Starting phenix.real_space_refine on Sat Jul 4 23:28:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jg9_36225/07_2026/8jg9_36225_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jg9_36225/07_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_36225/07_2026/8jg9_36225_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jg9_36225/07_2026/8jg9_36225_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jg9_36225/07_2026/8jg9_36225.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jg9_36225/07_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-dev-6108/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: 4.94, per 1000 atoms: 0.20 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: 2.30 Conformation dependent library (CDL) restraints added in 862.3 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: 3.12 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: 6.20 Time building geometry restraints manager: 2.96 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=" 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=" O3' U B 71 " pdb=" P U B 72 " ideal model delta sigma weight residual 1.607 1.679 -0.072 1.50e-02 4.44e+03 2.31e+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 bond pdb=" O3' U E 71 " pdb=" P U E 72 " ideal model delta sigma weight residual 1.607 1.678 -0.071 1.50e-02 4.44e+03 2.27e+01 ... (remaining 25144 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 30891 2.03 - 4.06: 3584 4.06 - 6.09: 411 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: 3233 0.111 - 0.221: 678 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: 3.340 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 25.620 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.110 ------------------------------------------------------------------------------- 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= 0.626 Angle : 1.267 10.151 34955 Z= 0.951 Chirality : 0.089 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 0.00846 / 0.63 (25149) covalent geometry : angle 1.26696 / 0.95 (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 : 0.862 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: 0.1899 time to fit residues: 55.7898 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 : 0.880 ------------------------------------------------------------------------------- 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: 20.0000 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 990 ASN A1025 GLN 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 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.076824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.064251 restraints weight = 245400.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.062963 restraints weight = 179764.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.062910 restraints weight = 147903.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.062751 restraints weight = 126087.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.062767 restraints weight = 119527.912| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6343 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 25149 Z= 0.236 Angle : 0.683 8.859 34955 Z= 0.387 Chirality : 0.044 0.195 4022 Planarity : 0.005 0.048 3683 Dihedral : 21.007 179.112 5863 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.62 % Allowed : 9.33 % Favored : 89.05 % 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: 0.20 (0.17), residues: 2412 helix: 0.99 (0.15), residues: 1192 sheet: -0.32 (0.33), residues: 242 loop : -0.74 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 208 TYR 0.030 0.002 TYR A 897 PHE 0.023 0.002 PHE C 136 TRP 0.014 0.001 TRP A 223 HIS 0.009 0.002 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.24 (25149) covalent geometry : angle 0.68322 / 0.39 (34955) hydrogen bonds : bond 0.06289 / 4.37 ( 1103) hydrogen bonds : angle 5.09663 / 3.65 ( 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: 34 poor density : 73 time to evaluate : 0.861 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: A 278 TYR cc_start: 0.7652 (p90) cc_final: 0.7356 (p90) REVERT: D 297 LYS cc_start: 0.6412 (OUTLIER) cc_final: 0.5958 (pptt) REVERT: D 1008 MET cc_start: 0.4252 (ptt) cc_final: 0.3526 (mpp) REVERT: F 1 MET cc_start: 0.8812 (tpp) cc_final: 0.8571 (tpp) outliers start: 34 outliers final: 16 residues processed: 102 average time/residue: 0.1731 time to fit residues: 28.4320 Evaluate side-chains 78 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.802 ------------------------------------------------------------------------------- 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 65 VAL 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: 9.9990 chunk 67 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 184 optimal weight: 9.9990 chunk 108 optimal weight: 10.0000 chunk 248 optimal weight: 20.0000 chunk 117 optimal weight: 20.0000 chunk 78 optimal weight: 0.6980 chunk 43 optimal weight: 5.9990 chunk 176 optimal weight: 7.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- 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** A 985 ASN ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 785 ASN ** F 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 159 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.076243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.063516 restraints weight = 246471.