Starting phenix.real_space_refine on Mon Aug 25 01:00:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jg9_36225/08_2025/8jg9_36225_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jg9_36225/08_2025/8jg9_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jg9_36225/08_2025/8jg9_36225.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jg9_36225/08_2025/8jg9_36225.map" model { file = "/net/cci-nas-00/data/ceres_data/8jg9_36225/08_2025/8jg9_36225_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jg9_36225/08_2025/8jg9_36225_neut.cif" } resolution = 3.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 220 5.49 5 S 34 5.16 5 C 14567 2.51 5 N 4203 2.21 5 O 5240 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 6.48, per 1000 atoms: 0.27 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: 2.45 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 3.51 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: 6.44 Time building geometry restraints manager: 3.19 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: 30846 2.03 - 4.06: 3625 4.06 - 6.09: 414 6.09 - 8.12: 59 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: 3.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 28.450 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 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:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4820 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= 0.620 Angle : 1.274 10.151 34955 Z= 0.947 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 aren 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 covalent geometry : bond 0.00850 (25149) covalent geometry : angle 1.27433 (34955) hydrogen bonds : bond 0.18678 ( 1103) hydrogen bonds : angle 8.12137 ( 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 : 0.880 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: 0.2140 time to fit residues: 62.3120 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 : 0.814 ------------------------------------------------------------------------------- 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: 10.0000 chunk 183 optimal weight: 20.0000 chunk 111 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN A 111 HIS 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 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 969 ASN A 985 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 472 ASN D 570 ASN D 580 ASN D 590 GLN D 695 ASN D 785 ASN D 863 ASN D 968 ASN F 54 GLN F 159 GLN C 163 HIS C 169 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.075816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.062609 restraints weight = 245478.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.061252 restraints weight = 180064.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.061167 restraints weight = 151934.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.061030 restraints weight = 134269.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.061088 restraints weight = 133920.065| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6495 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 25149 Z= 0.236 Angle : 0.687 10.393 34955 Z= 0.366 Chirality : 0.042 0.177 4022 Planarity : 0.005 0.056 3683 Dihedral : 20.974 177.219 5863 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.52 % Allowed : 9.33 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.17), residues: 2412 helix: 1.08 (0.15), residues: 1195 sheet: -0.39 (0.33), residues: 241 loop : -0.75 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 116 TYR 0.031 0.002 TYR A 897 PHE 0.019 0.002 PHE F 51 TRP 0.020 0.001 TRP A 223 HIS 0.008 0.002 HIS A 832 Details of bonding type rmsd covalent geometry : bond 0.00474 (25149) covalent geometry : angle 0.68729 (34955) hydrogen bonds : bond 0.05460 ( 1103) hydrogen bonds : angle 5.00692 ( 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 102 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 70 time to evaluate : 0.933 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: A 278 TYR cc_start: 0.7786 (p90) cc_final: 0.7427 (p90) REVERT: D 297 LYS cc_start: 0.6475 (OUTLIER) cc_final: 0.6137 (pptt) REVERT: D 1008 MET cc_start: 0.4367 (ptt) cc_final: 0.3677 (mpp) REVERT: F 1 MET cc_start: 0.8767 (tpp) cc_final: 0.8404 (tpp) outliers start: 32 outliers final: 20 residues processed: 98 average time/residue: 0.1913 time to fit residues: 29.6473 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 : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 415 ILE Chi-restraints excluded: chain D residue 475 ILE Chi-restraints excluded: chain D residue 590 GLN Chi-restraints excluded: chain D residue 975 ASN Chi-restraints excluded: chain D residue 1032 THR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 163 HIS Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 163 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 227 optimal weight: 20.0000 chunk 67 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 184 optimal weight: 0.0870 chunk 108 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 117 optimal weight: 10.0000 chunk 78 optimal weight: 0.0270 chunk 43 optimal weight: 0.4980 chunk 176 optimal weight: 30.0000 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 HIS A 154 GLN ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 590 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.077157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.064311 restraints weight = 244866.