Starting phenix.real_space_refine on Fri May 23 12:54:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jg9_36225/05_2025/8jg9_36225_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jg9_36225/05_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_36225/05_2025/8jg9_36225.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jg9_36225/05_2025/8jg9_36225.map" model { file = "/net/cci-nas-00/data/ceres_data/8jg9_36225/05_2025/8jg9_36225_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jg9_36225/05_2025/8jg9_36225_neut.cif" } resolution = 3.82 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 3, 'GLU:plan': 16, 'ASN:plan1': 3, 'ARG:plan': 4, 'ASP:plan': 2} 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: {'GLN:plan1': 3, 'GLU:plan': 15, 'ASN:plan1': 3, 'ARG:plan': 4, 'ASP:plan': 2} 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: {'GLU:plan': 7, 'ARG:plan': 2, '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: 15.92, per 1000 atoms: 0.66 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: 6.05 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 10.21 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: 13.88 Time building geometry restraints manager: 7.15 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: 5.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.870 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 68.050 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.850 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.011 0.002 TRP D 408 HIS 0.006 0.001 HIS A 773 PHE 0.019 0.002 PHE F 165 TYR 0.027 0.002 TYR D 256 ARG 0.008 0.001 ARG A 685 Details of bonding type rmsd hydrogen bonds : bond 0.18678 ( 1103) hydrogen bonds : angle 8.12137 ( 3045) covalent geometry : bond 0.00850 (25149) covalent geometry : angle 1.27433 (34955) *********************** 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 : 2.365 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: 0.4188 time to fit residues: 121.8637 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 : 2.306 ------------------------------------------------------------------------------- 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 221 optimal weight: 20.0000 chunk 198 optimal weight: 7.9990 chunk 110 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 133 optimal weight: 30.0000 chunk 106 optimal weight: 9.9990 chunk 205 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 237 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 ASN D 570 ASN D 580 ASN D 590 GLN D 695 ASN ** D 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 863 ASN D 968 ASN F 54 GLN ** F 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 HIS C 169 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.075918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.062366 restraints weight = 244669.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.060750 restraints weight = 174791.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.060652 restraints weight = 151950.765| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 25149 Z= 0.235 Angle : 0.689 10.557 34955 Z= 0.369 Chirality : 0.042 0.198 4022 Planarity : 0.005 0.052 3683 Dihedral : 20.968 177.309 5863 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.52 % Allowed : 9.19 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.17), residues: 2412 helix: 1.07 (0.15), residues: 1195 sheet: -0.39 (0.33), residues: 241 loop : -0.73 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 223 HIS 0.008 0.002 HIS A 832 PHE 0.021 0.002 PHE F 51 TYR 0.030 0.002 TYR A 897 ARG 0.020 0.001 ARG A 116 Details of bonding type rmsd hydrogen bonds : bond 0.05472 ( 1103) hydrogen bonds : angle 5.02851 ( 3045) covalent geometry : bond 0.00471 (25149) covalent geometry : angle 0.68902 (34955) *********************** 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 101 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 69 time to evaluate : 2.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 TYR cc_start: 0.7977 (p90) cc_final: 0.7598 (p90) REVERT: D 297 LYS cc_start: 0.6457 (OUTLIER) cc_final: 0.6148 (pptt) REVERT: D 1008 MET cc_start: 0.4647 (ptt) cc_final: 0.3899 (mpp) REVERT: F 1 MET cc_start: 0.8805 (tpp) cc_final: 0.8451 (tpp) outliers start: 32 outliers final: 20 residues processed: 97 average time/residue: 0.3746 time to fit residues: 58.4815 Evaluate side-chains 79 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 58 time to evaluate : 2.462 ------------------------------------------------------------------------------- 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 185 optimal weight: 9.9990 chunk 63 optimal weight: 0.9980 chunk 19 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 chunk 135 optimal weight: 20.0000 chunk 162 optimal weight: 30.0000 chunk 245 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 chunk 168 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 250 optimal weight: 0.7980 overall best weight: 1.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 D 785 ASN F 159 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.076171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.062841 restraints weight = 241688.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.061113 restraints weight = 178206.