027 1.23e-02 6.61e+03 4.76e+00 bond pdb=" C3' DG I 52 " pdb=" O3' DG I 52 " ideal model delta sigma weight residual 1.422 1.486 -0.064 3.00e-02 1.11e+03 4.51e+00 bond pdb=" N GLN B 93 " pdb=" CA GLN B 93 " ideal model delta sigma weight residual 1.456 1.484 -0.028 1.32e-02 5.74e+03 4.39e+00 ... (remaining 19798 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 27757 2.44 - 4.89: 344 4.89 - 7.33: 28 7.33 - 9.77: 11 9.77 - 12.22: 2 Bond angle restraints: 28142 Sorted by residual: angle pdb=" CA GLN K 920 " pdb=" CB GLN K 920 " pdb=" CG GLN K 920 " ideal model delta sigma weight residual 114.10 122.37 -8.27 2.00e+00 2.50e-01 1.71e+01 angle pdb=" CB MET A 90 " pdb=" CG MET A 90 " pdb=" SD MET A 90 " ideal model delta sigma weight residual 112.70 124.92 -12.22 3.00e+00 1.11e-01 1.66e+01 angle pdb=" CA ARG K 274 " pdb=" CB ARG K 274 " pdb=" CG ARG K 274 " ideal model delta sigma weight residual 114.10 122.22 -8.12 2.00e+00 2.50e-01 1.65e+01 angle pdb=" C GLY K 677 " pdb=" N ASP K 678 " pdb=" CA ASP K 678 " ideal model delta sigma weight residual 121.54 129.28 -7.74 1.91e+00 2.74e-01 1.64e+01 angle pdb=" C THR K 631 " pdb=" N LYS K 632 " pdb=" CA LYS K 632 " ideal model delta sigma weight residual 121.54 128.50 -6.96 1.91e+00 2.74e-01 1.33e+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: 2797 0.065 - 0.131: 350 0.131 - 0.196: 30 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.200 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: 0.060 Set scattering table: 0.050 Process input model: 21.410 Find NCS groups from input model: 0.160 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:7.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 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 0.064 19803 Z= 0.216 Angle : 0.740 12.215 28142 Z= 0.426 Chirality : 0.044 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 aren 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 covalent geometry : bond 0.00458 (19803) covalent geometry : angle 0.73961 (28142) hydrogen bonds : bond 0.12941 ( 1068) hydrogen bonds : angle 5.04650 ( 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 : 0.435 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: 0.8725 (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: 0.8692 time to fit residues: 220.6968 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 : 0.569 ------------------------------------------------------------------------------- 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: 3.9990 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... Flipped N/Q/H residues before XYZ refinement: B 93 GLN C 104 GLN K 129 ASN K 235 GLN K 653 ASN E 68 GLN ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 76 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.124290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.087528 restraints weight = 33683.354| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.94 r_work: 0.3323 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19803 Z= 0.169 Angle : 0.533 6.473 28142 Z= 0.316 Chirality : 0.036 0.140 3181 Planarity : 0.004 0.051 2486 Dihedral : 27.928 111.599 5199 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.95 % Allowed : 11.22 % Favored : 87.84 % 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 aren not related in a simple way. whole: 0.30 (0.21), residues: 1527 helix: 0.93 (0.17), residues: 897 sheet: 0.33 (0.50), residues: 97 loop : -1.02 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 92 TYR 0.011 0.001 TYR G 50 PHE 0.010 0.001 PHE E 67 TRP 0.010 0.001 TRP K 932 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00370 (19803) covalent geometry : angle 0.53265 (28142) hydrogen bonds : bond 0.03728 ( 1068) hydrogen bonds : angle 3.35137 ( 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 215 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 203 time to evaluate : 0.462 Fit side-chains REVERT: C 75 LYS cc_start: 0.9023 (mmtm) cc_final: 0.8800 (mmtt) REVERT: D 53 CYS cc_start: 0.8822 (m) cc_final: 0.8414 (t) REVERT: D 83 ARG cc_start: 0.8872 (mmt-90) cc_final: 0.8611 (mmt90) REVERT: H 44 GLN cc_start: 0.8908 (mt0) cc_final: 0.8671 (mt0) REVERT: H 90 GLU cc_start: 0.8736 (mp0) cc_final: 0.8270 (mp0) outliers start: 12 outliers final: 2 residues processed: 209 average time/residue: 0.9467 time to fit residues: 214.2666 Evaluate side-chains 188 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 186 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 453 CYS Chi-restraints excluded: chain E residue 45 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 99 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 14 optimal weight: 30.0000 chunk 152 optimal weight: 6.9990 chunk 79 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 159 optimal weight: 5.