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.061897 restraints weight = 188922.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.062014 restraints weight = 157349.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.061824 restraints weight = 134913.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.061804 restraints weight = 127093.800| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6419 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25149 Z= 0.153 Angle : 0.549 10.511 34955 Z= 0.317 Chirality : 0.040 0.230 4022 Planarity : 0.004 0.040 3683 Dihedral : 20.852 178.426 5860 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.62 % Allowed : 10.00 % Favored : 88.38 % 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: 0.46 (0.17), residues: 2412 helix: 1.26 (0.15), residues: 1194 sheet: -0.37 (0.32), residues: 251 loop : -0.66 (0.20), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 63 TYR 0.022 0.002 TYR A 897 PHE 0.026 0.002 PHE F 51 TRP 0.012 0.001 TRP A 223 HIS 0.006 0.001 HIS D 832 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.15 (25149) covalent geometry : angle 0.54941 / 0.32 (34955) hydrogen bonds : bond 0.05280 / 3.65 ( 1103) hydrogen bonds : angle 4.66906 / 3.34 ( 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 102 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 68 time to evaluate : 0.792 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: 0.7691 (p90) cc_final: 0.7376 (p90) REVERT: D 297 LYS cc_start: 0.6372 (OUTLIER) cc_final: 0.6154 (pptt) REVERT: D 1008 MET cc_start: 0.4177 (ptt) cc_final: 0.3220 (mpp) REVERT: F 1 MET cc_start: 0.8723 (tpp) cc_final: 0.8428 (tpp) outliers start: 34 outliers final: 20 residues processed: 92 average time/residue: 0.1555 time to fit residues: 23.2064 Evaluate side-chains 80 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 59 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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 491 ILE Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 260 ASN Chi-restraints excluded: chain D residue 297 LYS 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 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 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: 2.9990 chunk 50 optimal weight: 8.9990 chunk 252 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 165 optimal weight: 4.9990 chunk 229 optimal weight: 8.9990 chunk 132 optimal weight: 20.0000 chunk 218 optimal weight: 50.0000 chunk 81 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 228 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 930 ASN D 62 HIS D 236 HIS ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 780 ASN D 902 ASN D 990 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.073370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.060433 restraints weight = 242489.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.058394 restraints weight = 201996.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.058533 restraints weight = 171219.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.058423 restraints weight = 137923.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.058440 restraints weight = 131767.997| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 25149 Z= 0.257 Angle : 0.682 12.885 34955 Z= 0.380 Chirality : 0.043 0.375 4022 Planarity : 0.005 0.073 3683 Dihedral : 20.899 176.952 5858 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.90 % Allowed : 11.19 % Favored : 86.90 % 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: 0.10 (0.17), residues: 2412 helix: 0.96 (0.15), residues: 1184 sheet: -0.50 (0.31), residues: 263 loop : -0.81 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 92 TYR 0.027 0.002 TYR A 698 PHE 0.027 0.002 PHE C 51 TRP 0.017 0.002 TRP A 223 HIS 0.010 0.002 HIS A 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.26 (25149) covalent geometry : angle 0.68224 / 0.38 (34955) hydrogen bonds : bond 0.06566 / 4.62 ( 1103) hydrogen bonds : angle 4.83691 / 3.47 ( 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 98 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 58 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ILE cc_start: 0.7054 (mm) cc_final: 0.6808 (mp) REVERT: A 499 ARG cc_start: 0.8217 (ttp80) cc_final: 0.7938 (tmm160) REVERT: D 140 ARG cc_start: 0.6859 (mtm-85) cc_final: 0.6232 (tmt-80) REVERT: D 234 MET cc_start: -0.0091 (mpp) cc_final: -0.1179 (mtm) REVERT: D 297 LYS cc_start: 0.6630 (OUTLIER) cc_final: 0.6385 (pptt) REVERT: D 1008 MET cc_start: 0.3985 (ptt) cc_final: 0.3079 (mpp) outliers start: 40 outliers final: 24 residues processed: 92 average time/residue: 0.1788 time to fit residues: 26.5415 Evaluate side-chains 77 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 52 time to evaluate : 0.846 ------------------------------------------------------------------------------- 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 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 840 LEU Chi-restraints excluded: chain A residue 978 LEU 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 447 SER Chi-restraints excluded: chain D residue 475 ILE Chi-restraints excluded: chain D residue 957 SER 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 Chi-restraints excluded: chain C residue 163 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 211 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 50 optimal weight: 20.0000 chunk 227 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 204 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 chunk 134 optimal weight: 6.