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.061245 restraints weight = 157962.858| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6551 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 25149 Z= 0.126 Angle : 0.526 11.736 34955 Z= 0.283 Chirality : 0.037 0.158 4022 Planarity : 0.003 0.042 3683 Dihedral : 20.691 178.704 5860 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.33 % Allowed : 10.48 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.17), residues: 2412 helix: 1.51 (0.15), residues: 1194 sheet: -0.14 (0.32), residues: 251 loop : -0.59 (0.20), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 223 HIS 0.004 0.001 HIS D 832 PHE 0.013 0.001 PHE D 589 TYR 0.018 0.001 TYR D 897 ARG 0.006 0.001 ARG A 685 Details of bonding type rmsd hydrogen bonds : bond 0.04083 ( 1103) hydrogen bonds : angle 4.50698 ( 3045) covalent geometry : bond 0.00253 (25149) covalent geometry : angle 0.52631 (34955) *********************** 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 94 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 66 time to evaluate : 2.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 TYR cc_start: 0.7892 (p90) cc_final: 0.7655 (p90) REVERT: D 297 LYS cc_start: 0.6685 (OUTLIER) cc_final: 0.6407 (pptt) REVERT: D 1008 MET cc_start: 0.4244 (ptt) cc_final: 0.3389 (mpp) outliers start: 28 outliers final: 17 residues processed: 86 average time/residue: 0.3683 time to fit residues: 51.3704 Evaluate side-chains 77 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 2.352 ------------------------------------------------------------------------------- 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 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 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 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 116 optimal weight: 9.9990 chunk 39 optimal weight: 20.0000 chunk 61 optimal weight: 0.2980 chunk 60 optimal weight: 3.9990 chunk 97 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 chunk 145 optimal weight: 20.0000 chunk 166 optimal weight: 7.9990 chunk 254 optimal weight: 0.9990 chunk 186 optimal weight: 0.0980 chunk 239 optimal weight: 20.0000 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 557 HIS D 62 HIS D 393 HIS C 169 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.075717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.062674 restraints weight = 244221.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.061720 restraints weight = 170892.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.061726 restraints weight = 131272.017| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6454 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 25149 Z= 0.122 Angle : 0.501 12.346 34955 Z= 0.270 Chirality : 0.036 0.154 4022 Planarity : 0.003 0.036 3683 Dihedral : 20.475 179.252 5858 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.29 % Allowed : 11.33 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.17), residues: 2412 helix: 1.67 (0.15), residues: 1180 sheet: -0.16 (0.32), residues: 261 loop : -0.50 (0.20), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 229 HIS 0.005 0.001 HIS C 169 PHE 0.009 0.001 PHE F 51 TYR 0.016 0.001 TYR D 230 ARG 0.005 0.001 ARG D 63 Details of bonding type rmsd hydrogen bonds : bond 0.03614 ( 1103) hydrogen bonds : angle 4.29687 ( 3045) covalent geometry : bond 0.00248 (25149) covalent geometry : angle 0.50108 (34955) *********************** 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 90 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 63 time to evaluate : 2.383 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: 0.7694 (p90) cc_final: 0.7453 (p90) REVERT: A 996 MET cc_start: 0.8667 (tpp) cc_final: 0.7567 (mtm) REVERT: D 140 ARG cc_start: 0.6723 (mtm-85) cc_final: 0.6051 (tmt-80) REVERT: D 297 LYS cc_start: 0.6669 (pptt) cc_final: 0.6460 (pptt) REVERT: D 1008 MET cc_start: 0.4143 (ptt) cc_final: 0.3216 (mpp) outliers start: 27 outliers final: 16 residues processed: 83 average time/residue: 0.4198 time to fit residues: 54.5875 Evaluate side-chains 71 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 2.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 1000 THR 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 475 ILE Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 83 THR 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 243 optimal weight: 10.0000 chunk 242 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 238 optimal weight: 0.9990 chunk 213 optimal weight: 30.0000 chunk 236 optimal weight: 30.0000 chunk 231 optimal weight: 9.9990 chunk 117 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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** D 236 HIS D 252 ASN D 902 ASN F 163 HIS C 163 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.074322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.061617 restraints weight = 244302.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.060511 restraints weight = 178766.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.060605 restraints weight = 144914.365| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6496 moved from start: 0.4515 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= 0.139 Angle : 0.515 11.538 34955 Z= 0.279 Chirality : 0.037 0.164 4022 Planarity : 0.003 0.038 3683 Dihedral : 20.336 179.260 5854 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.52 % Allowed : 12.00 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.17), residues: 2412 helix: 1.71 (0.15), residues: 1171 sheet: -0.24 (0.31), residues: 270 loop : -0.40 (0.20), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 408 HIS 0.009 0.001 HIS F 163 PHE 0.017 0.001 PHE D 589 TYR 0.016 0.001 TYR D 230 ARG 0.006 0.000 ARG D 63 Details of bonding type rmsd hydrogen bonds : bond 0.03696 ( 1103) hydrogen bonds : angle 4.31765 ( 3045) covalent geometry : bond 0.00283 (25149) covalent geometry : angle 0.51456 (34955) *********************** 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 93 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 61 time to evaluate : 2.