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 HIS C 104 GLN K 222 HIS K 800 GLN ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.120396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.083734 restraints weight = 33562.300| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.86 r_work: 0.3238 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 19803 Z= 0.276 Angle : 0.581 5.950 28142 Z= 0.339 Chirality : 0.039 0.137 3181 Planarity : 0.004 0.044 2486 Dihedral : 28.305 98.150 5199 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.58 % Allowed : 13.27 % Favored : 85.15 % 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 aren not related in a simple way. whole: 0.71 (0.21), residues: 1527 helix: 1.31 (0.17), residues: 913 sheet: 0.37 (0.50), residues: 99 loop : -0.99 (0.25), residues: 515 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 0.017 0.002 PHE K 389 TRP 0.012 0.002 TRP K 932 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00625 (19803) covalent geometry : angle 0.58085 (28142) hydrogen bonds : bond 0.04928 ( 1068) hydrogen bonds : angle 3.30267 ( 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 200 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 0.609 Fit side-chains REVERT: C 75 LYS cc_start: 0.9055 (mmtm) cc_final: 0.8824 (mmmt) REVERT: D 83 ARG cc_start: 0.8881 (mmt-90) cc_final: 0.8584 (mmt90) REVERT: F 95 ARG cc_start: 0.9019 (mtt-85) cc_final: 0.8801 (mtt-85) REVERT: H 90 GLU cc_start: 0.8768 (mp0) cc_final: 0.8241 (mp0) REVERT: K 483 MET cc_start: 0.8940 (mmm) cc_final: 0.8555 (mmm) outliers start: 20 outliers final: 6 residues processed: 194 average time/residue: 0.9832 time to fit residues: 206.5065 Evaluate side-chains 179 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 173 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain K residue 560 MET Chi-restraints excluded: chain K residue 766 VAL Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 105 GLU 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: 0.8980 chunk 178 optimal weight: 1.9990 chunk 158 optimal weight: 0.2980 chunk 15 optimal weight: 50.0000 chunk 147 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 43 optimal weight: 0.0980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN A 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.121530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.084032 restraints weight = 33316.132| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.01 r_work: 0.3245 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 19803 Z= 0.181 Angle : 0.531 6.079 28142 Z= 0.315 Chirality : 0.036 0.134 3181 Planarity : 0.004 0.050 2486 Dihedral : 28.259 97.844 5199 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.34 % Allowed : 14.06 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.21), residues: 1527 helix: 1.57 (0.17), residues: 910 sheet: 0.44 (0.51), residues: 99 loop : -0.85 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 30 TYR 0.014 0.001 TYR K 494 PHE 0.011 0.001 PHE E 67 TRP 0.008 0.001 TRP K 311 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00402 (19803) covalent geometry : angle 0.53116 (28142) hydrogen bonds : bond 0.03902 ( 1068) hydrogen bonds : angle 3.18970 ( 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 197 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 180 time to evaluate : 0.565 Fit side-chains REVERT: C 75 LYS cc_start: 0.9020 (mmtm) cc_final: 0.8762 (mmmt) REVERT: C 92 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.7867 (mt-10) REVERT: D 83 ARG cc_start: 0.8930 (mmt-90) cc_final: 0.8574 (mmt90) REVERT: F 95 ARG cc_start: 0.9032 (mtt-85) cc_final: 0.8831 (mtt-85) REVERT: H 90 GLU cc_start: 0.8796 (mp0) cc_final: 0.8290 (mp0) REVERT: K 483 MET cc_start: 0.8962 (mmm) cc_final: 0.8560 (mmm) outliers start: 17 outliers final: 6 residues processed: 188 average time/residue: 0.9347 time to fit residues: 189.9901 Evaluate side-chains 183 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 176 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LYS 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 470 GLU Chi-restraints excluded: chain K residue 560 MET Chi-restraints excluded: chain E residue 45 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 175 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 148 optimal weight: 2.9990 chunk 15 optimal weight: 50.0000 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN A 68 GLN A 76 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.120877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.083717 restraints weight = 33394.050| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.94 r_work: 0.3254 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 19803 Z= 0.202 Angle : 0.528 5.478 28142 Z= 0.313 Chirality : 0.037 0.133 3181 Planarity : 0.004 0.041 2486 Dihedral : 28.085 91.906 5199 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.26 % Allowed : 15.17 % Favored : 83.57 % 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 aren not related in a simple way. whole: 1.23 (0.22), residues: 1527 helix: 1.75 (0.17), residues: 910 sheet: 0.45 (0.52), residues: 99 loop : -0.80 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 83 TYR 0.015 0.001 TYR K 494 PHE 0.010 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 covalent geometry : bond 0.00452 (19803) covalent geometry : angle 0.52799 (28142) hydrogen bonds : bond 0.03873 ( 1068) hydrogen