Starting phenix.real_space_refine on Mon May 4 09:58:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vls_65166/05_2026/9vls_65166.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vls_65166/05_2026/9vls_65166.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vls_65166/05_2026/9vls_65166.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vls_65166/05_2026/9vls_65166.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vls_65166/05_2026/9vls_65166.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vls_65166/05_2026/9vls_65166.map" } resolution = 4.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.022 sd= 0.307 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: 4 Type Number sf(0) Gaussians S 87 5.16 5 C 12354 2.51 5 N 3288 2.21 5 O 3843 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 130 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19572 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3304 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 16, 'TRANS': 412} Chain breaks: 1 Chain: "G" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1590 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 11, 'TRANS': 201} Chain breaks: 1 Chain: "H" Number of atoms: 1574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1574 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 15, 'TRANS': 195} Chain: "B" Number of atoms: 3304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3304 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 16, 'TRANS': 412} Chain breaks: 1 Chain: "I" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1590 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 11, 'TRANS': 201} Chain breaks: 1 Chain: "J" Number of atoms: 1574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1574 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 15, 'TRANS': 195} Chain: "C" Number of atoms: 3304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3304 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 16, 'TRANS': 412} Chain breaks: 1 Chain: "K" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1590 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 11, 'TRANS': 201} Chain breaks: 1 Chain: "L" Number of atoms: 1574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1574 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 15, 'TRANS': 195} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.41, per 1000 atoms: 0.23 Number of scatterers: 19572 At special positions: 0 Unit cell: (154.712, 151.916, 255.368, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 87 16.00 O 3843 8.00 N 3288 7.00 C 12354 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 148 " - pdb=" SG CYS G 204 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 90 " distance=2.03 Simple disulfide: pdb=" SG CYS H 138 " - pdb=" SG CYS H 197 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 148 " - pdb=" SG CYS I 204 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 90 " distance=2.03 Simple disulfide: pdb=" SG CYS J 138 " - pdb=" SG CYS J 197 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 148 " - pdb=" SG CYS K 204 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 138 " - pdb=" SG CYS L 197 " distance=2.03 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 709 " " NAG A1302 " - " ASN A1074 " " NAG A1303 " - " ASN A1098 " " NAG A1304 " - " ASN A1134 " " NAG B1301 " - " ASN B 709 " " NAG B1302 " - " ASN B1074 " " NAG B1303 " - " ASN B1098 " " NAG B1304 " - " ASN B1134 " " NAG C1301 " - " ASN C 709 " " NAG C1302 " - " ASN C1074 " " NAG C1303 " - " ASN C1098 " " NAG C1304 " - " ASN C1134 " Time building additional restraints: 1.79 Conformation dependent library (CDL) restraints added in 895.7 milliseconds 5058 Ramachandran restraints generated. 2529 Oldfield, 0 Emsley, 2529 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4722 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 45 sheets defined 29.3% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 703 through 708 removed outlier: 3.566A pdb=" N SER A 708 " --> pdb=" O VAL A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.893A pdb=" N CYS A 743 " --> pdb=" O THR A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.676A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 769 removed outlier: 3.515A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 823 removed outlier: 3.661A pdb=" N ILE A 818 " --> pdb=" O LYS A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 842 Processing helix chain 'A' and resid 844 through 850 removed outlier: 3.718A pdb=" N ARG A 847 " --> pdb=" O ILE A 844 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP A 848 " --> pdb=" O ALA A 845 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 849 " --> pdb=" O ALA A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 895 through 1032 removed outlier: 3.577A pdb=" N ALA A 899 " --> pdb=" O GLN A 895 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET A 902 " --> pdb=" O PHE A 898 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER A1003 " --> pdb=" O GLY A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'G' and resid 161 through 165 removed outlier: 3.688A pdb=" N SER G 164 " --> pdb=" O SER G 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 198 removed outlier: 