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 728 MET cc_start: 0.5335 (tpt) cc_final: 0.4991 (mmt) REVERT: D 234 MET cc_start: 0.0010 (mpp) cc_final: -0.1014 (mtm) REVERT: D 1008 MET cc_start: 0.3503 (ptt) cc_final: 0.2785 (mpp) outliers start: 32 outliers final: 16 residues processed: 87 average time/residue: 0.3716 time to fit residues: 52.2246 Evaluate side-chains 66 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 2.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 805 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 975 ASN Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 128 ASN Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 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 3 optimal weight: 1.9990 chunk 161 optimal weight: 8.9990 chunk 246 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 185 optimal weight: 30.0000 chunk 12 optimal weight: 10.0000 chunk 261 optimal weight: 7.9990 chunk 188 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 214 optimal weight: 20.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 GLN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 401 ASN D 658 ASN D 780 ASN ** D1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.072420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.057738 restraints weight = 234319.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.056141 restraints weight = 197490.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.055852 restraints weight = 179082.237| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.5489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25149 Z= 0.196 Angle : 0.596 17.070 34955 Z= 0.317 Chirality : 0.039 0.202 4022 Planarity : 0.004 0.059 3683 Dihedral : 20.502 178.137 5854 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.00 % Allowed : 12.43 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.17), residues: 2412 helix: 1.39 (0.15), residues: 1177 sheet: -0.40 (0.31), residues: 271 loop : -0.48 (0.21), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 408 HIS 0.007 0.002 HIS F 163 PHE 0.016 0.002 PHE A 221 TYR 0.028 0.002 TYR C 53 ARG 0.006 0.001 ARG D 63 Details of bonding type rmsd hydrogen bonds : bond 0.04520 ( 1103) hydrogen bonds : angle 4.49112 ( 3045) covalent geometry : bond 0.00398 (25149) covalent geometry : angle 0.59612 (34955) *********************** 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 97 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 55 time to evaluate : 2.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 TYR cc_start: 0.8174 (p90) cc_final: 0.7774 (p90) REVERT: D 1008 MET cc_start: 0.3679 (ptt) cc_final: 0.3132 (mpp) outliers start: 42 outliers final: 22 residues processed: 92 average time/residue: 0.3710 time to fit residues: 55.0837 Evaluate side-chains 72 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 50 time to evaluate : 2.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 84 SER 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 957 SER Chi-restraints excluded: chain D residue 975 ASN Chi-restraints excluded: chain D residue 997 ILE Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 142 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 184 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 204 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 93 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 50 optimal weight: 20.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 557 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 ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 557 HIS ** D 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 ASN ** F 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.071809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.058027 restraints weight = 243965.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.056572 restraints weight = 180095.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.056511 restraints weight = 156190.575| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.6149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25149 Z= 0.186 Angle : 0.579 12.584 34955 Z= 0.309 Chirality : 0.038 0.232 4022 Planarity : 0.004 0.051 3683 Dihedral : 20.641 179.094 5854 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.57 % Allowed : 13.14 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.17), residues: 2412 helix: 1.38 (0.15), residues: 1180 sheet: -0.41 (0.31), residues: 276 loop : -0.53 (0.21), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 408 HIS 0.007 0.001 HIS A 890 PHE 0.024 0.002 PHE C 51 TYR 0.017 0.002 TYR A 176 ARG 0.011 0.001 ARG D 781 Details of bonding type rmsd hydrogen bonds : bond 0.04186 ( 1103) hydrogen bonds : angle 4.52507 ( 3045) covalent geometry : bond 0.00377 (25149) covalent geometry : angle 0.57866 (34955) *********************** 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 : 2.