Starting phenix.real_space_refine on Fri Aug 7 21:46:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jg9_36225/08_2026/8jg9_36225_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jg9_36225/08_2026/8jg9_36225.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jg9_36225/08_2026/8jg9_36225_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jg9_36225/08_2026/8jg9_36225_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jg9_36225/08_2026/8jg9_36225.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jg9_36225/08_2026/8jg9_36225.map" } resolution = 3.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.015 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 220 5.49 5 S 34 5.16 5 C 14567 2.51 5 N 4203 2.21 5 O 5240 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24264 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8436 Classifications: {'peptide': 1041} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 25, 'TRANS': 1015} Chain breaks: 1 Unresolved non-hydrogen bonds: 209 Unresolved non-hydrogen angles: 244 Unresolved non-hydrogen dihedrals: 174 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 16, 'ASN:plan1': 3, 'ASP:plan': 2, 'ARG:plan': 4, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 111 Chain: "B" Number of atoms: 1820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1820 Classifications: {'RNA': 86} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 6, 'rna3p_pur': 39, 'rna3p_pyr': 38} Link IDs: {'rna2p': 8, 'rna3p': 77} Chain breaks: 1 Chain: "D" Number of atoms: 8443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8443 Classifications: {'peptide': 1041} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 25, 'TRANS': 1015} Chain breaks: 1 Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 235 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 15, 'ASN:plan1': 3, 'ASP:plan': 2, 'ARG:plan': 4, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 107 Chain: "E" Number of atoms: 1820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1820 Classifications: {'RNA': 86} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 6, 'rna3p_pur': 39, 'rna3p_pyr': 38} Link IDs: {'rna2p': 8, 'rna3p': 77} Chain breaks: 1 Chain: "F" Number of atoms: 1354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1354 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 170} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 7, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 47 Chain: "G" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 514 Classifications: {'DNA': 25} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 24} Chain: "H" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 505 Classifications: {'DNA': 25} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 24} Chain: "C" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1372 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'TRANS': 170} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 37 Time building chain proxies: 5.53, per 1000 atoms: 0.23 Number of scatterers: 24264 At special positions: 0 Unit cell: (130, 132.08, 176.8, 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 34 16.00 P 220 15.00 O 5240 8.00 N 4203 7.00 C 14567 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: 2.26 Conformation dependent library (CDL) restraints added in 927.2 milliseconds 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4644 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 20 sheets defined 53.9% alpha, 9.8% beta 61 base pairs and 140 stacking pairs defined. Time for finding SS restraints: 3.53 Creating SS restraints... Processing helix chain 'A' and resid 40 through 74 removed outlier: 4.413A pdb=" N ASN A 44 " --> pdb=" O ASN A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 96 Processing helix chain 'A' and resid 101 through 115 Processing helix chain 'A' and resid 120 through 124 removed outlier: 4.015A pdb=" N VAL A 124 " --> pdb=" O VAL A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 145 Processing helix chain 'A' and resid 149 through 161 Processing helix chain 'A' and resid 172 through 188 removed outlier: 3.621A pdb=" N TYR A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 186 " --> pdb=" O GLN A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 207 Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 250 through 265 Processing helix chain 'A' and resid 276 through 291 Processing helix chain 'A' and resid 295 through 304 Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 326 through 336 removed outlier: 3.741A pdb=" N ILE A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.682A pdb=" N ILE A 342 " --> pdb=" O ARG A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 358 Processing helix chain 'A' and resid 360 through 371 Processing helix chain 'A' and resid 376 through 384 removed outlier: 3.523A pdb=" N GLU A 381 " --> pdb=" O GLN A 377 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN A 382 " --> pdb=" O GLU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 410 Processing helix chain 'A' and resid 413 through 422 Processing helix chain 'A' and resid 438 through 444 removed outlier: 4.188A pdb=" N ASP A 442 " --> pdb=" O THR A 438 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASP A 443 " --> pdb=" O THR A 439 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 438 through 444' Processing helix chain 'A' and resid 447 through 469 Processing helix chain 'A' and resid 483 through 513 Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 520 through 530 removed outlier: 3.685A pdb=" N ASP A 528 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET A 529 " --> pdb=" O LYS A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 549 Processing helix chain 'A' and resid 560 through 565 Processing helix chain 'A' and resid 568 through 570 No H-bonds generated for 'chain 'A' and resid 568 through 570' Processing helix chain 'A' and resid 577 through 584 Processing helix chain 'A' and resid 587 through 594 Processing helix chain 'A' and resid 600 through 614 Processing helix chain 'A' and resid 615 through 617 No H-bonds generated for 'chain 'A' and resid 615 through 617' Processing helix chain 'A' and resid 619 through 627 removed outlier: 3.562A pdb=" N GLU A 624 " --> pdb=" O LYS A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 646 Processing helix chain 'A' and resid 650 through 667 Processing helix chain 'A' and resid 