bonds : angle 3.09215 ( 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 200 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 184 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: C 92 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7900 (mt-10) REVERT: D 53 CYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8488 (t) REVERT: D 83 ARG cc_start: 0.8854 (mmt-90) cc_final: 0.8574 (mmt90) REVERT: H 90 GLU cc_start: 0.8710 (mp0) cc_final: 0.8269 (mp0) REVERT: K 229 THR cc_start: 0.8428 (OUTLIER) cc_final: 0.8165 (p) REVERT: K 483 MET cc_start: 0.8936 (mmm) cc_final: 0.8608 (mmm) REVERT: K 692 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8216 (mpt) outliers start: 16 outliers final: 7 residues processed: 193 average time/residue: 0.8199 time to fit residues: 171.1718 Evaluate side-chains 186 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 175 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 92 GLU 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 692 MET Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 105 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 57 optimal weight: 0.7980 chunk 118 optimal weight: 0.0970 chunk 6 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 147 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 16 optimal weight: 50.0000 chunk 70 optimal weight: 0.8980 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN K 486 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.121457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.084033 restraints weight = 33356.440| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.97 r_work: 0.3270 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19803 Z= 0.160 Angle : 0.519 5.379 28142 Z= 0.309 Chirality : 0.035 0.133 3181 Planarity : 0.003 0.053 2486 Dihedral : 28.092 91.509 5199 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.58 % Allowed : 15.48 % Favored : 82.94 % 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 aren not related in a simple way. whole: 1.32 (0.22), residues: 1527 helix: 1.84 (0.17), residues: 910 sheet: 0.41 (0.52), residues: 99 loop : -0.75 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG D 30 TYR 0.013 0.001 TYR K 494 PHE 0.010 0.001 PHE E 67 TRP 0.010 0.001 TRP K 311 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00353 (19803) covalent geometry : angle 0.51852 (28142) hydrogen bonds : bond 0.03645 ( 1068) hydrogen bonds : angle 3.07373 ( 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 198 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 178 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: C 92 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7841 (mt-10) REVERT: D 53 CYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8444 (t) REVERT: D 83 ARG cc_start: 0.8825 (mmt-90) cc_final: 0.8556 (mmt90) REVERT: H 90 GLU cc_start: 0.8739 (mp0) cc_final: 0.8294 (mp0) REVERT: K 229 THR cc_start: 0.8406 (OUTLIER) cc_final: 0.8140 (p) REVERT: K 483 MET cc_start: 0.8936 (mmm) cc_final: 0.8483 (mmm) REVERT: K 692 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8196 (mpt) REVERT: E 59 GLU cc_start: 0.8766 (pm20) cc_final: 0.8366 (pm20) outliers start: 20 outliers final: 7 residues processed: 190 average time/residue: 0.8694 time to fit residues: 178.8484 Evaluate side-chains 185 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 174 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain K residue 204 LEU Chi-restraints excluded: chain K residue 229 THR Chi-restraints excluded: chain K residue 246 CYS Chi-restraints excluded: chain K residue 453 CYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 114 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 162 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 163 optimal weight: 20.0000 chunk 103 optimal weight: 0.1980 chunk 68 optimal weight: 4.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN K 339 GLN K 486 ASN A 68 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.121790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.084282 restraints weight = 33455.010| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.97 r_work: 0.3270 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19803 Z= 0.159 Angle : 0.514 7.192 28142 Z= 0.306 Chirality : 0.035 0.132 3181 Planarity : 0.003 0.057 2486 Dihedral : 28.063 90.822 5199 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.58 % Allowed : 15.40 % Favored : 83.02 % 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 aren not related in a simple way. whole: 1.38 (0.22), residues: 1527 helix: 1.88 (0.17), residues: 910 sheet: 0.43 (0.53), residues: 99 loop : -0.73 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 30 TYR 0.013 0.001 TYR K 494 PHE 0.010 0.001 PHE E 67 TRP 0.010 0.001 TRP K 311 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00351 (19803) covalent geometry : angle 0.51367 (28142) hydrogen bonds : bond 0.03435 ( 1068) hydrogen bonds : angle 3.05727 ( 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 198 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 178 time to evaluate : 0.589 Fit