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.062468 restraints weight = 177138.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.062684 restraints weight = 146158.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.062406 restraints weight = 127547.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.062486 restraints weight = 119115.854| |-----------------------------------------------------------------------------| r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6454 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.079 25149 Z= 0.110 Angle : 0.516 11.229 34955 Z= 0.277 Chirality : 0.037 0.152 4022 Planarity : 0.003 0.042 3683 Dihedral : 20.605 179.860 5860 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.14 % Allowed : 10.38 % Favored : 88.48 % 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 aren not related in a simple way. whole: 0.77 (0.17), residues: 2412 helix: 1.54 (0.15), residues: 1198 sheet: -0.08 (0.31), residues: 261 loop : -0.59 (0.20), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 499 TYR 0.016 0.001 TYR D 897 PHE 0.014 0.001 PHE D 589 TRP 0.007 0.001 TRP A 229 HIS 0.004 0.001 HIS D 832 Details of bonding type rmsd covalent geometry : bond 0.00222 (25149) covalent geometry : angle 0.51591 (34955) hydrogen bonds : bond 0.03983 ( 1103) hydrogen bonds : angle 4.43591 ( 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 95 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 71 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 297 LYS cc_start: 0.6585 (pptt) cc_final: 0.6310 (pptt) REVERT: D 1008 MET cc_start: 0.4180 (ptt) cc_final: 0.3353 (mpp) outliers start: 24 outliers final: 15 residues processed: 90 average time/residue: 0.1887 time to fit residues: 27.2581 Evaluate side-chains 75 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.815 ------------------------------------------------------------------------------- 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 D residue 41 VAL Chi-restraints excluded: chain D residue 260 ASN Chi-restraints excluded: chain D residue 327 LYS Chi-restraints excluded: chain D residue 415 ILE 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 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: 0.9980 chunk 50 optimal weight: 10.0000 chunk 252 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 165 optimal weight: 0.9990 chunk 229 optimal weight: 20.0000 chunk 132 optimal weight: 30.0000 chunk 218 optimal weight: 40.0000 chunk 81 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 chunk 228 optimal weight: 20.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 HIS ** 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 930 ASN D 62 HIS D 236 HIS D 252 ASN D 780 ASN D 902 ASN F 163 HIS C 169 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.073350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.060099 restraints weight = 244630.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.058853 restraints weight = 180981.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.058724 restraints weight = 154507.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.058651 restraints weight = 129736.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.058686 restraints weight = 128140.884| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 25149 Z= 0.240 Angle : 0.660 11.289 34955 Z= 0.352 Chirality : 0.041 0.210 4022 Planarity : 0.005 0.070 3683 Dihedral : 20.791 179.163 5858 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.86 % Allowed : 11.14 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.17), residues: 2412 helix: 1.28 (0.15), residues: 1178 sheet: -0.41 (0.33), residues: 241 loop : -0.54 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 21 TYR 0.026 0.002 TYR A 947 PHE 0.026 0.002 PHE C 51 TRP 0.019 0.002 TRP A 223 HIS 0.007 0.002 HIS D 832 Details of bonding type rmsd covalent geometry : bond 0.00483 (25149) covalent geometry : angle 0.66012 (34955) hydrogen bonds : bond 0.05481 ( 1103) hydrogen bonds : angle 4.69231 ( 3045) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 60 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 499 ARG cc_start: 0.8223 (ttp80) cc_final: 0.7989 (ttp80) REVERT: D 1008 MET cc_start: 0.3968 (ptt) cc_final: 0.3151 (mpp) REVERT: F 1 MET cc_start: 0.8757 (tpp) cc_final: 0.8537 (tpp) outliers start: 39 outliers final: 18 residues processed: 91 average time/residue: 0.1988 time to fit residues: 28.3318 Evaluate side-chains 68 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 327 LYS Chi-restraints excluded: chain D residue 475 ILE Chi-restraints excluded: chain D residue 775 VAL Chi-restraints excluded: chain D residue 975 ASN Chi-restraints excluded: chain D residue 997 ILE Chi-restraints excluded: chain D residue 1000 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 142 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 211 optimal weight: 0.4980 chunk 45 optimal weight: 0.9990 chunk 50 optimal weight: 20.0000 chunk 227 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 143 optimal weight: 0.0570 chunk 97 optimal weight: 9.9990 chunk 26 optimal weight: 30.0000 chunk 204 optimal weight: 0.8980 chunk 12 optimal weight: 10.0000 chunk 134 optimal weight: 8.9990 overall best weight: 2.0902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 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** A 930 ASN D 252 ASN ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 590 GLN 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 = 0.4305 r_free = 0.4305 target = 0.074050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.060897 restraints weight = 242594.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.059835 restraints weight = 176138.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.059681 restraints weight = 143062.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.059630 restraints weight = 122119.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.059607 restraints weight = 117142.022| |-----------------------------------------------------------------------------| r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6563 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25149 Z= 0.127 Angle : 0.515 12.852 34955 Z= 0.276 Chirality : 0.037 0.160 4022 Planarity : 0.003 0.043 3683 Dihedral : 20.522 179.922 5854 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.14 % Allowed : 12.52 % 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 aren not related in a simple way. whole: 0.76 (0.17), residues: 2412 helix: 1.54 (0.15), residues: 1178 sheet: -0.48 (0.32), residues: 251 loop : -0.43 (0.20), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 63 TYR 0.019 0.001 TYR A 278 PHE 0.025 0.001 PHE C 51 TRP 0.014 0.001 TRP D 408 HIS 0.004 0.001 HIS D 890 Details of bonding type rmsd covalent geometry : bond 0.00259 (25149) covalent geometry : angle 0.51494 (34955) hydrogen bonds : bond 0.03580 ( 1103) hydrogen bonds : angle 4.39572 ( 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 76 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 52 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 TYR cc_start: 0.7854 (p90) cc_final: 0.7484 (p90) REVERT: A 657 MET cc_start: 0.7444 (mmm) cc_final: 0.7203 (mmm) REVERT: A 784 ILE cc_start: 0.9348 (tp) cc_final: 0.8906 (mm) REVERT: A 996 MET cc_start: 0.8718 (tpp) cc_final: 0.7758 (mtm) REVERT: D 1008 MET cc_start: 0.3631 (ptt) cc_final: 0.2902 (mpp) outliers start: 24 outliers final: 12 residues processed: 71 average time/residue: 0.1658 time to fit residues: 19.1271 Evaluate side-chains 62 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 327 LYS Chi-restraints excluded: chain D residue 475 ILE 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 142 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 22 optimal weight: 10.0000 chunk 242 optimal weight: 10.0000 chunk 143 optimal weight: 40.0000 chunk 156 optimal weight: 20.0000 chunk 128 optimal weight: 0.9980 chunk 59 optimal weight: 9.9990 chunk 80 optimal weight: 0.0370 chunk 246 optimal weight: 8.9990 chunk 11 optimal weight: 7.9990 chunk 218 optimal weight: 40.0000 chunk 85 optimal weight: 0.9990 overall best weight: 3.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN A 182 GLN A 365 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** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 ASN D 401 ASN ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 658 ASN ** D1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.072040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.057960 restraints weight = 234104.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.056647 restraints weight = 176249.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.056134 restraints weight = 155960.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.056142 restraints weight = 133044.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.056126 restraints weight = 125282.545| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.5637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25149 Z= 0.199 Angle : 0.595 13.197 34955 Z= 0.318 Chirality : 0.039 0.203 4022 Planarity : 0.004 0.066 3683 Dihedral : 20.646 179.188 5854 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.10 % Favored : 95.85 % Rotamer: Outliers : 1.33 % Allowed : 12.81 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.17), residues: 2412 helix: 1.35 (0.15), residues: 1178 sheet: -0.40 (0.31), residues: 277 loop : -0.55 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 63 TYR 0.020 0.002 TYR A 912 PHE 0.020 0.002 PHE C 51 TRP 0.013 0.002 TRP A 223 HIS 0.008 0.002 HIS D 890 Details of bonding type rmsd covalent geometry : bond 0.00402 (25149) covalent