677 through 688 removed outlier: 3.767A pdb=" N THR A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER A 682 " --> pdb=" O GLY A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 714 removed outlier: 3.637A pdb=" N ALA A 702 " --> pdb=" O TYR A 698 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA A 705 " --> pdb=" O HIS A 701 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP A 712 " --> pdb=" O ILE A 708 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE A 713 " --> pdb=" O ALA A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 720 No H-bonds generated for 'chain 'A' and resid 718 through 720' Processing helix chain 'A' and resid 721 through 730 Processing helix chain 'A' and resid 746 through 755 Processing helix chain 'A' and resid 760 through 766 removed outlier: 3.900A pdb=" N LYS A 764 " --> pdb=" O ILE A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 823 Processing helix chain 'A' and resid 824 through 827 Processing helix chain 'A' and resid 828 through 833 Processing helix chain 'A' and resid 833 through 847 removed outlier: 3.919A pdb=" N TYR A 837 " --> pdb=" O ASP A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 862 Processing helix chain 'A' and resid 943 through 954 Processing helix chain 'A' and resid 1000 through 1007 Processing helix chain 'D' and resid 40 through 74 removed outlier: 4.413A pdb=" N ASN D 44 " --> pdb=" O ASN D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 96 Processing helix chain 'D' and resid 101 through 115 Processing helix chain 'D' and resid 120 through 124 removed outlier: 4.015A pdb=" N VAL D 124 " --> pdb=" O VAL D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 145 Processing helix chain 'D' and resid 149 through 161 Processing helix chain 'D' and resid 172 through 188 removed outlier: 3.621A pdb=" N TYR D 176 " --> pdb=" O LYS D 172 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL D 186 " --> pdb=" O GLN D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 207 Processing helix chain 'D' and resid 225 through 235 Processing helix chain 'D' and resid 250 through 265 Processing helix chain 'D' and resid 276 through 291 Processing helix chain 'D' and resid 295 through 304 Processing helix chain 'D' and resid 306 through 308 No H-bonds generated for 'chain 'D' and resid 306 through 308' Processing helix chain 'D' and resid 326 through 336 removed outlier: 3.742A pdb=" N ILE D 335 " --> pdb=" O ASP D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 343 removed outlier: 3.682A pdb=" N ILE D 342 " --> pdb=" O ARG D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 358 Processing helix chain 'D' and resid 360 through 371 Processing helix chain 'D' and resid 376 through 384 removed outlier: 3.523A pdb=" N GLU D 381 " --> pdb=" O GLN D 377 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN D 382 " --> pdb=" O GLU D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 410 Processing helix chain 'D' and resid 413 through 422 Processing helix chain 'D' and resid 438 through 444 removed outlier: 4.187A pdb=" N ASP D 442 " --> pdb=" O THR D 438 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP D 443 " --> pdb=" O THR D 439 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE D 444 " --> pdb=" O LEU D 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 438 through 444' Processing helix chain 'D' and resid 447 through 469 Processing helix chain 'D' and resid 483 through 513 Processing helix chain 'D' and resid 515 through 519 Processing helix chain 'D' and resid 520 through 530 removed outlier: 3.685A pdb=" N ASP D 528 " --> pdb=" O ILE D 524 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET D 529 " --> pdb=" O LYS D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 549 removed outlier: 3.763A pdb=" N LEU D 546 " --> pdb=" O PRO D 542 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU D 547 " --> pdb=" O LEU D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 565 Processing helix chain 'D' and resid 568 through 570 No H-bonds generated for 'chain 'D' and resid 568 through 570' Processing helix chain 'D' and resid 577 through 584 Processing helix chain 'D' and resid 587 through 594 Processing helix chain 'D' and resid 600 through 614 Processing helix chain 'D' and resid 615 through 617 No H-bonds generated for 'chain 'D' and resid 615 through 617' Processing helix chain 'D' and resid 619 through 627 removed outlier: 3.562A pdb=" N GLU D 624 " --> pdb=" O LYS D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 646 Processing helix chain 'D' and resid 650 through 667 Processing helix chain 'D' and resid 677 through 688 removed outlier: 3.767A pdb=" N THR D 681 " --> pdb=" O ASN D 677 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER D 682 " --> pdb=" O GLY D 678 " (cutoff:3.500A) Processing helix chain 'D' and resid 698 through 714 removed outlier: 3.637A pdb=" N ALA D 702 " --> pdb=" O TYR D 698 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA D 705 " --> pdb=" O HIS D 701 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP D 712 " --> pdb=" O ILE D 708 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE D 713 " --> pdb=" O ALA D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 718 through 720 No H-bonds generated for 'chain 'D' and resid 718 through 720' Processing helix chain 'D' and resid 721 through 729 Processing helix chain 'D' and resid 746 through 755 Processing helix chain 'D' and resid 760 through 766 removed outlier: 3.900A pdb=" N LYS D 764 " --> pdb=" O ILE D 760 " (cutoff:3.500A) Processing helix chain 'D' and resid 814 through 823 Processing helix chain 'D' and resid 824 through 827 Processing helix chain 'D' and resid 828 through 833 Processing helix chain 'D' and resid 833 through 847 removed outlier: 3.919A pdb=" N TYR D 837 " --> pdb=" O ASP D 833 " (cutoff:3.500A) Processing helix chain 'D' and resid 852 through 862 Processing helix chain 'D' and resid 943 through 954 Processing helix chain 'D' and resid 1000 through 1007 Processing helix chain 'F' and resid 1 through 10 Processing helix chain 'F' and resid 14 through 23 Processing helix chain 'F' and resid 25 through 35 Processing helix chain 'F' and resid 38 through 42 Processing helix chain 'F' and resid 43 through 57 removed outlier: 3.626A pdb=" N GLU F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N MET F 57 " --> pdb=" O TYR F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 