3.523A pdb=" N GLY G 198 " --> pdb=" O SER G 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 195 through 198' Processing helix chain 'H' and resid 25 through 30 Processing helix chain 'H' and resid 125 through 130 Processing helix chain 'H' and resid 185 through 192 Processing helix chain 'B' and resid 703 through 708 removed outlier: 3.522A pdb=" N SER B 708 " --> pdb=" O VAL B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.916A pdb=" N CYS B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.682A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 769 Processing helix chain 'B' and resid 814 through 823 removed outlier: 3.667A pdb=" N ILE B 818 " --> pdb=" O LYS B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 842 Processing helix chain 'B' and resid 844 through 850 removed outlier: 3.704A pdb=" N ARG B 847 " --> pdb=" O ILE B 844 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP B 848 " --> pdb=" O ALA B 845 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU B 849 " --> pdb=" O ALA B 846 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 895 through 1032 removed outlier: 3.550A pdb=" N ALA B 899 " --> pdb=" O GLN B 895 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER B1003 " --> pdb=" O GLY B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'I' and resid 161 through 165 removed outlier: 3.671A pdb=" N SER I 164 " --> pdb=" O SER I 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 198 removed outlier: 3.507A pdb=" N GLY I 198 " --> pdb=" O SER I 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 195 through 198' Processing helix chain 'J' and resid 25 through 30 Processing helix chain 'J' and resid 125 through 130 Processing helix chain 'J' and resid 185 through 192 Processing helix chain 'C' and resid 703 through 708 removed outlier: 3.558A pdb=" N SER C 708 " --> pdb=" O VAL C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.878A pdb=" N CYS C 743 " --> pdb=" O THR C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.687A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 769 removed outlier: 3.511A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 823 removed outlier: 3.674A pdb=" N ILE C 818 " --> pdb=" O LYS C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 842 Processing helix chain 'C' and resid 844 through 850 removed outlier: 3.699A pdb=" N ARG C 847 " --> pdb=" O ILE C 844 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP C 848 " --> pdb=" O ALA C 845 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU C 849 " --> pdb=" O ALA C 846 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 895 through 1032 removed outlier: 3.585A pdb=" N ALA C 899 " --> pdb=" O GLN C 895 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N MET C 902 " --> pdb=" O PHE C 898 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER C1003 " --> pdb=" O GLY C 999 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'K' and resid 161 through 165 removed outlier: 3.666A pdb=" N SER K 164 " --> pdb=" O SER K 161 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 198 removed outlier: 3.512A pdb=" N GLY K 198 " --> pdb=" O SER K 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 195 through 198' Processing helix chain 'L' and resid 25 through 30 Processing helix chain 'L' and resid 125 through 130 Processing helix chain 'L' and resid 185 through 192 Processing sheet with id=AA1, first strand: chain 'A' and resid 712 through 718 removed outlier: 4.695A pdb=" N ILE A 712 " --> pdb=" O PHE A1075 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE A1075 " --> pdb=" O ILE A 712 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 723 through 727 removed outlier: 3.514A pdb=" N THR A 723 " --> pdb=" O HIS A1064 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL A1061 " --> pdb=" O GLN A1054 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 853 through 854 Processing sheet with id=AA4, first strand: chain 'A' and resid 1088 through 1090 Processing sheet with id=AA5, first strand: chain 'A' and resid 1094 through 1097 removed outlier: 3.711A pdb=" N GLN A1113 " --> pdb=" O VAL A1104 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 19 through 23 removed outlier: 4.079A pdb=" N SER G 78 " --> pdb=" O ASP G 73 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER G 71 " --> pdb=" O PHE G 80 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 58 through 60 removed outlier: 6.650A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR G 94 " --> pdb=" O THR G 115 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR G 115 " --> pdb=" O TYR G 94 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 128 through 132 removed outlier: 3.972A pdb=" N LEU G 146 " --> pdb=" O VAL G 190 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N CYS G 148 " --> pdb=" O SER G 188 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP G 152 " --> pdb=" O TYR G 184 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N TYR G 184 " --> pdb=" O ASP G 152 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 128 through 132 removed outlier: 3.972A pdb=" N LEU G 146 " --> pdb=" O VAL G 190 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N CYS G 148 " --> pdb=" O SER G 188 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP G 152 " --> pdb=" O TYR G 184 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N TYR G 184 " --> pdb=" O ASP G 152 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 204 through 208 Processing sheet with id=AB2, first strand: chain 'H' and resid 19 through 23 Processing sheet with id=AB3, first strand: chain 'H' and resid 48 through 51 removed outlier: 4.906A pdb=" N VAL H 48 " --> pdb=" O ARG H 39 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ARG H 39 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE H 50 " --> pdb=" O TRP H 37 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER H 36 " --> pdb=" O CYS H 91 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER H 92 " --> pdb=" O ILE H 100 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE H 100 " --> pdb=" O SER H 92 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 120 through 122 removed outlier: 3.628A pdb=" N VAL H 137 " --> pdb=" O PHE H 122 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N SER H 179 " --> pdb=" O THR H 165 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N THR H 165 " --> pdb=" O SER H 179 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N TYR H 181 " --> pdb=" O VAL H 163 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 195 through 196 removed outlier: 4.124A pdb=" N TYR H 195 " --> pdb=" O VAL H 210 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 199 through 201 removed outlier: 3.763A pdb=" N VAL H 199 " --> pdb=" O VAL H 206 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL H 206 " --> pdb=" O VAL H 199 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 711 through 718 removed outlier: 4.492A pdb=" N ILE B 712 " --> pdb=" O PHE B1075 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE B1075 " --> pdb=" O ILE B 712 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 723 through 727 removed outlier: 3.534A pdb=" N THR B 723 " --> pdb=" O HIS B1064 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS B1064 " --> pdb=" O THR B 723 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL B1061 " --> pdb=" O GLN B1054 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 853 through 854 Processing sheet with id=AC1, first strand: chain 'B' and resid 1088 through 1090 Processing sheet with id=AC2, first strand: chain 'B' and resid 1094 through 1097 removed outlier: 3.719A pdb=" N GLN B1113 " --> pdb=" O VAL B1104 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 17 through 23 removed outlier: 3.637A pdb=" N LEU I 18 " --> pdb=" O MET I 83 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N SER I 78 " --> pdb=" O ASP I 73 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER I 71 " --> pdb=" O PHE I 80 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 58 through 60 removed outlier: 3.504A pdb=" N SER I 59 " --> pdb=" O ARG I 50 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN I 39 " --> pdb=" O LEU I 93 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR I 94 " --> pdb=" O THR I 115 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR I 115 " --> pdb=" O TYR I 94 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 128 through 132 removed outlier: 3.518A pdb=" N VAL I 192 " --> pdb=" O ALA I 144 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU I 146 " --> pdb=" O VAL I 190 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N CYS I 148 " --> pdb=" O SER I 188 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP I 152 " --> pdb=" O TYR I 184 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N TYR I 184 " --> pdb=" O ASP I 152 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 128 through 132 removed outlier: 3.518A pdb=" N VAL I 192 " --> pdb=" O ALA I 144 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU I 146 " --> pdb=" O VAL I 190 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N CYS I 148 " --> pdb=" O SER I 188 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP I 152 " --> pdb=" O TYR I 184 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N TYR I 184 " --> pdb=" O ASP I 152 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 204 through 208 removed outlier: 3.515A pdb=" N LYS I 217 " --> pdb=" O CYS I 204 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 19 through 23 Processing sheet with id=AC9, first strand: chain 'J' and resid 48 through 51 removed outlier: 4.969A pdb=" N VAL J 48 " --> pdb=" O ARG J 39 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ARG J 39 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE J 50 " --> pdb=" O TRP J 37 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER J 92 " --> pdb=" O ILE J 100 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE J 100 " --> pdb=" O SER J 92 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 120 through 122 removed outlier: 3.596A pdb=" N VAL J 137 " --> pdb=" O PHE J 122 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N TYR J 181 " --> pdb=" O GLU J 164 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU J 164 " --> pdb=" O TYR J 181 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 195 through 196 removed outlier: 4.126A pdb=" N TYR J 195 " --> pdb=" O VAL J 210 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 199 through 201 removed outlier: 3.787A pdb=" N VAL J 199 " --> pdb=" O VAL J 206 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL J 206 " --> pdb=" O VAL J 199 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 711 through 718 removed outlier: 4.538A pdb=" N ILE C 712 " --> pdb=" O PHE C1075 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE C1075 " --> pdb=" O ILE C 712 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 723 through 727 removed outlier: 3.541A pdb=" N THR C 723 " --> pdb=" O HIS C1064 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL C1061 " --> pdb=" O GLN C1054 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 853 through 854 Processing sheet with id=AD7, first strand: chain 'C' and resid 1088 through 1090 Processing sheet with id=AD8, first strand: chain 'C' and resid 1094 through 1097 removed outlier: 3.708A pdb=" N GLN C1113 " --> pdb=" O VAL C1104 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 17 through 23 removed outlier: 3.643A pdb=" N LEU K 18 " --> pdb=" O MET K 83 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SER K 78 " --> pdb=" O ASP K 73 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER K 71 " --> pdb=" O PHE K 80 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 58 through 60 removed outlier: 3.519A pdb=" N SER K 59 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 128 through 132 removed outlier: 3.985A pdb=" N LEU K 146 " --> pdb=" O VAL K 190 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N CYS K 148 " --> pdb=" O SER K 188 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP K 152 " --> pdb=" O TYR K 184 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N TYR K 184 " --> pdb=" O ASP K 152 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 128 through 132 removed outlier: 3.985A pdb=" N LEU K 146 " --> pdb=" O VAL K 190 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N CYS K 148 " --> pdb=" O SER K 188 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP K 152 " --> pdb=" O TYR K 184 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N TYR K 184 " --> pdb=" O ASP K 152 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 204 through 208 Processing sheet with id=AE5, first strand: chain 'L' and resid 19 through 23 Processing sheet with id=AE6, first strand: chain 'L' and resid 48 through 51 removed outlier: 4.979A pdb=" N VAL L 48 " --> pdb=" O ARG L 39 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ARG L 39 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE L 50 " --> pdb=" O TRP L 37 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER L 36 " --> pdb=" O CYS L 91 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER L 92 " --> pdb=" O ILE L 100 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE L 100 " --> pdb=" O SER L 92 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 120 through 122 removed outlier: 3.636A pdb=" N VAL L 137 " --> pdb=" O PHE L 122 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N SER L 179 " --> pdb=" O THR L 165 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N THR L 165 " --> pdb=" O SER L 179 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N TYR L 181 " --> pdb=" O VAL L 163 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 195 through 196 removed outlier: 4.097A pdb=" N TYR L 195 " --> pdb=" O VAL L 210 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 199 through 201 removed outlier: 3.734A pdb=" N VAL L 199 " --> pdb=" O VAL L 206 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL L 206 " --> pdb=" O VAL L 199 " (cutoff:3.500A) 824 hydrogen bonds defined for protein. 2292 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.29 Time building geometry restraints manager: 2.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6325 1.34 - 1.46: 4389 1.46 - 1.58: 9143 1.58 - 1.69: 0 1.69 - 1.81: 117 Bond restraints: 19974 Sorted by residual: bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.04e+00 bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.04e+00 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 2.01e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.99e+00 ... (remaining 19969 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.06: 26344 1.06 - 2.12: 587 2.12 - 3.19: 185 3.19 - 4.25: 26 4.25 - 5.31: 14 Bond angle restraints: 27156 Sorted by residual: angle pdb=" N ILE C 834 " pdb=" CA ILE C 834 " pdb=" C ILE C 834 " ideal model delta sigma weight residual 111.62 109.77 1.85 7.90e-01 1.60e+00 5.47e+00 angle pdb=" C VAL L 53 " pdb=" N ASN L 54 " pdb=" CA ASN L 54 " ideal model delta sigma weight residual 125.66 129.97 -4.31 1.85e+00 2.92e-01 5.43e+00 angle pdb=" C VAL J 53 " pdb=" N ASN J 54 " pdb=" CA ASN J 54 " ideal model delta sigma weight residual 125.66 129.95 -4.29 1.85e+00 2.92e-01 5.38e+00 angle pdb=" C VAL H 53 " pdb=" N ASN H 54 " pdb=" CA ASN H 54 " ideal model delta sigma weight residual 125.66 129.91 -4.25 1.85e+00 2.92e-01 5.27e+00 angle pdb=" N ILE A 794 " pdb=" CA ILE A 794 " pdb=" C ILE A 794 " ideal model delta sigma weight residual 112.98 110.15 2.83 1.25e+00 6.40e-01 5.12e+00 ... (remaining 27151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 11644 17.76 - 35.51: 438 35.51 - 53.27: 64 53.27 - 71.03: 4 71.03 - 88.79: 3 Dihedral angle restraints: 12153 sinusoidal: 4791 harmonic: 7362 Sorted by residual: dihedral pdb=" CB GLU J 164 " pdb=" CG GLU J 164 " pdb=" CD GLU J 164 " pdb=" OE1 GLU J 164 " ideal model delta sinusoidal sigma weight residual 0.00 -88.79 88.79 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB GLU L 164 " pdb=" CG GLU L 164 " pdb=" CD GLU L 164 " pdb=" OE1 GLU L 164 " ideal model delta sinusoidal sigma weight residual 0.00 -88.78 88.78 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB GLU H 164 " pdb=" CG GLU H 164 " pdb=" CD GLU H 164 " pdb=" OE1 GLU H 164 " ideal model delta sinusoidal sigma weight residual 0.00 -88.55 88.55 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 12150 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2217 0.034 - 0.068: 636 0.068 - 0.102: 248 0.102 - 0.136: 71 0.136 - 0.170: 2 Chirality restraints: 3174 Sorted by residual: chirality pdb=" C2 NAG C1302 " pdb=" C1 NAG C1302 " pdb=" C3 NAG C1302 " pdb=" N2 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.49 -2.32 -0.17 2.00e-01 2.50e+01 7.25e-01 chirality pdb=" C2 NAG B1302 " pdb=" C1 NAG B1302 " pdb=" C3 NAG B1302 " pdb=" N2 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.49 -2.32 -0.17 2.00e-01 2.50e+01 7.08e-01 chirality pdb=" CA ILE H 100 " pdb=" N ILE H 100 " pdb=" C ILE H 100 " pdb=" CB ILE H 100 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.02e-01 ... (remaining 3171 not shown) Planarity restraints: 3486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B1111 " -0.022 5.00e-02 4.00e+02 3.34e-02 1.79e+00 pdb=" N PRO B1112 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO B1112 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B1112 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C1111 " -0.022 5.00e-02 4.00e+02 3.33e-02 1.77e+00 pdb=" N PRO C1112 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO C1112 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C1112 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A1111 " 0.022 5.00e-02 4.00e+02 3.32e-02 1.76e+00 pdb=" N PRO A1112 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A1112 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A1112 " 0.018 5.00e-02 4.00e+02 ... (remaining 3483 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4152 2.78 - 3.31: 19294 3.31 - 3.84: 31973 3.84 - 4.37: 35109 4.37 - 4.90: 61697 Nonbonded interactions: 152225 Sorted by model distance: nonbonded pdb=" OG1 THR A1105 " pdb=" O PHE A1109 " model vdw 2.254 3.040 nonbonded pdb=" OG1 THR C1105 " pdb=" O PHE C1109 " model vdw 2.261 3.040 nonbonded pdb=" OG1 THR B1105 " pdb=" O PHE B1109 " model vdw 2.261 3.040 nonbonded pdb=" O VAL J 53 " pdb=" ND2 ASN J 54 " model vdw 2.265 3.120 nonbonded pdb=" O VAL L 53 " pdb=" ND2 ASN L 54 " model vdw 2.267 3.120 ... (remaining 152220 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 17.970 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 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 : 0.002 0.042 20013 Z= 0.102 Angle : 0.434 5.311 27246 Z= 0.228 Chirality : 0.039 0.170 3174 Planarity : 0.003 0.033 3474 Dihedral : 8.697 88.785 7350 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 5.14 % Allowed : 6.38 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.16), residues: 2529 helix: 1.08 (0.19), residues: 747 sheet: -1.36 (0.21), residues: 528 loop : -3.15 (0.15), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 995 TYR 0.006 0.000 TYR C1067 PHE 0.004 0.001 PHE C 718 TRP 0.003 0.000 TRP I 36 HIS 0.001 0.000 HIS K 35 Details of bonding type rmsd covalent geometry : bond 0.00200 (19974) covalent geometry : angle 0.43365 (27156) SS BOND : bond 0.00169 ( 27) SS BOND : angle 0.49098 ( 54) hydrogen bonds : bond 0.19849 ( 789) hydrogen bonds : angle 6.75391 ( 2292) link_NAG-ASN : bond 0.00165 ( 12) link_NAG-ASN : angle 0.79669 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5058 Ramachandran restraints generated. 2529 Oldfield, 0 Emsley, 2529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5058 Ramachandran restraints generated. 2529 Oldfield, 0 Emsley, 2529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 543 time to evaluate : 0.784 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 844 ILE cc_start: 0.7034 (mt) cc_final: 0.6542 (mm) REVERT: A 900 MET cc_start: 0.6770 (mmt) cc_final: 0.5669 (mmt) REVERT: A 921 LYS cc_start: 0.9107 (mtmm) cc_final: 0.8704 (mtmm) REVERT: A 990 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7827 (mt-10) REVERT: G 6 GLU cc_start: 0.6184 (pp20) cc_final: 0.5556 (pm20) REVERT: G 54 ASP cc_start: 0.8344 (p0) cc_final: 0.8004 (p0) REVERT: G 107 ASP cc_start: 0.7833 (m-30) cc_final: 0.7619 (m-30) REVERT: H 34 PHE cc_start: 0.7666 (m-80) cc_final: 0.7343 (m-10) REVERT: H 93 TYR cc_start: 0.7451 (t80) cc_final: 0.7167 (t80) REVERT: H 112 GLN cc_start: 0.7189 (OUTLIER) cc_final: 0.6902 (pm20) REVERT: B 739 THR cc_start: 0.8283 (m) cc_final: 0.7950 (m) REVERT: B 745 ASP cc_start: 0.7589 (m-30) cc_final: 0.7143 (m-30) REVERT: B 900 MET cc_start: 0.7444 (mmt) cc_final: 0.6736 (mmt) REVERT: B 933 LYS cc_start: 0.8650 (mmmm) cc_final: 0.8150 (mmmm) REVERT: I 5 VAL cc_start: 0.8500 (OUTLIER) cc_final: 0.8172 (m) REVERT: I 6 GLU cc_start: 0.6797 (pp20) cc_final: 0.6235 (pm20) REVERT: I 27 PHE cc_start: 0.8150 (p90) cc_final: 0.7906 (p90) REVERT: I 54 ASP cc_start: 0.8653 (p0) cc_final: 