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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** ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 888 ASN F 163 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.074370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.061725 restraints weight = 242300.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.060070 restraints weight = 191427.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.060159 restraints weight = 162518.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.060058 restraints weight = 129998.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.060103 restraints weight = 124184.868| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6501 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 25149 Z= 0.123 Angle : 0.510 12.096 34955 Z= 0.291 Chirality : 0.038 0.167 4022 Planarity : 0.003 0.052 3683 Dihedral : 20.744 178.648 5856 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.52 % Allowed : 12.14 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.17), residues: 2412 helix: 1.30 (0.15), residues: 1182 sheet: -0.62 (0.31), residues: 271 loop : -0.61 (0.20), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 21 TYR 0.025 0.001 TYR C 53 PHE 0.021 0.001 PHE C 51 TRP 0.007 0.001 TRP D 408 HIS 0.003 0.001 HIS A 890 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 (25149) covalent geometry : angle 0.51050 / 0.29 (34955) hydrogen bonds : bond 0.04279 / 2.94 ( 1103) hydrogen bonds : angle 4.54959 / 3.26 ( 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 87 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 55 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 844 MET cc_start: 0.5993 (mmm) cc_final: 0.5722 (tpt) REVERT: A 879 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7823 (ptmm) REVERT: A 996 MET cc_start: 0.8689 (tpp) cc_final: 0.7786 (mtm) REVERT: D 140 ARG cc_start: 0.6806 (mtm-85) cc_final: 0.6183 (tmt-80) REVERT: D 297 LYS cc_start: 0.6633 (OUTLIER) cc_final: 0.6410 (pptt) REVERT: D 780 ASN cc_start: 0.5678 (OUTLIER) cc_final: 0.5371 (t0) REVERT: D 996 MET cc_start: 0.6910 (pmm) cc_final: 0.5886 (ppp) REVERT: D 1008 MET cc_start: 0.3967 (ptt) cc_final: 0.3075 (mpp) outliers start: 32 outliers final: 14 residues processed: 80 average time/residue: 0.1919 time to fit residues: 24.4525 Evaluate side-chains 69 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL 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 879 LYS Chi-restraints excluded: chain D residue 297 LYS 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 780 ASN Chi-restraints excluded: chain F residue 24 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 22 optimal weight: 9.9990 chunk 242 optimal weight: 40.0000 chunk 143 optimal weight: 0.0020 chunk 156 optimal weight: 8.9990 chunk 128 optimal weight: 30.0000 chunk 59 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 246 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 218 optimal weight: 40.0000 chunk 85 optimal weight: 1.9990 overall best weight: 4.7996 ------------------------------------------------------------------------------- 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 462 ASN ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 HIS D 252 ASN D 401 ASN D 658 ASN D 888 ASN ** 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 = 0.4274 r_free = 0.4274 target = 0.072547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.059190 restraints weight = 245644.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.057226 restraints weight = 203778.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.057532 restraints weight = 184771.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.057288 restraints weight = 151848.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.057408 restraints weight = 139383.738| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.4862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 25149 Z= 0.233 Angle : 0.620 19.867 34955 Z= 0.344 Chirality : 0.041 0.208 4022 Planarity : 0.004 0.066 3683 Dihedral : 20.752 179.448 5854 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.95 % Allowed : 12.86 % Favored : 85.19 % 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: 0.20 (0.17), residues: 2412 helix: 1.10 (0.15), residues: 1190 sheet: -0.72 (0.31), residues: 257 loop : -0.78 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 21 TYR 0.026 0.002 TYR C 53 PHE 0.023 0.002 PHE A 221 TRP 0.018 0.002 TRP D 408 HIS 0.009 0.002 HIS C 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.23 (25149) covalent geometry : angle 0.61975 / 0.34 (34955) hydrogen