side-chains revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8887 (ptpp) cc_final: 0.8585 (ptpp) REVERT: C 92 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7866 (mt-10) REVERT: D 53 CYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8436 (t) REVERT: D 83 ARG cc_start: 0.8858 (mmt-90) cc_final: 0.8543 (mmt90) REVERT: G 92 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7781 (mt-10) REVERT: H 90 GLU cc_start: 0.8743 (mp0) cc_final: 0.8271 (mp0) REVERT: K 229 THR cc_start: 0.8388 (OUTLIER) cc_final: 0.8119 (p) REVERT: K 483 MET cc_start: 0.8944 (mmm) cc_final: 0.8481 (mmm) REVERT: K 692 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8205 (mpt) outliers start: 20 outliers final: 9 residues processed: 192 average time/residue: 0.8433 time to fit residues: 175.6145 Evaluate side-chains 189 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 175 time to evaluate : 0.550 ------------------------------------------------------------------------------- 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 109 SER Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain K residue 204 LEU Chi-restraints excluded: chain K residue 229 THR Chi-restraints excluded: chain K residue 246 CYS Chi-restraints excluded: chain K residue 453 CYS 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 Chi-restraints excluded: chain E residue 57 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 68 optimal weight: 0.9990 chunk 162 optimal weight: 0.0770 chunk 141 optimal weight: 0.9990 chunk 108 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 chunk 154 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN K 339 GLN K 486 ASN A 68 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.122000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.084595 restraints weight = 33399.031| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.88 r_work: 0.3280 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19803 Z= 0.148 Angle : 0.513 5.408 28142 Z= 0.306 Chirality : 0.035 0.128 3181 Planarity : 0.003 0.064 2486 Dihedral : 28.055 90.836 5199 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.66 % Allowed : 15.48 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.22), residues: 1527 helix: 1.93 (0.17), residues: 910 sheet: 0.42 (0.52), residues: 99 loop : -0.72 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 30 TYR 0.013 0.001 TYR K 494 PHE 0.010 0.001 PHE E 67 TRP 0.011 0.001 TRP K 311 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00323 (19803) covalent geometry : angle 0.51259 (28142) hydrogen bonds : bond 0.03327 ( 1068) hydrogen bonds : angle 3.04702 ( 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 198 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 177 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.8860 (ptpp) cc_final: 0.8564 (ptpp) REVERT: C 92 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7836 (mt-10) REVERT: D 53 CYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8447 (t) REVERT: D 83 ARG cc_start: 0.8827 (mmt-90) cc_final: 0.8543 (mmt90) REVERT: H 90 GLU cc_start: 0.8724 (mp0) cc_final: 0.8283 (mp0) REVERT: K 229 THR cc_start: 0.8405 (OUTLIER) cc_final: 0.8158 (p) REVERT: K 692 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8195 (mpt) outliers start: 21 outliers final: 12 residues processed: 192 average time/residue: 0.9123 time to fit residues: 189.8703 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 : 0.580 ------------------------------------------------------------------------------- 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 109 SER Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain K residue 204 LEU Chi-restraints excluded: chain K residue 229 THR Chi-restraints excluded: chain K residue 246 CYS Chi-restraints excluded: chain K residue 339 GLN Chi-restraints excluded: chain K residue 453 CYS 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 Chi-restraints excluded: chain E residue 57 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 20 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 167 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 43 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN ** K 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 486 ASN K 667 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.119048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.081964 restraints weight = 32915.372| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.12 r_work: 0.3204 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 19803 Z= 0.294 Angle : 0.578 5.659 28142 Z= 0.339 Chirality : 0.040 0.133 3181 Planarity : 0.004 0.046 2486 Dihedral : 28.305 93.930 5199 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.50 % Allowed : 15.96 % 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 aren not related in a simple way. whole: 1.11 (0.21), residues: 1527 helix: 1.67 (0.17), residues: 918 sheet: 0.33 (0.51), residues: 99 loop : -0.88 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 30 TYR 0.016 0.002 TYR K 494 PHE 0.013 0.002 PHE C 25 TRP 0.013 0.002 TRP K 932 