0.8138 (p0) REVERT: I 64 VAL cc_start: 0.6746 (OUTLIER) cc_final: 0.6266 (p) REVERT: I 107 ASP cc_start: 0.8103 (m-30) cc_final: 0.7839 (m-30) REVERT: J 28 ASP cc_start: 0.8259 (m-30) cc_final: 0.7825 (m-30) REVERT: J 181 TYR cc_start: 0.6733 (m-80) cc_final: 0.6508 (m-10) REVERT: C 739 THR cc_start: 0.8501 (m) cc_final: 0.8178 (m) REVERT: C 745 ASP cc_start: 0.8008 (m-30) cc_final: 0.7101 (m-30) REVERT: C 828 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7027 (tm) REVERT: C 900 MET cc_start: 0.7255 (mmt) cc_final: 0.6567 (mmt) REVERT: C 933 LYS cc_start: 0.8703 (mmmm) cc_final: 0.8035 (mmmm) REVERT: C 990 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8172 (pt0) REVERT: K 54 ASP cc_start: 0.8543 (p0) cc_final: 0.8199 (p0) REVERT: K 107 ASP cc_start: 0.7952 (m-30) cc_final: 0.7750 (m-30) outliers start: 112 outliers final: 19 residues processed: 629 average time/residue: 0.1695 time to fit residues: 155.3014 Evaluate side-chains 370 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 347 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 247 optimal weight: 9.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 872 GLN ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A 992 GLN A1011 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1108 ASN A1135 ASN G 13 GLN ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 179 GLN G 205 ASN H 16 GLN H 130 GLN ** H 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 872 GLN B 949 GLN B 957 GLN B 992 GLN B1011 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1108 ASN B1135 ASN I 13 GLN I 179 GLN I 205 ASN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 16 GLN J 130 GLN ** J 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 872 GLN ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C 992 GLN C1011 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1108 ASN C1135 ASN K 13 GLN K 113 GLN K 179 GLN K 205 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 16 GLN L 130 GLN ** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.081779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.058419 restraints weight = 123527.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.060754 restraints weight = 87027.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.060306 restraints weight = 63127.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.060763 restraints weight = 60959.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.060773 restraints weight = 58048.969| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.136 20013 Z= 0.449 Angle : 0.908 9.841 27246 Z= 0.474 Chirality : 0.052 0.311 3174 Planarity : 0.006 0.084 3474 Dihedral : 5.987 57.661 2967 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 23.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 0.05 % Allowed : 5.51 % Favored : 94.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.16), residues: 2529 helix: 1.02 (0.19), residues: 735 sheet: -1.73 (0.19), residues: 615 loop : -2.65 (0.17), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG I 76 TYR 0.030 0.003 TYR I 95 PHE 0.032 0.003 PHE H 143 TRP 0.015 0.003 TRP K 36 HIS 0.010 0.002 HIS J 201 Details of bonding type rmsd covalent geometry : bond 0.00953 (19974) covalent geometry : angle 0.89507 (27156) SS BOND : bond 0.00892 ( 27) SS BOND : angle 1.95462 ( 54) hydrogen bonds : bond 0.05564 ( 789) hydrogen bonds : angle 5.79900 ( 2292) link_NAG-ASN : bond 0.00417 ( 12) link_NAG-ASN : angle 3.78758 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5058 Ramachandran restraints generated. 2529 Oldfield, 0 Emsley, 2529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5058 Ramachandran restraints generated. 2529 Oldfield, 0 Emsley, 2529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 432 time to evaluate : 0.791 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 853 GLN cc_start: 0.8192 (tm-30) cc_final: 0.7885 (tm-30) REVERT: A 866 THR cc_start: 0.9361 (p) cc_final: 0.9032 (p) REVERT: A 900 MET cc_start: 0.7269 (mmt) cc_final: 0.6393 (mmt) REVERT: A 902 MET cc_start: 0.9488 (mtm) cc_final: 0.9283 (mtm) REVERT: A 905 ARG cc_start: 0.8823 (mtp-110) cc_final: 0.8392 (mtp-110) REVERT: A 986 LYS cc_start: 0.8744 (tppt) cc_final: 0.8462 (tppp) REVERT: A 1038 LYS cc_start: 0.9083 (mppt) cc_final: 0.8768 (mppt) REVERT: G 5 VAL cc_start: 0.8447 (m) cc_final: 0.8164 (m) REVERT: G 27 PHE cc_start: 0.8425 (p90) cc_final: 0.8203 (p90) REVERT: G 30 LYS cc_start: 0.9048 (tmmt) cc_final: 0.8553 (mmmm) REVERT: G 31 ASP cc_start: 0.8807 (p0) cc_final: 0.8474 (p0) REVERT: G 54 ASP cc_start: 0.9126 (p0) cc_final: 0.8589 (p0) REVERT: G 107 ASP cc_start: 0.8278 (m-30) cc_final: 0.7355 (m-30) REVERT: G 172 HIS cc_start: 0.8494 (t70) cc_final: 0.8223 (t70) REVERT: G 174 PHE cc_start: 0.7474 (m-80) cc_final: 0.7273 (m-80) REVERT: H 51 TYR cc_start: 0.6312 (p90) cc_final: 0.5511 (p90) REVERT: H 52 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7177 (mp0) REVERT: H 100 ILE cc_start: 0.8912 (mp) cc_final: 0.8711 (mm) REVERT: H 139 LEU cc_start: 0.7602 (mt) cc_final: 0.7393 (mt) REVERT: H 181 TYR cc_start: 0.8764 (m-10) cc_final: 0.8397 (m-10) REVERT: B 853 GLN cc_start: 0.8238 (tm-30) cc_final: 0.7923 (tm-30) REVERT: B 900 MET cc_start: 0.7798 (mmt) cc_final: 0.6889 (mmt) REVERT: B 986 LYS cc_start: 0.8692 (tppt) cc_final: 0.8460 (tppp) REVERT: B 1014 ARG cc_start: 0.8800 (mmm160) cc_final: 0.8583 (mmm-85) REVERT: B 1048 HIS cc_start: 0.6344 (t70) cc_final: 0.5963 (t70) REVERT: B 1114 ILE cc_start: 0.8531 (tp) cc_final: 0.8329 (tp) REVERT: I 5 VAL cc_start: 0.8680 (m) cc_final: 0.8311 (t) REVERT: I 6 GLU cc_start: 0.8277 (pp20) cc_final: 0.6697 (pm20) REVERT: I 27 PHE cc_start: 0.8659 (p90) cc_final: 0.8403 (p90) REVERT: I 30 LYS cc_start: 0.9146 (tmmt) cc_final: 0.8779 (tppt) REVERT: I 31 ASP cc_start: 0.8603 (p0) cc_final: 0.7965 (p0) REVERT: I 32 TYR cc_start: 0.7681 (m-10) cc_final: 0.7395 (m-10) REVERT: I 74 ASN cc_start: 0.8591 (m-40) cc_final: 0.8287 (m-40) REVERT: I 107 ASP cc_start: 0.8210 (m-30) cc_final: 0.7854 (m-30) REVERT: I 108 PHE cc_start: 0.8244 (t80) cc_final: 0.8003 (t80) REVERT: I 179 GLN cc_start: 0.9452 (pt0) cc_final: 0.9145 (pm20) REVERT: J 6 GLN cc_start: 0.8467 (tt0) cc_final: 0.8208 (tt0) REVERT: J 100 ILE cc_start: 0.8736 (mp) cc_final: 0.8452 (mm) REVERT: J 181 TYR cc_start: 0.8383 (m-80) cc_final: 0.7732 (m-10) REVERT: C 866 THR cc_start: 0.9163 (p) cc_final: 0.8933 (p) REVERT: C 900 MET cc_start: 0.7622 (mmt) cc_final: 0.7017 (mmt) REVERT: C 909 ILE cc_start: 0.9190 (mt) cc_final: 0.8964 (mt) REVERT: C 986 LYS cc_start: 0.8846 (tppt) cc_final: 0.8603 (tppp) REVERT: K 30 LYS cc_start: 0.9228 (tmmt) cc_final: 0.8750 (ttmm) REVERT: K 54 ASP cc_start: 0.9193 (p0) cc_final: 0.8830 (p0) REVERT: K 74 ASN cc_start: 0.8657 (t0) cc_final: 0.8422 (t0) REVERT: K 107 ASP cc_start: 0.8067 (m-30) cc_final: 0.7115 (m-30) REVERT: K 152 ASP cc_start: 0.9151 (t70) cc_final: 0.8911 (t70) REVERT: K 179 GLN cc_start: 0.9403 (pt0) cc_final: 0.9150 (pm20) REVERT: L 52 GLU cc_start: 0.7954 (tp30) cc_final: 0.7726 (tp30) REVERT: L 93 TYR cc_start: 0.8825 (t80) cc_final: 0.8139 (t80) outliers start: 1 outliers final: 0 residues processed: 433 average time/residue: 0.1846 time to fit residues: 113.3673 Evaluate side-chains 292 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 20 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 60 optimal weight: 10.0000 chunk 160 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 209 optimal weight: 0.9980 chunk 134 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 949 GLN A 957 GLN A 965 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 179 GLN G 205 ASN ** H 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 113 GLN I 172 HIS I 179 GLN J 16 GLN J 171 GLN ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 179 GLN L 6 GLN ** L 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 171 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.084651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.061396 restraints weight = 123725.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.063130 restraints weight = 80479.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.064121 restraints weight = 62277.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.064702 restraints weight = 53685.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.065040 restraints weight = 49351.961| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20013 Z= 0.154 Angle : 0.627 9.424 27246 Z= 0.320 Chirality : 0.044 0.204 3174 Planarity : 0.005 0.086 3474 Dihedral : 5.246 56.053 2967 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.05 % Allowed : 4.09 % Favored : 95.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.16), residues: 2529 helix: 1.72 (0.19), residues: 714 sheet: -1.29 (0.20), residues: 555 loop : -2.65 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C1014 TYR 0.034 0.002 TYR B 873 PHE 0.034 0.002 PHE A1062 TRP 0.016 0.001 TRP J 152 HIS 0.008 0.001 HIS L 82 Details of bonding type rmsd covalent geometry : bond 0.00338 (19974) covalent geometry : angle 0.61482 (27156) SS BOND : bond 0.00472 ( 27) SS BOND : angle 1.41271 ( 54) hydrogen bonds : bond 0.04147 ( 789) hydrogen bonds : angle 4.98474 ( 2292) link_NAG-ASN : bond 0.00675 ( 12) link_NAG-ASN : angle 3.07919 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5058 Ramachandran restraints generated. 2529 Oldfield, 0 Emsley, 2529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5058 Ramachandran restraints generated. 2529 Oldfield, 0 Emsley, 2529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 384 time to evaluate : 0.797 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: 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: 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 844 ILE cc_start: 0.8289 (mp) cc_final: 0.8069 (mm) REVERT: A 900 MET cc_start: 0.7075 (mmt) cc_final: 0.6126 (mmt) REVERT: A 902 MET cc_start: 0.9379 (mtm) cc_final: 0.9044 (mtm) REVERT: A 1068 VAL cc_start: 0.8550 (p) cc_final: 0.8309 (p) REVERT: G 5 VAL cc_start: 0.8421 (m) cc_final: 0.8053 (m) REVERT: G 27 PHE cc_start: 0.7881 (p90) cc_final: 0.7633 (p90) REVERT: G 31 ASP cc_start: 0.8866 (p0) cc_final: 0.8497 (p0) REVERT: G 54 ASP cc_start: 0.9053 (p0) cc_final: 0.8487 (p0) REVERT: G 151 LYS cc_start: 0.9268 (ptpp) cc_final: 0.9000 (pttt) REVERT: G 172 HIS cc_start: 0.8369 (t70) cc_final: 0.8137 (t70) REVERT: G 174 PHE cc_start: 0.7637 (m-80) cc_final: 0.7431 (m-80) REVERT: H 38 TYR cc_start: 0.6247 (m-80) cc_final: 0.5893 (m-80) REVERT: H 93 