bonds : bond 0.05674 / 3.95 ( 1103) hydrogen bonds : angle 4.67843 / 3.35 ( 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 92 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 51 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 297 LYS cc_start: 0.6556 (OUTLIER) cc_final: 0.6318 (pptt) REVERT: D 888 ASN cc_start: 0.5363 (OUTLIER) cc_final: 0.4978 (m-40) REVERT: D 996 MET cc_start: 0.7250 (pmm) cc_final: 0.6288 (ppp) REVERT: D 1008 MET cc_start: 0.4066 (ptt) cc_final: 0.3351 (mpp) outliers start: 41 outliers final: 27 residues processed: 87 average time/residue: 0.1811 time to fit residues: 25.0833 Evaluate side-chains 76 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 47 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 280 LYS 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 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 297 LYS 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 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 1 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 199 optimal weight: 10.0000 chunk 216 optimal weight: 20.0000 chunk 52 optimal weight: 0.1980 chunk 65 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 247 optimal weight: 20.0000 chunk 257 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 171 optimal weight: 30.0000 chunk 97 optimal weight: 0.2980 overall best weight: 2.8986 ------------------------------------------------------------------------------- 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** D 137 GLN D 141 ASN ** D 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 401 ASN D 888 ASN C 169 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.073076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.060155 restraints weight = 243635.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.058506 restraints weight = 187690.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.058685 restraints weight = 163707.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.058527 restraints weight = 134901.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.058557 restraints weight = 125429.793| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.5022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25149 Z= 0.148 Angle : 0.523 13.550 34955 Z= 0.295 Chirality : 0.038 0.186 4022 Planarity : 0.004 0.061 3683 Dihedral : 20.685 178.397 5854 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.52 % Allowed : 13.52 % Favored : 84.95 % 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: 0.43 (0.17), residues: 2412 helix: 1.27 (0.15), residues: 1178 sheet: -0.72 (0.30), residues: 271 loop : -0.57 (0.21), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 140 TYR 0.015 0.001 TYR F 95 PHE 0.012 0.001 PHE C 51 TRP 0.009 0.001 TRP D 408 HIS 0.006 0.001 HIS D 890 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.15 (25149) covalent geometry : angle 0.52293 / 0.30 (34955) hydrogen bonds : bond 0.04323 / 3.00 ( 1103) hydrogen bonds : angle 4.58521 / 3.29 ( 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 83 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 51 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 784 ILE cc_start: 0.9331 (tp) cc_final: 0.8966 (mm) REVERT: A 996 MET cc_start: 0.8670 (tpp) cc_final: 0.7812 (mtm) REVERT: D 297 LYS cc_start: 0.6611 (OUTLIER) cc_final: 0.5555 (pptt) REVERT: D 307 GLU cc_start: 0.6936 (pm20) cc_final: 0.6481 (mt-10) REVERT: D 996 MET cc_start: 0.7324 (pmm) cc_final: 0.6588 (ppp) REVERT: D 1008 MET cc_start: 0.3989 (ptt) cc_final: 0.3322 (mpp) outliers start: 32 outliers final: 21 residues processed: 78 average time/residue: 0.1698 time to fit residues: 21.7371 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 : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL 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 491 ILE Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 1000 THR 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 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 975 ASN Chi-restraints excluded: chain F residue 24 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 173 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 182 optimal weight: 9.9990 chunk 177 optimal weight: 20.0000 chunk 226 optimal weight: 30.0000 chunk 260 optimal weight: 7.9990 chunk 148 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 121 optimal weight: 6.9990 chunk 222 optimal weight: 30.0000 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 182 GLN ** 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** ** D 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 ASN C 169 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.072340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.058783 restraints weight = 244556.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.057381 restraints weight = 178197.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.057323 restraints weight = 149998.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.057197 restraints weight = 133155.