95 Processing helix chain 'F' and resid 103 through 114 Processing helix chain 'F' and resid 116 through 121 Processing helix chain 'F' and resid 129 through 139 Processing helix chain 'F' and resid 148 through 155 Processing helix chain 'C' and resid 1 through 10 Processing helix chain 'C' and resid 14 through 23 Processing helix chain 'C' and resid 25 through 35 Processing helix chain 'C' and resid 38 through 42 Processing helix chain 'C' and resid 43 through 59 removed outlier: 3.806A pdb=" N GLU C 56 " --> pdb=" O GLU C 52 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET C 57 " --> pdb=" O TYR C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 95 Processing helix chain 'C' and resid 96 through 100 Processing helix chain 'C' and resid 103 through 114 Processing helix chain 'C' and resid 116 through 121 Processing helix chain 'C' and resid 129 through 139 Processing helix chain 'C' and resid 148 through 155 Processing sheet with id=AA1, first strand: chain 'A' and resid 672 through 675 removed outlier: 4.025A pdb=" N ASP A 473 " --> pdb=" O TYR A 5 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA A 31 " --> pdb=" O LYS A 770 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N SER A 772 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL A 33 " --> pdb=" O SER A 772 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 266 through 267 Processing sheet with id=AA3, first strand: chain 'A' and resid 553 through 557 Processing sheet with id=AA4, first strand: chain 'A' and resid 791 through 793 Processing sheet with id=AA5, first strand: chain 'A' and resid 803 through 805 Processing sheet with id=AA6, first strand: chain 'A' and resid 891 through 892 Processing sheet with id=AA7, first strand: chain 'A' and resid 922 through 929 removed outlier: 3.694A pdb=" N ALA A 964 " --> pdb=" O VAL A 916 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU A 918 " --> pdb=" O PHE A 962 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N PHE A 962 " --> pdb=" O LEU A 918 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 933 through 936 Processing sheet with id=AA9, first strand: chain 'A' and resid 1017 through 1019 removed outlier: 7.507A pdb=" N ARG A 991 " --> pdb=" O VAL A 984 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N VAL A 984 " --> pdb=" O ARG A 991 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLU A 993 " --> pdb=" O ILE A 982 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 672 through 675 removed outlier: 4.025A pdb=" N ASP D 473 " --> pdb=" O TYR D 5 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA D 31 " --> pdb=" O LYS D 770 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N SER D 772 " --> pdb=" O ALA D 31 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL D 33 " --> pdb=" O SER D 772 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 266 through 267 Processing sheet with id=AB3, first strand: chain 'D' and resid 553 through 557 Processing sheet with id=AB4, first strand: chain 'D' and resid 791 through 793 Processing sheet with id=AB5, first strand: chain 'D' and resid 803 through 805 Processing sheet with id=AB6, first strand: chain 'D' and resid 891 through 892 Processing sheet with id=AB7, first strand: chain 'D' and resid 922 through 929 removed outlier: 3.694A pdb=" N ALA D 964 " --> pdb=" O VAL D 916 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU D 918 " --> pdb=" O PHE D 962 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N PHE D 962 " --> pdb=" O LEU D 918 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 933 through 936 Processing sheet with id=AB9, first strand: chain 'D' and resid 1017 through 1019 removed outlier: 7.506A pdb=" N ARG D 991 " --> pdb=" O VAL D 984 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N VAL D 984 " --> pdb=" O ARG D 991 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLU D 993 " --> pdb=" O ILE D 982 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 76 through 81 Processing sheet with id=AC2, first strand: chain 'C' and resid 76 through 81 removed outlier: 3.674A pdb=" N GLU C 170 " --> pdb=" O ASP C 61 " (cutoff:3.500A) 964 hydrogen bonds defined for protein. 2775 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 139 hydrogen bonds 270 hydrogen bond angles 0 basepair planarities 61 basepair parallelities 140 stacking parallelities Total time for adding SS restraints: 7.49 Time building geometry restraints manager: 3.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3594 1.31 - 1.43: 7654 1.43 - 1.56: 13403 1.56 - 1.68: 436 1.68 - 1.81: 62 Bond restraints: 25149 Sorted by residual: bond pdb=" O3' U B 71 " pdb=" P U B 72 " ideal model delta sigma weight residual 1.607 1.679 -0.072 1.20e-02 6.94e+03 3.61e+01 bond pdb=" O3' U E 71 " pdb=" P U E 72 " ideal model delta sigma weight residual 1.607 1.678 -0.071 1.20e-02 6.94e+03 3.54e+01 bond pdb=" C ARG D 47 " pdb=" O ARG D 47 " ideal model delta sigma weight residual 1.237 1.180 0.057 1.17e-02 7.31e+03 2.39e+01 bond pdb=" C ARG A 47 " pdb=" O ARG A 47 " ideal model delta sigma weight residual 1.237 1.180 0.057 1.17e-02 7.31e+03 2.35e+01 bond pdb=" N ILE A 541 " pdb=" CA ILE A 541 " ideal model delta sigma weight residual 1.456 1.498 -0.041 8.70e-03 1.32e+04 2.27e+01 ... (remaining 25144 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 30815 2.03 - 4.06: 3655 4.06 - 6.09: 416 6.09 - 8.12: 58 8.12 - 10.15: 11 Bond angle restraints: 34955 Sorted by residual: angle pdb=" N ARG A 51 " pdb=" CA ARG A 51 " pdb=" C ARG A 51 " ideal model delta sigma weight residual 111.28 102.87 8.41 1.09e+00 8.42e-01 5.95e+01 angle pdb=" N ARG D 51 " pdb=" CA ARG D 51 " pdb=" C ARG D 51 " ideal model delta sigma weight residual 111.28 102.91 8.37 1.09e+00 8.42e-01 5.89e+01 angle pdb=" N LEU D 110 " pdb=" CA LEU D 110 " pdb=" C LEU D 110 " ideal model delta sigma weight residual 111.28 103.45 7.83 1.09e+00 8.42e-01 5.17e+01 angle pdb=" N LEU A 110 " pdb=" CA LEU A 110 " pdb=" C LEU A 110 " ideal model delta sigma weight residual 111.28 103.45 7.83 1.09e+00 8.42e-01 5.16e+01 angle pdb=" N GLU D 45 " pdb=" CA GLU D 45 " pdb=" C GLU D 45 " ideal model delta sigma weight residual 111.82 103.56 8.26 1.16e+00 7.43e-01 5.07e+01 ... (remaining 34950 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 14449 35.58 - 71.15: 875 71.15 - 106.73: 62 106.73 - 142.31: 4 142.31 - 177.88: 4 Dihedral angle restraints: 15394 