geometry : angle 0.59462 (34955) hydrogen bonds : bond 0.04715 ( 1103) hydrogen bonds : angle 4.60485 ( 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 81 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 53 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 996 MET cc_start: 0.8857 (tpp) cc_final: 0.7867 (mtm) REVERT: D 1008 MET cc_start: 0.3632 (ptt) cc_final: 0.3155 (mpp) REVERT: F 73 MET cc_start: 0.2877 (ptt) cc_final: 0.2672 (ptt) outliers start: 28 outliers final: 17 residues processed: 79 average time/residue: 0.1784 time to fit residues: 22.8726 Evaluate side-chains 63 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 46 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 GLU 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 D residue 41 VAL Chi-restraints excluded: chain D residue 327 LYS Chi-restraints excluded: chain D residue 475 ILE Chi-restraints excluded: chain D residue 997 ILE 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 147 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 199 optimal weight: 30.0000 chunk 216 optimal weight: 20.0000 chunk 52 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 247 optimal weight: 5.9990 chunk 257 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 171 optimal weight: 30.0000 chunk 97 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1025 GLN ** D 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 557 HIS ** D1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.071848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.057323 restraints weight = 234457.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.056022 restraints weight = 175881.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.056093 restraints weight = 153791.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.055688 restraints weight = 143434.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.055818 restraints weight = 133279.664| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.6195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25149 Z= 0.175 Angle : 0.563 13.433 34955 Z= 0.300 Chirality : 0.038 0.235 4022 Planarity : 0.004 0.153 3683 Dihedral : 20.654 179.507 5854 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.57 % Allowed : 13.10 % Favored : 85.33 % 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 aren not related in a simple way. whole: 0.59 (0.17), residues: 2412 helix: 1.37 (0.15), residues: 1178 sheet: -0.42 (0.31), residues: 274 loop : -0.53 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 33 TYR 0.020 0.002 TYR F 95 PHE 0.021 0.002 PHE C 51 TRP 0.014 0.001 TRP D 408 HIS 0.006 0.001 HIS A 890 Details of bonding type rmsd covalent geometry : bond 0.00355 (25149) covalent geometry : angle 0.56327 (34955) hydrogen bonds : bond 0.04059 ( 1103) hydrogen bonds : angle 4.57128 ( 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: 33 poor density : 50 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 657 MET cc_start: 0.7510 (mmm) cc_final: 0.7078 (mmm) REVERT: A 784 ILE cc_start: 0.9351 (tp) cc_final: 0.9098 (pt) REVERT: D 1008 MET cc_start: 0.3682 (ptt) cc_final: 0.3406 (mpp) REVERT: F 73 MET cc_start: 0.3174 (ptt) cc_final: 0.2885 (ptt) REVERT: F 153 PHE cc_start: 0.1419 (m-80) cc_final: 0.1158 (m-10) outliers start: 33 outliers final: 21 residues processed: 78 average time/residue: 0.1733 time to fit residues: 22.7055 Evaluate side-chains 70 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 49 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 840 LEU Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 327 LYS Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 475 ILE Chi-restraints excluded: chain D residue 775 VAL Chi-restraints excluded: chain D residue 957 SER Chi-restraints excluded: chain D residue 997 ILE 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 147 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 173 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 182 optimal weight: 50.0000 chunk 177 optimal weight: 5.9990 chunk 226 optimal weight: 50.0000 chunk 260 optimal weight: 9.9990 chunk 148 optimal weight: 8.9990 chunk 52 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 121 optimal weight: 50.0000 chunk 222 optimal weight: 20.0000 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 401 ASN D 985 ASN ** D1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.071079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.057454 restraints weight = 236392.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.056253 restraints weight = 179646.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.056167 restraints weight = 154114.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.055890 restraints weight = 131079.