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.057246 restraints weight = 128305.736| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.5497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25149 Z= 0.173 Angle : 0.541 13.087 34955 Z= 0.304 Chirality : 0.039 0.184 4022 Planarity : 0.004 0.067 3683 Dihedral : 20.636 178.708 5854 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.62 % Allowed : 13.62 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.17), residues: 2412 helix: 1.30 (0.15), residues: 1175 sheet: -0.68 (0.30), residues: 277 loop : -0.63 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 499 TYR 0.017 0.002 TYR C 53 PHE 0.015 0.002 PHE A 221 TRP 0.011 0.001 TRP D 408 HIS 0.005 0.001 HIS A 890 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.17 (25149) covalent geometry : angle 0.54095 / 0.30 (34955) hydrogen bonds : bond 0.04673 / 3.25 ( 1103) hydrogen bonds : angle 4.58706 / 3.29 ( 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 90 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 56 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 728 MET cc_start: 0.6199 (tpt) cc_final: 0.5826 (mmt) REVERT: A 784 ILE cc_start: 0.9335 (tp) cc_final: 0.8977 (mm) REVERT: A 996 MET cc_start: 0.8819 (tpp) cc_final: 0.7924 (mtm) REVERT: D 297 LYS cc_start: 0.6569 (OUTLIER) cc_final: 0.6347 (pptt) REVERT: D 844 MET cc_start: -0.3432 (ptt) cc_final: -0.3879 (ptt) REVERT: D 1008 MET cc_start: 0.3906 (ptt) cc_final: 0.3352 (mpp) REVERT: C 157 SER cc_start: 0.8676 (OUTLIER) cc_final: 0.8414 (p) outliers start: 34 outliers final: 24 residues processed: 86 average time/residue: 0.1580 time to fit residues: 22.3758 Evaluate side-chains 78 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 52 time to evaluate : 0.854 ------------------------------------------------------------------------------- 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 41 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 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 297 LYS 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 975 ASN 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 Chi-restraints excluded: chain C residue 157 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 148 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 227 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 198 optimal weight: 20.0000 chunk 7 optimal weight: 0.9990 chunk 224 optimal weight: 20.0000 chunk 111 optimal weight: 20.0000 chunk 164 optimal weight: 10.0000 chunk 229 optimal weight: 6.9990 chunk 193 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** A1025 GLN ** D 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.071840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.057571 restraints weight = 234532.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.055398 restraints weight = 208915.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.055517 restraints weight = 204801.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.055182 restraints weight = 156948.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.055162 restraints weight = 141767.356| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.5835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 25149 Z= 0.182 Angle : 0.548 14.095 34955 Z= 0.306 Chirality : 0.039 0.194 4022 Planarity : 0.004 0.100 3683 Dihedral : 20.709 178.335 5854 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.71 % Allowed : 13.62 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.17), residues: 2412 helix: 1.22 (0.15), residues: 1177 sheet: -0.70 (0.30), residues: 277 loop : -0.62 (0.21), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG F 33 TYR 0.020 0.002 TYR F 95 PHE 0.015 0.002 PHE C 136 TRP 0.012 0.001 TRP D 408 HIS 0.006 0.001 HIS A 393 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.18 (25149) covalent geometry : angle 0.54775 / 0.31 (34955) hydrogen bonds : bond 0.04663 / 3.25 ( 1103) hydrogen bonds : angle 4.63440 / 3.33 ( 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 89 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 53 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 GLU cc_start: 0.4717 (OUTLIER) cc_final: 0.4516 (pm20) REVERT: A 728 MET cc_start: 0.6162 (tpt) cc_final: 0.5813 (mmt) REVERT: A 784 ILE cc_start: 0.9358 (tp) cc_final: 0.9056 (mm) REVERT: A 996 MET cc_start: 0.8869 (tpp) cc_final: 0.7944 (mtm) REVERT: D 297 LYS cc_start: 0.6620 (OUTLIER) cc_final: 0.6413 (pptt) REVERT: D 844 MET cc_start: -0.3294 (ptt) cc_final: -0.3672 (ptm) REVERT: D 1008 MET cc_start: 0.4110 (ptt) cc_final: 0.3587 (mpp) REVERT: C 157 SER cc_start: 0.8652 (OUTLIER) cc_final: 0.8384 (p) outliers start: 36 outliers final: 28 residues processed: 84 average time/residue: 0.1517 time to fit residues: 21.2908 Evaluate side-chains 82 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 51 time to evaluate : 0.660 ------------------------------------------------------------------------------- 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 41 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 271 GLU 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 438 THR 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 297 LYS 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 975 ASN 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 Chi-restraints excluded: chain C residue 157 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 169 optimal weight: 10.0000 chunk 89 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 chunk 257 optimal weight: 0.7980 chunk 14 optimal weight: 9.9990 chunk 122 optimal weight: 7.9990 chunk 225 optimal weight: 40.0000 chunk 37 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 overall best weight: 2.