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 657 MET cc_start: 0.7183 (mmm) cc_final: 0.6787 (mmm) REVERT: D 1008 MET cc_start: 0.3836 (ptt) cc_final: 0.3384 (mpp) outliers start: 33 outliers final: 24 residues processed: 78 average time/residue: 0.3890 time to fit residues: 48.6614 Evaluate side-chains 70 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 46 time to evaluate : 2.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain A residue 805 LEU 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 D residue 957 SER Chi-restraints excluded: chain D residue 975 ASN 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 Chi-restraints excluded: chain C residue 167 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 241 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 99 optimal weight: 0.6980 chunk 235 optimal weight: 9.9990 chunk 145 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 chunk 155 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- 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 557 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 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 888 ASN D 985 ASN ** D1048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 ASN ** F 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.071322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.057782 restraints weight = 237719.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.056227 restraints weight = 175665.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.056305 restraints weight = 149674.747| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.6634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 25149 Z= 0.181 Angle : 0.577 15.952 34955 Z= 0.306 Chirality : 0.038 0.206 4022 Planarity : 0.004 0.056 3683 Dihedral : 20.583 179.282 5854 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.38 % Allowed : 13.33 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.17), residues: 2412 helix: 1.37 (0.15), residues: 1178 sheet: -0.31 (0.31), residues: 270 loop : -0.55 (0.21), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 408 HIS 0.006 0.001 HIS A 890 PHE 0.035 0.002 PHE C 51 TYR 0.019 0.002 TYR F 95 ARG 0.011 0.001 ARG C 21 Details of bonding type rmsd hydrogen bonds : bond 0.04362 ( 1103) hydrogen bonds : angle 4.50311 ( 3045) covalent geometry : bond 0.00370 (25149) covalent geometry : angle 0.57669 (34955) *********************** 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 77 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 48 time to evaluate : 2.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 996 MET cc_start: 0.8747 (tpp) cc_final: 0.8179 (mtp) REVERT: D 844 MET cc_start: -0.2942 (ptt) cc_final: -0.3472 (ptt) REVERT: D 1008 MET cc_start: 0.3629 (ptt) cc_final: 0.3330 (mpp) REVERT: F 147 TYR cc_start: 0.8444 (OUTLIER) cc_final: 0.7670 (p90) outliers start: 29 outliers final: 20 residues processed: 76 average time/residue: 0.3424 time to fit residues: 44.4644 Evaluate side-chains 67 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 46 time to evaluate : 2.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 805 LEU 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 475 ILE Chi-restraints excluded: chain D residue 775 VAL Chi-restraints excluded: chain D residue 957 SER Chi-restraints excluded: chain D residue 975 ASN 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 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 48 optimal weight: 7.9990 chunk 97 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 178 optimal weight: 0.0470 chunk 160 optimal weight: 0.4980 chunk 24 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 231 optimal weight: 9.9990 chunk 132 optimal weight: 0.0970 overall best weight: 1.5280 ------------------------------------------------------------------------------- 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 557 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 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 ASN ** F 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.072165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.057714 restraints weight = 240927.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.055892 restraints weight = 190365.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.056192 restraints weight = 174970.798| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.6661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 25149 Z= 0.116 Angle : 0.520 15.534 34955 Z= 0.275 Chirality : 0.037 0.222 4022 Planarity : 0.003 0.047 3683 Dihedral : 20.402 178.911 5854 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.10 % Allowed : 13.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.18), residues: 2412 helix: 1.59 (0.15), residues: 1179 sheet: -0.30 (0.32), residues: 264 loop : -0.42 (0.21), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 408 HIS 0.006 0.001 HIS D 890 PHE 0.026 0.001 PHE C 51 TYR 0.017 0.001 TYR A 809 ARG 0.011 0.001 ARG A 499 Details of bonding type rmsd hydrogen bonds : bond 0.03492 ( 1103) hydrogen bonds : angle 4.32519 ( 3045) covalent geometry : bond 0.00238 (25149) covalent geometry : angle 0.52027 (34955) *********************** 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 73 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 50 time to evaluate : 2.