sinusoidal: 8182 harmonic: 7212 Sorted by residual: dihedral pdb=" C4' U B 73 " pdb=" C3' U B 73 " pdb=" C2' U B 73 " pdb=" C1' U B 73 " ideal model delta sinusoidal sigma weight residual -35.00 33.95 -68.95 1 8.00e+00 1.56e-02 9.61e+01 dihedral pdb=" C4' U E 73 " pdb=" C3' U E 73 " pdb=" C2' U E 73 " pdb=" C1' U E 73 " ideal model delta sinusoidal sigma weight residual -35.00 33.91 -68.91 1 8.00e+00 1.56e-02 9.60e+01 dihedral pdb=" O4' U B 73 " pdb=" C2' U B 73 " pdb=" C1' U B 73 " pdb=" C3' U B 73 " ideal model delta sinusoidal sigma weight residual -35.00 31.41 -66.41 1 8.00e+00 1.56e-02 9.00e+01 ... (remaining 15391 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 3237 0.111 - 0.221: 674 0.221 - 0.332: 106 0.332 - 0.443: 4 0.443 - 0.553: 1 Chirality restraints: 4022 Sorted by residual: chirality pdb=" CA ASP F 61 " pdb=" N ASP F 61 " pdb=" C ASP F 61 " pdb=" CB ASP F 61 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.65e+00 chirality pdb=" CA PRO D1014 " pdb=" N PRO D1014 " pdb=" C PRO D1014 " pdb=" CB PRO D1014 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CA PRO A1014 " pdb=" N PRO A1014 " pdb=" C PRO A1014 " pdb=" CB PRO A1014 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 3.07e+00 ... (remaining 4019 not shown) Planarity restraints: 3683 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS D 973 " -0.018 2.00e-02 2.50e+03 3.64e-02 1.32e+01 pdb=" C LYS D 973 " 0.063 2.00e-02 2.50e+03 pdb=" O LYS D 973 " -0.024 2.00e-02 2.50e+03 pdb=" N ILE D 974 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 973 " -0.018 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C LYS A 973 " 0.063 2.00e-02 2.50e+03 pdb=" O LYS A 973 " -0.024 2.00e-02 2.50e+03 pdb=" N ILE A 974 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A1006 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C GLU A1006 " -0.056 2.00e-02 2.50e+03 pdb=" O GLU A1006 " 0.021 2.00e-02 2.50e+03 pdb=" N ASN A1007 " 0.019 2.00e-02 2.50e+03 ... (remaining 3680 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5728 2.79 - 3.32: 23443 3.32 - 3.85: 41547 3.85 - 4.37: 49991 4.37 - 4.90: 76178 Nonbonded interactions: 196887 Sorted by model distance: nonbonded pdb=" O ARG A 209 " pdb=" O2' U B 16 " model vdw 2.265 3.040 nonbonded pdb=" O ARG D 209 " pdb=" O2' U E 16 " model vdw 2.265 3.040 nonbonded pdb=" OG SER D 957 " pdb=" OE1 GLN D 959 " model vdw 2.271 3.040 nonbonded pdb=" OG SER A 957 " pdb=" OE1 GLN A 959 " model vdw 2.271 3.040 nonbonded pdb=" OD2 ASP D 545 " pdb=" OH TYR D 553 " model vdw 2.287 3.040 ... (remaining 196882 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 'D' and (resid 1 through 542 or (resid 543 through 544 and (name N or nam \ e CA or name C or name O or name CB )) or resid 545 through 1053)) } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = (chain 'C' and (resid 0 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 20 or (resid 21 and (name N or name CA \ or name C or name O or name CB )) or resid 22 through 54 or (resid 55 through 5 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 57 through 5 \ 9 or (resid 60 and (name N or name CA or name C or name O or name CB )) or resid \ 61 through 170)) selection = (chain 'F' and (resid 0 through 51 or (resid 52 and (name N or name CA or name C \ or name O or name CB )) or resid 53 through 170)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.650 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: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 28.510 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4805 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 : 0.008 0.073 25149 Z= 0.637 Angle : 1.271 10.151 34955 Z= 0.956 Chirality : 0.088 0.553 4022 Planarity : 0.005 0.041 3683 Dihedral : 19.257 177.883 10750 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.19 % Allowed : 5.62 % Favored : 93.19 % Cbeta Deviations : 0.22 % 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: 0.03 (0.17), residues: 2412 helix: 0.75 (0.15), residues: 1148 sheet: -0.02 (0.36), residues: 203 loop : -0.71 (0.18), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 685 TYR 0.027 0.002 TYR D 256 PHE 0.019 0.002 PHE F 165 TRP 0.011 0.002 TRP D 408 HIS 0.006 0.001 HIS A 773 Details of bonding type rmsd/Z covalent geometry : bond 0.00849 / 0.64 (25149) covalent geometry : angle 1.27137 / 0.96 (34955) hydrogen bonds : bond 0.18678 / 12.74 ( 1103) hydrogen bonds : angle 8.12137 / 5.75 ( 3045) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 234 MET cc_start: -0.0683 (mmm) cc_final: -0.1233 (mtm) outliers start: 25 outliers final: 5 residues processed: 195 average time/residue: 0.1957 time to fit residues: 57.5588 Evaluate side-chains 82 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 54 GLN Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 163 HIS Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 163 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 40.0000 chunk 183 optimal weight: 20.0000 chunk 111 optimal weight: 30.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 ASN A 111 HIS A 154 GLN A 252 ASN A 411 ASN ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 ASN ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN A 580 ASN A 695 ASN A 758 HIS A 785 ASN A 863 ASN A 968 ASN A 969 ASN A 985 ASN A 990 ASN D 75 ASN D 154 GLN D 252 ASN D 411 ASN ** D 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 ASN D 570 ASN D 580 ASN D 590 GLN D 695 ASN ** D 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 863 ASN D 968 ASN D 990 ASN F 54 GLN ** F 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.077135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.064644 restraints weight = 245919.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.063603 restraints weight = 179904.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.063488 restraints weight = 142899.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.063289 restraints weight = 126725.