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.071930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.058803 restraints weight = 237443.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.057289 restraints weight = 183448.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.057331 restraints weight = 155981.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.057026 restraints weight = 142235.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.057109 restraints weight = 127581.542| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6650 moved from start: 0.6021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25149 Z= 0.144 Angle : 0.526 14.722 34955 Z= 0.293 Chirality : 0.038 0.185 4022 Planarity : 0.003 0.064 3683 Dihedral : 20.668 179.134 5854 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.43 % Allowed : 14.10 % Favored : 84.48 % 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: 0.46 (0.17), residues: 2412 helix: 1.30 (0.15), residues: 1175 sheet: -0.69 (0.30), residues: 274 loop : -0.56 (0.21), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 499 TYR 0.017 0.001 TYR C 53 PHE 0.012 0.001 PHE C 51 TRP 0.013 0.001 TRP D 408 HIS 0.005 0.001 HIS A 890 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (25149) covalent geometry : angle 0.52552 / 0.29 (34955) hydrogen bonds : bond 0.04240 / 2.95 ( 1103) hydrogen bonds : angle 4.56467 / 3.28 ( 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 82 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 52 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 GLU cc_start: 0.4485 (OUTLIER) cc_final: 0.4277 (pm20) REVERT: A 728 MET cc_start: 0.6179 (tpt) cc_final: 0.5844 (mmt) REVERT: A 784 ILE cc_start: 0.9320 (tp) cc_final: 0.8970 (mm) REVERT: A 996 MET cc_start: 0.8836 (tpp) cc_final: 0.7983 (mtm) REVERT: D 297 LYS cc_start: 0.6643 (OUTLIER) cc_final: 0.6399 (pptt) REVERT: D 844 MET cc_start: -0.3117 (ptt) cc_final: -0.3673 (ptt) REVERT: D 1008 MET cc_start: 0.3564 (ptt) cc_final: 0.3139 (mpp) REVERT: F 153 PHE cc_start: 0.1370 (m-80) cc_final: 0.1026 (m-10) REVERT: C 157 SER cc_start: 0.8641 (OUTLIER) cc_final: 0.8388 (p) outliers start: 30 outliers final: 25 residues processed: 78 average time/residue: 0.1525 time to fit residues: 19.9347 Evaluate side-chains 81 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 53 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 41 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 271 GLU 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 438 THR Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 1000 THR 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 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 975 ASN 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 142 VAL Chi-restraints excluded: chain C residue 157 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 67 optimal weight: 0.9980 chunk 131 optimal weight: 6.9990 chunk 61 optimal weight: 0.3980 chunk 231 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 191 optimal weight: 20.0000 chunk 184 optimal weight: 10.0000 chunk 209 optimal weight: 0.9980 chunk 14 optimal weight: 9.9990 chunk 203 optimal weight: 20.0000 chunk 127 optimal weight: 20.0000 overall best weight: 3.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 557 HIS ** D1048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.071519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.058601 restraints weight = 237085.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.058336 restraints weight = 185265.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.057742 restraints weight = 161863.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.057459 restraints weight = 149405.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.057399 restraints weight = 128049.133| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6571 moved from start: 0.6351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25149 Z= 0.161 Angle : 0.537 14.506 34955 Z= 0.299 Chirality : 0.038 0.202 4022 Planarity : 0.004 0.070 3683 Dihedral : 20.621 179.063 5854 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.48 % Allowed : 14.24 % 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: 0.47 (0.17), residues: 2412 helix: 1.30 (0.15), residues: 1176 sheet: -0.71 (0.30), residues: 277 loop : -0.54 (0.21), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 499 TYR 0.019 0.001 TYR F 95 PHE 0.012 0.002 PHE A 221 TRP 0.012 0.001 TRP D 408 HIS 0.005 0.001 HIS D 890 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.16 (25149) covalent geometry : angle 0.53732 / 0.30 (34955) hydrogen bonds : bond 0.04585 / 3.20 ( 1103) hydrogen bonds : angle 4.58118 / 3.30 ( 3045) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3797.81 seconds wall clock time: 66 minutes 59.40 seconds (4019.40 seconds total)