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.055899 restraints weight = 124464.219| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.6711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 25149 Z= 0.183 Angle : 0.572 15.524 34955 Z= 0.304 Chirality : 0.038 0.204 4022 Planarity : 0.004 0.065 3683 Dihedral : 20.625 179.040 5854 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.48 % Allowed : 13.33 % 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 aren not related in a simple way. whole: 0.55 (0.17), residues: 2412 helix: 1.37 (0.15), residues: 1176 sheet: -0.51 (0.31), residues: 277 loop : -0.56 (0.21), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 499 TYR 0.021 0.002 TYR F 95 PHE 0.015 0.002 PHE C 51 TRP 0.009 0.001 TRP D 408 HIS 0.007 0.001 HIS A 890 Details of bonding type rmsd covalent geometry : bond 0.00373 (25149) covalent geometry : angle 0.57212 (34955) hydrogen bonds : bond 0.04490 ( 1103) hydrogen bonds : angle 4.58223 ( 3045) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 47 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 MET cc_start: 0.8238 (mtp) cc_final: 0.7995 (mtt) REVERT: A 784 ILE cc_start: 0.9332 (tp) cc_final: 0.8971 (mm) REVERT: D 1008 MET cc_start: 0.3638 (ptt) cc_final: 0.3368 (mpp) REVERT: F 73 MET cc_start: 0.3184 (ptt) cc_final: 0.2837 (ptt) REVERT: F 147 TYR cc_start: 0.8551 (OUTLIER) cc_final: 0.7806 (p90) REVERT: F 153 PHE cc_start: 0.1637 (m-80) cc_final: 0.1384 (m-10) outliers start: 31 outliers final: 23 residues processed: 76 average time/residue: 0.1781 time to fit residues: 22.5147 Evaluate side-chains 71 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 47 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 327 LYS Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 475 ILE Chi-restraints excluded: chain D residue 775 VAL Chi-restraints excluded: chain D residue 957 SER Chi-restraints excluded: chain D residue 997 ILE 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 F residue 147 TYR Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 147 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 148 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 227 optimal weight: 40.0000 chunk 8 optimal weight: 4.9990 chunk 198 optimal weight: 0.2980 chunk 7 optimal weight: 0.9980 chunk 224 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 chunk 164 optimal weight: 9.9990 chunk 229 optimal weight: 9.9990 chunk 193 optimal weight: 0.7980 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 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 = 0.4258 r_free = 0.4258 target = 0.071559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.057993 restraints weight = 238017.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.056714 restraints weight = 185283.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.056592 restraints weight = 159099.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.056283 restraints weight = 147261.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.056428 restraints weight = 129197.141| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.6883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25149 Z= 0.138 Angle : 0.527 15.379 34955 Z= 0.280 Chirality : 0.037 0.210 4022 Planarity : 0.003 0.058 3683 Dihedral : 20.469 179.508 5854 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.24 % Allowed : 13.76 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.17), residues: 2412 helix: 1.51 (0.15), residues: 1181 sheet: -0.46 (0.31), residues: 274 loop : -0.49 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 499 TYR 0.018 0.001 TYR A 809 PHE 0.017 0.001 PHE C 51 TRP 0.011 0.001 TRP D 408 HIS 0.005 0.001 HIS A 890 Details of bonding type rmsd covalent geometry : bond 0.00283 (25149) covalent geometry : angle 0.52743 (34955) hydrogen bonds : bond 0.03769 ( 1103) hydrogen bonds : angle 4.46035 ( 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 76 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 50 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 MET cc_start: 0.7919 (mmt) cc_final: 0.7624 (mmp) REVERT: A 657 MET cc_start: 0.7428 (mmm) cc_final: 0.6887 (mmm) REVERT: A 996 MET cc_start: 0.8624 (tpp) cc_final: 0.8128 (mtp) REVERT: D 232 MET cc_start: 0.6060 (mmm) cc_final: 0.5752 (mmm) REVERT: F 73 MET cc_start: 0.3058 (ptt) cc_final: 0.2714 (ptt) REVERT: F 147 TYR cc_start: 0.8519 (OUTLIER) cc_final: 0.7881 (p90) REVERT: F 153 PHE cc_start: 0.1732 (m-80) cc_final: 0.1477 (m-10) REVERT: C 135 GLU cc_start: 0.9235 (OUTLIER) cc_final: 0.8910 (tm-30) outliers start: 26 outliers final: 20 residues processed: 71 average time/residue: 0.1809 time to fit residues: 21.7429 Evaluate side-chains 70 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 48 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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 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 840 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 327 LYS Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 475 ILE Chi-restraints excluded: chain D residue 775 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 147 TYR Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 147 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 169 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 98 optimal weight: 9.9990 chunk 257 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 225 optimal weight: 30.0000 chunk 37 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 43 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 590 GLN A 813 ASN ** D 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.071864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.057824 restraints weight = 244268.