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.063329 restraints weight = 121474.811| |-----------------------------------------------------------------------------| r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6301 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 25149 Z= 0.229 Angle : 0.677 9.386 34955 Z= 0.382 Chirality : 0.044 0.234 4022 Planarity : 0.004 0.059 3683 Dihedral : 20.836 179.203 5863 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.43 % Allowed : 9.29 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.17), residues: 2412 helix: 1.06 (0.15), residues: 1192 sheet: -0.24 (0.33), residues: 241 loop : -0.74 (0.19), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 208 TYR 0.029 0.002 TYR A 897 PHE 0.020 0.002 PHE C 136 TRP 0.012 0.001 TRP A 223 HIS 0.006 0.001 HIS A 758 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.23 (25149) covalent geometry : angle 0.67742 / 0.38 (34955) hydrogen bonds : bond 0.06541 / 4.54 ( 1103) hydrogen bonds : angle 5.18161 / 3.71 ( 3045) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 77 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 TYR cc_start: 0.7628 (p90) cc_final: 0.7308 (p90) REVERT: A 657 MET cc_start: 0.7685 (mmm) cc_final: 0.7053 (mmm) REVERT: D 297 LYS cc_start: 0.6191 (OUTLIER) cc_final: 0.5677 (pptt) REVERT: D 1008 MET cc_start: 0.4141 (ptt) cc_final: 0.3314 (mpp) REVERT: F 1 MET cc_start: 0.8797 (tpp) cc_final: 0.8532 (tpp) outliers start: 30 outliers final: 16 residues processed: 102 average time/residue: 0.1708 time to fit residues: 27.8465 Evaluate side-chains 82 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 297 LYS Chi-restraints excluded: chain D residue 327 LYS Chi-restraints excluded: chain D residue 475 ILE Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 163 HIS Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 163 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 227 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 184 optimal weight: 9.9990 chunk 108 optimal weight: 10.0000 chunk 248 optimal weight: 8.9990 chunk 117 optimal weight: 20.0000 chunk 78 optimal weight: 0.7980 chunk 43 optimal weight: 0.0050 chunk 176 optimal weight: 9.9990 overall best weight: 2.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 ASN ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 785 ASN F 159 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.076378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.063231 restraints weight = 246777.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.061342 restraints weight = 183342.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.061579 restraints weight = 163664.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.061262 restraints weight = 147391.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.061312 restraints weight = 131627.457| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6503 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25149 Z= 0.155 Angle : 0.557 10.212 34955 Z= 0.317 Chirality : 0.040 0.198 4022 Planarity : 0.004 0.042 3683 Dihedral : 20.750 178.410 5860 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.48 % Allowed : 9.95 % Favored : 88.57 % 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 are not related in a simple way. whole: 0.47 (0.17), residues: 2412 helix: 1.26 (0.15), residues: 1195 sheet: -0.33 (0.32), residues: 251 loop : -0.64 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 63 TYR 0.023 0.002 TYR A 897 PHE 0.025 0.002 PHE C 51 TRP 0.014 0.001 TRP A 223 HIS 0.008 0.001 HIS A 393 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.16 (25149) covalent geometry : angle 0.55675 / 0.32 (34955) hydrogen bonds : bond 0.05134 / 3.55 ( 1103) hydrogen bonds : angle 4.69660 / 3.35 ( 3045) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 65 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1008 MET cc_start: 0.4394 (ptt) cc_final: 0.3365 (mpp) REVERT: F 1 MET cc_start: 0.8817 (tpp) cc_final: 0.8508 (tpp) outliers start: 31 outliers final: 19 residues processed: 87 average time/residue: 0.1733 time to fit residues: 24.4176 Evaluate side-chains 77 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 327 LYS Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 447 SER Chi-restraints excluded: chain D residue 475 ILE Chi-restraints excluded: chain D residue 1032 THR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 163 HIS Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 163 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 13 optimal weight: 7.9990 chunk 50 optimal weight: 20.0000 chunk 252 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 165 optimal weight: 0.0970 chunk 229 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 chunk 218 optimal weight: 50.0000 chunk 81 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 228 optimal weight: 9.9990 overall best weight: 5.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 ASN ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 930 ASN D 62 HIS D 236 HIS ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 780 ASN D 902 ASN D 990 ASN F 74 ASN ** F 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.073554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.060319 restraints weight = 242431.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.058128 restraints weight = 201962.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.058163 restraints weight = 185057.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.058102 restraints weight = 144898.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.058123 restraints weight = 140416.709| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6664 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 25149 Z= 0.241 Angle : 0.682 14.249 34955 Z= 0.372 Chirality : 0.044 0.215 4022 Planarity : 0.005 0.069 3683 Dihedral : 20.802 178.760 5859 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.90 % Allowed : 11.14 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.17), residues: 2412 helix: 1.00 (0.15), residues: 1182 sheet: -0.52 (0.33), residues: 242 loop : -0.83 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 92 TYR 0.028 0.002 TYR C 53 PHE 0.028 0.002 PHE C 51 TRP 0.017 0.002 TRP D 229 HIS 0.009 0.002 HIS A 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.24 (25149) covalent geometry : angle 0.68162 / 0.37 (34955) hydrogen bonds : bond 0.06560 / 4.58 ( 1103) hydrogen bonds : angle 4.77676 / 3.42 ( 3045) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 59 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 TYR cc_start: 0.7830 (p90) cc_final: 0.7539 (p90) REVERT: A 499 ARG cc_start: 0.8251 (ttp80) cc_final: 0.7991 (tmm160) REVERT: A 657 MET cc_start: 0.7371 (mmm) cc_final: 0.6685 (mmm) REVERT: D 140 ARG cc_start: 0.6924 (mtm-85) cc_final: 0.6287 (tmt-80) REVERT: D 234 MET cc_start: -0.0483 (mpp) cc_final: -0.1756 (mtm) REVERT: D 1008 MET cc_start: 0.4112 (ptt) cc_final: 0.3179 (mpp) REVERT: F 73 MET cc_start: 0.3961 (ptt) cc_final: 0.3536 (ptp) outliers start: 40 outliers final: 22 residues processed: 93 average time/residue: 0.1778 time to fit residues: 26.3248 Evaluate side-chains 72 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 50 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 978 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 327 LYS Chi-restraints excluded: chain D residue 447 SER Chi-restraints excluded: chain D residue 475 ILE Chi-restraints excluded: chain D residue 1032 THR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 142 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 211 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 chunk 50 optimal weight: 20.0000 chunk 227 optimal weight: 20.0000 chunk 0 optimal weight: 4.9990 chunk 143 optimal weight: 20.0000 chunk 97 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 chunk 204 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 134 optimal weight: 9.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 GLN ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 ASN A 930 ASN D 252 ASN D 658 ASN D 888 ASN F 163 HIS ** C 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.072712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.059390 restraints weight = 243899.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.057520 restraints weight = 189475.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.057432 restraints weight = 163557.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.057330 restraints weight = 139201.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.057349 restraints weight = 135564.080| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 25149 Z= 0.246 Angle : 0.635 13.725 34955 Z= 0.351 Chirality : 0.042 0.231 4022 Planarity : 0.004 0.075 3683 Dihedral : 20.836 176.827 5854 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.05 % Allowed : 11.81 % Favored : 86.14 % 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: -0.02 (0.17), residues: 2412 helix: 0.92 (0.15), residues: 1192 sheet: -0.69 (0.33), residues: 237 loop : -0.93 (0.20), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 63 TYR 0.024 0.002 TYR A 912 PHE 0.022 0.002 PHE A 221 TRP 0.014 0.001 TRP A 223 HIS 0.008 0.002 HIS F 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.25 (25149) covalent geometry : angle 0.63490 / 0.35 (34955) hydrogen bonds : bond 0.05521 / 3.82 ( 1103) hydrogen bonds : angle 4.79525 / 3.44 ( 3045) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 52 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 996 MET cc_start: 0.8762 (tpp) cc_final: 0.7759 (mtm) REVERT: D 1008 MET cc_start: 0.4240 (ptt) cc_final: 0.3350 (mpp) REVERT: F 57 MET cc_start: 0.6740 (pmm) cc_final: 0.6361 (pmm) outliers start: 43 outliers final: 23 residues processed: 92 average time/residue: 0.1676 time to fit residues: 25.0447 Evaluate side-chains 71 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 48 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain D residue 327 LYS Chi-restraints excluded: chain D residue 447 SER Chi-restraints excluded: chain D residue 475 ILE Chi-restraints excluded: chain D residue 775 VAL Chi-restraints excluded: chain D residue 975 ASN Chi-restraints excluded: chain D residue 1032 THR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 167 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 22 optimal weight: 4.9990 chunk 242 optimal weight: 40.0000 chunk 143 optimal weight: 0.8980 chunk 156 optimal weight: 30.0000 chunk 128 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 chunk 80 optimal weight: 0.9990 chunk 246 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 218 optimal weight: 50.0000 chunk 85 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 ASN ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 ASN D 137 GLN D 141 ASN D 252 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.073850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.060874 restraints weight = 244725.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.059644 restraints weight = 177898.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.059604 restraints weight = 147396.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.059492 restraints weight = 125490.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.059568 restraints weight = 120136.508| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6536 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 25149 Z= 0.116 Angle : 0.522 13.771 34955 Z= 0.291 Chirality : 0.038 0.176 4022 Planarity : 0.004 0.065 3683 Dihedral : 20.632 179.185 5854 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.10 % Allowed : 13.19 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.17), residues: 2412 helix: 1.16 (0.15), residues: 1190 sheet: -0.69 (0.31), residues: 271 loop : -0.70 (0.20), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 140 TYR 0.017 0.001 TYR A 882 PHE 0.014 0.001 PHE C 51 TRP 0.016 0.001 TRP D 408 HIS 0.005 0.001 HIS F 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.12 (25149) covalent geometry : angle 0.52174 / 0.29 (34955) hydrogen bonds : bond 0.04152 / 2.86 ( 1103) hydrogen bonds : angle 4.53057 / 3.24 ( 3045) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 52 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 784 ILE cc_start: 0.9321 (tp) cc_final: 0.8946 (mm) REVERT: A 996 MET cc_start: 0.8713 (tpp) cc_final: 0.7788 (mtm) REVERT: D 1008 MET cc_start: 0.4024 (ptt) cc_final: 0.3196 (mpp) outliers start: 23 outliers final: 17 residues processed: 72 average time/residue: 0.1617 time to fit residues: 19.3935 Evaluate side-chains 65 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 327 LYS Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 447 SER Chi-restraints excluded: chain D residue 475 ILE Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 142 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 199 optimal weight: 5.9990 chunk 216 optimal weight: 40.0000 chunk 52 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 247 optimal weight: 5.9990 chunk 257 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 171 optimal weight: 30.0000 chunk 97 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 GLN A 191 HIS ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 ASN ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 HIS ** A 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 ASN D 401 ASN D 888 ASN ** D 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.071027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.056591 restraints weight = 237035.