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00664 (19803) covalent geometry : angle 0.57837 (28142) hydrogen bonds : bond 0.05193 ( 1068) hydrogen bonds : angle 3.19771 ( 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: 19 poor density : 178 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 92 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.7947 (mt-10) REVERT: D 53 CYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8450 (t) REVERT: D 83 ARG cc_start: 0.8896 (mmt-90) cc_final: 0.8649 (mmt90) REVERT: H 90 GLU cc_start: 0.8761 (mp0) cc_final: 0.8286 (mp0) REVERT: K 229 THR cc_start: 0.8267 (OUTLIER) cc_final: 0.8019 (p) REVERT: K 483 MET cc_start: 0.8941 (mmm) cc_final: 0.8509 (mmm) outliers start: 19 outliers final: 9 residues processed: 191 average time/residue: 0.9360 time to fit residues: 193.4363 Evaluate side-chains 182 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 170 time to evaluate : 0.415 ------------------------------------------------------------------------------- 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 109 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain K residue 204 LEU Chi-restraints excluded: chain K residue 229 THR Chi-restraints excluded: chain K residue 246 CYS Chi-restraints excluded: chain K residue 339 GLN 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 E residue 45 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 100 optimal weight: 0.9980 chunk 147 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 93 optimal weight: 40.0000 chunk 71 optimal weight: 0.7980 chunk 102 optimal weight: 0.5980 chunk 41 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN K 339 GLN K 486 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.119882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.083364 restraints weight = 33281.418| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.08 r_work: 0.3236 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2742 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= 0.195 Angle : 0.551 5.996 28142 Z= 0.324 Chirality : 0.037 0.133 3181 Planarity : 0.004 0.056 2486 Dihedral : 28.303 92.500 5199 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.95 % Allowed : 16.67 % Favored : 82.39 % 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 aren not related in a simple way. whole: 1.19 (0.21), residues: 1527 helix: 1.72 (0.17), residues: 916 sheet: 0.37 (0.52), residues: 99 loop : -0.83 (0.26), residues: 512 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 0.010 0.001 TRP K 932 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00434 (19803) covalent geometry : angle 0.55076 (28142) hydrogen bonds : bond 0.04215 ( 1068) hydrogen bonds : angle 3.16735 ( 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 186 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 174 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: D 53 CYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8439 (t) REVERT: H 90 GLU cc_start: 0.8723 (mp0) cc_final: 0.8278 (mp0) REVERT: K 229 THR cc_start: 0.8245 (OUTLIER) cc_final: 0.8006 (p) REVERT: K 483 MET cc_start: 0.8894 (mmm) cc_final: 0.8517 (mmm) REVERT: K 692 MET cc_start: 0.8788 (mpp) cc_final: 0.8350 (mpt) outliers start: 12 outliers final: 9 residues processed: 183 average time/residue: 0.8811 time to fit residues: 174.4715 Evaluate side-chains 181 residues out of total 1345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 170 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain K residue 204 LEU Chi-restraints excluded: chain K residue 229 THR Chi-restraints excluded: chain K residue 246 CYS 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 E residue 45 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 172 optimal weight: 0.9990 chunk 92 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 16 optimal weight: 50.0000 chunk 37 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN K 339 GLN K 486 ASN A 68 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.120032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.083785 restraints weight = 33540.757| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.00 r_work: 0.3228 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 19803 Z= 0.207 Angle : 0.539 6.205 28142 Z= 0.319 Chirality : 0.037 0.132 3181 Planarity : 0.004 0.054 2486 Dihedral : 28.125 92.322 5199 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.11 % Allowed : 16.75 % Favored : 82.15 % 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 aren not related in a simple way. whole: 1.27 (0.22), residues: 1527 helix: 1.79 (0.17), residues: 919 sheet: 0.43 (0.52), residues: 99 loop : -0.82 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 30 TYR 0.015 0.001 TYR K 494 PHE 0.009 0.001 PHE E 67 TRP 0.009 0.001 TRP K 932 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00463 (19803) covalent geometry : angle 0.53942 (28142) hydrogen bonds : bond 0.03861 ( 1068) hydrogen bonds : angle 3.10932 ( 2741) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10090.58 seconds wall clock time: 171 minutes 22.35 seconds (10282.35 seconds total)