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 MET cc_start: 0.7906 (mmt) cc_final: 0.7596 (mmp) REVERT: A 657 MET cc_start: 0.7294 (mmm) cc_final: 0.7045 (mmm) REVERT: A 996 MET cc_start: 0.8668 (tpp) cc_final: 0.8130 (mtp) REVERT: D 844 MET cc_start: -0.3084 (ptt) cc_final: -0.3604 (ptt) REVERT: D 1008 MET cc_start: 0.3642 (ptt) cc_final: 0.3371 (mpp) REVERT: C 135 GLU cc_start: 0.9269 (OUTLIER) cc_final: 0.8927 (tm-30) outliers start: 23 outliers final: 20 residues processed: 69 average time/residue: 0.3481 time to fit residues: 41.0183 Evaluate side-chains 69 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 48 time to evaluate : 3.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 283 ILE 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 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 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 8 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 135 optimal weight: 30.0000 chunk 27 optimal weight: 7.9990 chunk 242 optimal weight: 10.0000 chunk 174 optimal weight: 30.0000 chunk 6 optimal weight: 4.9990 chunk 221 optimal weight: 20.0000 chunk 93 optimal weight: 6.9990 chunk 248 optimal weight: 0.2980 chunk 217 optimal weight: 40.0000 overall best weight: 4.0586 ------------------------------------------------------------------------------- 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 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1025 GLN ** D 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 888 ASN ** D1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 ASN ** F 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.070709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.057072 restraints weight = 245202.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.055739 restraints weight = 174945.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.055469 restraints weight = 178464.495| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.7294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.127 25149 Z= 0.204 Angle : 0.612 15.107 34955 Z= 0.321 Chirality : 0.039 0.266 4022 Planarity : 0.004 0.068 3683 Dihedral : 20.583 179.401 5854 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.29 % Allowed : 13.62 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.17), residues: 2412 helix: 1.39 (0.15), residues: 1175 sheet: -0.23 (0.32), residues: 252 loop : -0.64 (0.20), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 408 HIS 0.009 0.001 HIS A 890 PHE 0.020 0.002 PHE C 51 TYR 0.022 0.002 TYR F 95 ARG 0.011 0.001 ARG A 499 Details of bonding type rmsd hydrogen bonds : bond 0.04668 ( 1103) hydrogen bonds : angle 4.57898 ( 3045) covalent geometry : bond 0.00422 (25149) covalent geometry : angle 0.61237 (34955) ********************** 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 76 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 49 time to evaluate : 2.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 MET cc_start: 0.8181 (mtp) cc_final: 0.7974 (mtt) REVERT: A 996 MET cc_start: 0.8765 (tpp) cc_final: 0.8211 (mtp) REVERT: D 307 GLU cc_start: 0.7278 (pm20) cc_final: 0.6706 (mt-10) REVERT: D 844 MET cc_start: -0.2963 (ptt) cc_final: -0.3509 (ptt) REVERT: D 888 ASN cc_start: 0.5695 (OUTLIER) cc_final: 0.5356 (m-40) REVERT: F 147 TYR cc_start: 0.8542 (OUTLIER) cc_final: 0.7828 (p90) REVERT: C 135 GLU cc_start: 0.9221 (OUTLIER) cc_final: 0.8858 (tm-30) outliers start: 27 outliers final: 19 residues processed: 74 average time/residue: 0.3606 time to fit residues: 44.8688 Evaluate side-chains 68 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 46 time to evaluate : 2.487 ------------------------------------------------------------------------------- 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 491 ILE Chi-restraints excluded: chain A residue 805 LEU 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 D residue 888 ASN 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 30 optimal weight: 0.9980 chunk 231 optimal weight: 2.9990 chunk 255 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 150 optimal weight: 20.0000 chunk 8 optimal weight: 4.9990 chunk 162 optimal weight: 8.9990 chunk 137 optimal weight: 50.0000 chunk 22 optimal weight: 3.9990 chunk 196 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 888 ASN ** D1048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 ASN F 163 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.070562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.056318 restraints weight = 245492.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.055133 restraints weight = 175284.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.054848 restraints weight = 161770.145| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.7568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25149 Z= 0.189 Angle : 0.593 14.681 34955 Z= 0.311 Chirality : 0.039 0.436 4022 Planarity : 0.004 0.071 3683 Dihedral : 20.572 178.992 5854 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.14 % Allowed : 13.95 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.17), residues: 2412 helix: 1.36 (0.15), residues: 1177 sheet: -0.34 (0.33), residues: 246 loop : -0.59 (0.20), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 223 HIS 0.006 0.001 HIS A 890 PHE 0.018 0.002 PHE C 51 TYR 0.025 0.002 TYR F 66 ARG 0.010 0.001 ARG A 499 Details of bonding type rmsd hydrogen bonds : bond 0.04304 ( 1103) hydrogen bonds : angle 4.57615 ( 3045) covalent geometry : bond 0.00383 (25149) covalent geometry : angle 0.59250 (34955) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7119.66 seconds wall clock time: 126 minutes 39.23 seconds (7599.23 seconds total)