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.055066 restraints weight = 191614.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.054973 restraints weight = 181000.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.054707 restraints weight = 150181.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.054826 restraints weight = 140760.853| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.5696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 25149 Z= 0.299 Angle : 0.728 16.159 34955 Z= 0.395 Chirality : 0.046 0.222 4022 Planarity : 0.006 0.097 3683 Dihedral : 20.824 177.194 5854 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 21.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.43 % Favored : 94.53 % Rotamer: Outliers : 2.19 % Allowed : 13.24 % Favored : 84.57 % 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 are not related in a simple way. whole: -0.18 (0.17), residues: 2412 helix: 0.76 (0.15), residues: 1175 sheet: -0.83 (0.32), residues: 253 loop : -0.91 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.034 0.001 ARG C 21 TYR 0.029 0.003 TYR A 912 PHE 0.031 0.003 PHE A 221 TRP 0.015 0.002 TRP A 223 HIS 0.009 0.002 HIS A 393 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.30 (25149) covalent geometry : angle 0.72774 / 0.39 (34955) hydrogen bonds : bond 0.07058 / 4.88 ( 1103) hydrogen bonds : angle 4.99443 / 3.59 ( 3045) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 53 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 996 MET cc_start: 0.9001 (tpp) cc_final: 0.8090 (mtm) REVERT: D 844 MET cc_start: -0.3892 (ptt) cc_final: -0.4126 (ptt) REVERT: D 888 ASN cc_start: 0.5417 (OUTLIER) cc_final: 0.4907 (m-40) REVERT: D 1008 MET cc_start: 0.4163 (ptt) cc_final: 0.3535 (mpp) outliers start: 46 outliers final: 31 residues processed: 95 average time/residue: 0.1584 time to fit residues: 24.8859 Evaluate side-chains 80 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 48 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 901 ARG Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 327 LYS Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 447 SER Chi-restraints excluded: chain D residue 475 ILE Chi-restraints excluded: chain D residue 775 VAL Chi-restraints excluded: chain D residue 888 ASN Chi-restraints excluded: chain D residue 1000 THR Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 167 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 173 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 182 optimal weight: 50.0000 chunk 177 optimal weight: 6.9990 chunk 226 optimal weight: 20.0000 chunk 260 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 121 optimal weight: 6.9990 chunk 222 optimal weight: 40.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 401 ASN ** D 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1048 GLN C 169 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.071886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.058508 restraints weight = 242854.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.056780 restraints weight = 185890.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.056860 restraints weight = 159987.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.056835 restraints weight = 131180.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.056811 restraints weight = 128877.755| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.5780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25149 Z= 0.164 Angle : 0.563 14.065 34955 Z= 0.311 Chirality : 0.039 0.166 4022 Planarity : 0.004 0.077 3683 Dihedral : 20.748 177.986 5854 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.43 % Allowed : 14.29 % Favored : 84.29 % 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: 0.12 (0.17), residues: 2412 helix: 1.03 (0.15), residues: 1178 sheet: -0.61 (0.32), residues: 255 loop : -0.82 (0.20), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 499 TYR 0.021 0.002 TYR F 95 PHE 0.016 0.002 PHE A 690 TRP 0.012 0.001 TRP D 408 HIS 0.012 0.001 HIS D 890 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.16 (25149) covalent geometry : angle 0.56310 / 0.31 (34955) hydrogen bonds : bond 0.04623 / 3.22 ( 1103) hydrogen bonds : angle 4.71177 / 3.39 ( 3045) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 48 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 784 ILE cc_start: 0.9327 (tp) cc_final: 0.9009 (mm) REVERT: A 996 MET cc_start: 0.8925 (tpp) cc_final: 0.8064 (mtm) REVERT: D 844 MET cc_start: -0.3252 (ptt) cc_final: -0.3557 (ptt) REVERT: D 1008 MET cc_start: 0.4146 (ptt) cc_final: 0.3556 (mpp) outliers start: 30 outliers final: 23 residues processed: 76 average time/residue: 0.1492 time to fit residues: 19.0393 Evaluate side-chains 70 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 47 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 327 LYS Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 447 SER Chi-restraints excluded: chain D residue 475 ILE Chi-restraints excluded: chain D residue 775 VAL Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 142 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 148 optimal weight: 8.9990 chunk 35 optimal weight: 0.9980 chunk 227 optimal weight: 20.0000 chunk 8 optimal weight: 7.9990 chunk 198 optimal weight: 20.0000 chunk 7 optimal weight: 0.9990 chunk 224 optimal weight: 0.3980 chunk 111 optimal weight: 30.0000 chunk 164 optimal weight: 0.2980 chunk 229 optimal weight: 5.9990 chunk 193 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 ASN ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.072955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.059106 restraints weight = 234560.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.057541 restraints weight = 182530.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.057709 restraints weight = 163074.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.057374 restraints weight = 129770.