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.056379 restraints weight = 175883.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.056365 restraints weight = 159118.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.056124 restraints weight = 135735.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.056129 restraints weight = 144676.131| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.7047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25149 Z= 0.121 Angle : 0.514 15.354 34955 Z= 0.272 Chirality : 0.036 0.201 4022 Planarity : 0.003 0.055 3683 Dihedral : 20.297 178.867 5854 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.05 % Allowed : 14.19 % 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 aren not related in a simple way. whole: 0.88 (0.18), residues: 2412 helix: 1.65 (0.15), residues: 1176 sheet: -0.21 (0.34), residues: 250 loop : -0.46 (0.21), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 499 TYR 0.018 0.001 TYR A 809 PHE 0.015 0.001 PHE C 51 TRP 0.008 0.001 TRP D 408 HIS 0.004 0.001 HIS D 890 Details of bonding type rmsd covalent geometry : bond 0.00252 (25149) covalent geometry : angle 0.51448 (34955) hydrogen bonds : bond 0.03588 ( 1103) hydrogen bonds : angle 4.39456 ( 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 69 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 47 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 MET cc_start: 0.8159 (mtp) cc_final: 0.7887 (mtt) REVERT: A 234 MET cc_start: 0.7887 (mmt) cc_final: 0.7562 (mmp) REVERT: A 657 MET cc_start: 0.7437 (mmm) cc_final: 0.7028 (mmm) REVERT: A 996 MET cc_start: 0.8531 (tpp) cc_final: 0.8180 (mtp) REVERT: D 232 MET cc_start: 0.5779 (mmm) cc_final: 0.5508 (mmm) REVERT: D 307 GLU cc_start: 0.7312 (pm20) cc_final: 0.6773 (mt-10) REVERT: F 73 MET cc_start: 0.3335 (ptt) cc_final: 0.2986 (ptt) REVERT: F 147 TYR cc_start: 0.8586 (OUTLIER) cc_final: 0.7963 (p90) REVERT: F 153 PHE cc_start: 0.1628 (m-80) cc_final: 0.1365 (m-10) REVERT: C 135 GLU cc_start: 0.9206 (OUTLIER) cc_final: 0.8890 (tm-30) outliers start: 22 outliers final: 17 residues processed: 67 average time/residue: 0.1849 time to fit residues: 20.3695 Evaluate side-chains 66 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 47 time to evaluate : 0.892 ------------------------------------------------------------------------------- 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 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 590 GLN Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 327 LYS Chi-restraints excluded: chain D residue 475 ILE Chi-restraints excluded: chain D residue 775 VAL Chi-restraints excluded: chain D residue 997 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 147 TYR Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 142 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 67 optimal weight: 10.0000 chunk 131 optimal weight: 0.9990 chunk 61 optimal weight: 30.0000 chunk 231 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 191 optimal weight: 0.7980 chunk 184 optimal weight: 20.0000 chunk 209 optimal weight: 30.0000 chunk 14 optimal weight: 7.9990 chunk 203 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 ASN A 813 ASN ** D 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.071716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.057352 restraints weight = 241015.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.055915 restraints weight = 177125.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.055988 restraints weight = 164007.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.055677 restraints weight = 142194.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.055670 restraints weight = 132810.324| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.7054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.120 25149 Z= 0.156 Angle : 0.675 59.106 34955 Z= 0.379 Chirality : 0.039 0.971 4022 Planarity : 0.003 0.054 3683 Dihedral : 20.297 178.870 5854 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.05 % Allowed : 14.14 % Favored : 84.81 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.18), residues: 2412 helix: 1.64 (0.15), residues: 1176 sheet: -0.20 (0.34), residues: 250 loop : -0.46 (0.21), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 499 TYR 0.046 0.001 TYR D 256 PHE 0.014 0.001 PHE C 51 TRP 0.008 0.001 TRP D 408 HIS 0.004 0.001 HIS D 832 Details of bonding type rmsd covalent geometry : bond 0.00312 (25149) covalent geometry : angle 0.67535 (34955) hydrogen bonds : bond 0.03592 ( 1103) hydrogen bonds : angle 4.39821 ( 3045) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4365.04 seconds wall clock time: 76 minutes 38.55 seconds (4598.55 seconds total)