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.057369 restraints weight = 116959.759| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6665 moved from start: 0.5752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 25149 Z= 0.106 Angle : 0.497 14.470 34955 Z= 0.277 Chirality : 0.037 0.160 4022 Planarity : 0.003 0.057 3683 Dihedral : 20.473 179.286 5854 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.14 % Allowed : 14.48 % Favored : 84.38 % 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: 0.50 (0.17), residues: 2412 helix: 1.36 (0.15), residues: 1175 sheet: -0.62 (0.30), residues: 274 loop : -0.60 (0.21), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 499 TYR 0.018 0.001 TYR A 882 PHE 0.012 0.001 PHE C 91 TRP 0.013 0.001 TRP D 408 HIS 0.009 0.001 HIS D 890 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.11 (25149) covalent geometry : angle 0.49707 / 0.28 (34955) hydrogen bonds : bond 0.03830 / 2.65 ( 1103) hydrogen bonds : angle 4.43222 / 3.19 ( 3045) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 54 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 728 MET cc_start: 0.6052 (tpt) cc_final: 0.5706 (mmp) REVERT: A 996 MET cc_start: 0.8891 (tpp) cc_final: 0.8139 (mtm) REVERT: D 844 MET cc_start: -0.3032 (ptt) cc_final: -0.3321 (ptt) REVERT: D 996 MET cc_start: 0.7157 (pmm) cc_final: 0.6461 (ppp) REVERT: D 1008 MET cc_start: 0.3825 (ptt) cc_final: 0.3377 (mpp) REVERT: F 57 MET cc_start: 0.6512 (pmm) cc_final: 0.5563 (pmm) REVERT: F 153 PHE cc_start: 0.1200 (m-80) cc_final: 0.0933 (m-10) outliers start: 24 outliers final: 16 residues processed: 75 average time/residue: 0.1597 time to fit residues: 19.9402 Evaluate side-chains 68 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 327 LYS Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 475 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 142 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 169 optimal weight: 50.0000 chunk 89 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 257 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 122 optimal weight: 10.0000 chunk 225 optimal weight: 40.0000 chunk 37 optimal weight: 8.9990 chunk 102 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 ASN ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.071101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.057921 restraints weight = 237220.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.055675 restraints weight = 210480.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.055551 restraints weight = 187066.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.055441 restraints weight = 149090.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.055475 restraints weight = 135832.434| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.6270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 25149 Z= 0.223 Angle : 0.612 14.204 34955 Z= 0.334 Chirality : 0.041 0.198 4022 Planarity : 0.004 0.080 3683 Dihedral : 20.556 178.047 5854 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.05 % Allowed : 14.71 % Favored : 84.24 % 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: 0.16 (0.17), residues: 2412 helix: 1.04 (0.15), residues: 1192 sheet: -0.73 (0.32), residues: 249 loop : -0.75 (0.20), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 499 TYR 0.049 0.002 TYR D 256 PHE 0.017 0.002 PHE A 221 TRP 0.015 0.002 TRP D 408 HIS 0.008 0.002 HIS A 700 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.22 (25149) covalent geometry : angle 0.61176 / 0.33 (34955) hydrogen bonds : bond 0.05436 / 3.77 ( 1103) hydrogen bonds : angle 4.67894 / 3.37 ( 3045) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 49 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 728 MET cc_start: 0.6278 (tpt) cc_final: 0.5811 (mmt) REVERT: A 996 MET cc_start: 0.8965 (tpp) cc_final: 0.8215 (mtm) REVERT: D 844 MET cc_start: -0.3149 (ptt) cc_final: -0.3454 (ptt) REVERT: D 996 MET cc_start: 0.7282 (pmm) cc_final: 0.6660 (ppp) REVERT: D 1008 MET cc_start: 0.3831 (ptt) cc_final: 0.3323 (mpp) REVERT: F 57 MET cc_start: 0.6567 (pmm) cc_final: 0.5922 (pmm) REVERT: F 153 PHE cc_start: 0.1606 (m-80) cc_final: 0.1268 (m-10) outliers start: 22 outliers final: 20 residues processed: 69 average time/residue: 0.1522 time to fit residues: 17.6644 Evaluate side-chains 69 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 49 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 327 LYS Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 475 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 128 ASN Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 142 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 67 optimal weight: 5.9990 chunk 131 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 231 optimal weight: 9.9990 chunk 41 optimal weight: 20.0000 chunk 191 optimal weight: 4.9990 chunk 184 optimal weight: 7.9990 chunk 209 optimal weight: 30.0000 chunk 14 optimal weight: 8.9990 chunk 203 optimal weight: 20.0000 chunk 127 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 141 ASN ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.071087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.057126 restraints weight = 236853.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.055747 restraints weight = 181322.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.055506 restraints weight = 156675.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.055450 restraints weight = 132730.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.055586 restraints weight = 126746.323| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.6277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.165 25149 Z= 0.253 Angle : 0.732 59.192 34955 Z= 0.422 Chirality : 0.043 0.721 4022 Planarity : 0.004 0.079 3683 Dihedral : 20.564 178.027 5854 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.14 % Allowed : 14.81 % Favored : 84.05 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.14 (0.17), residues: 2412 helix: 1.03 (0.15), residues: 1192 sheet: -0.74 (0.32), residues: 249 loop : -0.78 (0.20), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 499 TYR 0.033 0.002 TYR D 256 PHE 0.016 0.002 PHE A 221 TRP 0.014 0.001 TRP D 408 HIS 0.007 0.002 HIS A 700 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.25 (25149) covalent geometry : angle 0.73191 / 0.42 (34955) hydrogen bonds : bond 0.05437 / 3.77 ( 1103) hydrogen bonds : angle 4.67981 / 3.37 ( 3045) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3896.62 seconds wall clock time: 68 minutes 49.94 seconds (4129.94 seconds total)