TYR cc_start: 0.8791 (t80) cc_final: 0.8587 (t80) REVERT: H 100 ILE cc_start: 0.8613 (mp) cc_final: 0.8323 (mm) REVERT: H 139 LEU cc_start: 0.7519 (mt) cc_final: 0.7252 (mt) REVERT: H 181 TYR cc_start: 0.8576 (m-80) cc_final: 0.8371 (m-10) REVERT: B 844 ILE cc_start: 0.7640 (mm) cc_final: 0.7410 (mm) REVERT: B 900 MET cc_start: 0.7683 (mmt) cc_final: 0.7030 (mmt) REVERT: B 990 GLU cc_start: 0.7966 (pt0) cc_final: 0.7758 (pp20) REVERT: B 1048 HIS cc_start: 0.5812 (t70) cc_final: 0.5514 (t70) REVERT: I 27 PHE cc_start: 0.8220 (p90) cc_final: 0.7909 (p90) REVERT: I 54 ASP cc_start: 0.9119 (p0) cc_final: 0.8644 (p0) REVERT: I 107 ASP cc_start: 0.8239 (m-30) cc_final: 0.8003 (m-30) REVERT: I 152 ASP cc_start: 0.9223 (m-30) cc_final: 0.8692 (t70) REVERT: J 100 ILE cc_start: 0.8538 (mp) cc_final: 0.8335 (mm) REVERT: J 181 TYR cc_start: 0.8067 (m-80) cc_final: 0.7174 (m-10) REVERT: C 725 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7795 (tm-30) REVERT: C 900 MET cc_start: 0.7372 (mmt) cc_final: 0.6651 (mmt) REVERT: C 986 LYS cc_start: 0.8802 (tppt) cc_final: 0.8528 (tppp) REVERT: C 1052 PHE cc_start: 0.8119 (m-10) cc_final: 0.7886 (m-10) REVERT: K 30 LYS cc_start: 0.9099 (tmmt) cc_final: 0.8741 (ttmm) REVERT: K 31 ASP cc_start: 0.8801 (p0) cc_final: 0.7631 (p0) REVERT: K 54 ASP cc_start: 0.9074 (p0) cc_final: 0.8550 (p0) REVERT: K 74 ASN cc_start: 0.8227 (t0) cc_final: 0.7735 (t0) REVERT: K 152 ASP cc_start: 0.8872 (t70) cc_final: 0.8645 (t70) REVERT: K 179 GLN cc_start: 0.9284 (pt0) cc_final: 0.8948 (mp10) REVERT: L 89 TYR cc_start: 0.7663 (m-80) cc_final: 0.7420 (m-10) REVERT: L 93 TYR cc_start: 0.8719 (t80) cc_final: 0.8519 (t80) REVERT: L 152 TRP cc_start: 0.5117 (m100) cc_final: 0.4372 (m100) outliers start: 1 outliers final: 0 residues processed: 384 average time/residue: 0.1861 time to fit residues: 101.3439 Evaluate side-chains 289 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 78 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 149 optimal weight: 7.9990 chunk 163 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 217 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 208 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 179 GLN ** H 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 ASN B 957 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 172 HIS I 179 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 179 GLN ** L 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.083908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.060322 restraints weight = 122553.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.062108 restraints weight = 80852.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.063144 restraints weight = 62679.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.063674 restraints weight = 53955.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.064056 restraints weight = 49692.549| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.4871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 20013 Z= 0.171 Angle : 0.627 9.068 27246 Z= 0.320 Chirality : 0.044 0.213 3174 Planarity : 0.005 0.100 3474 Dihedral : 5.168 56.078 2967 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 0.05 % Allowed : 3.49 % Favored : 96.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.17), residues: 2529 helix: 1.74 (0.20), residues: 735 sheet: -1.35 (0.20), residues: 591 loop : -2.64 (0.16), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 905 TYR 0.031 0.002 TYR A 873 PHE 0.025 0.002 PHE L 143 TRP 0.013 0.001 TRP J 152 HIS 0.006 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00381 (19974) covalent geometry : angle 0.61659 (27156) SS BOND : bond 0.00469 ( 27) SS BOND : angle 1.45497 ( 54) hydrogen bonds : bond 0.03999 ( 789) hydrogen bonds : angle 4.74422 ( 2292) link_NAG-ASN : bond 0.00553 ( 12) link_NAG-ASN : angle 2.79388 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5058 Ramachandran restraints generated. 2529 Oldfield, 0 Emsley, 2529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5058 Ramachandran restraints generated. 2529 Oldfield, 0 Emsley, 2529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 357 time to evaluate : 0.726 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.7185 (mmt) cc_final: 0.6313 (mmt) REVERT: A 902 MET cc_start: 0.9448 (mtm) cc_final: 0.9125 (mtm) REVERT: A 1068 VAL cc_start: 0.8675 (p) cc_final: 0.8345 (p) REVERT: G 3 GLN cc_start: 0.7707 (pp30) cc_final: 0.7446 (pp30) REVERT: G 5 VAL cc_start: 0.8543 (m) cc_final: 0.8026 (m) REVERT: G 27 PHE cc_start: 0.8241 (p90) cc_final: 0.7941 (p90) REVERT: G 30 LYS cc_start: 0.8865 (tptm) cc_final: 0.8416 (mmmm) REVERT: G 31 ASP cc_start: 0.8930 (p0) cc_final: 0.8404 (p0) REVERT: G 54 ASP cc_start: 0.9192 (p0) cc_final: 0.8665 (p0) REVERT: G 69 ILE cc_start: 0.8827 (mm) cc_final: 0.8582 (tp) REVERT: G 151 LYS cc_start: 0.9182 (ptpp) cc_final: 0.8934 (pttt) REVERT: H 38 TYR cc_start: 0.6264 (m-80) cc_final: 0.5924 (m-80) REVERT: H 52 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7624 (tp30) REVERT: H 100 ILE cc_start: 0.8660 (mp) cc_final: 0.8390 (mm) REVERT: H 139 LEU cc_start: 0.7560 (mt) cc_final: 0.7297 (mt) REVERT: H 181 TYR cc_start: 0.8703 (m-80) cc_final: 0.8439 (m-10) REVERT: B 725 GLU cc_start: 0.8298 (tm-30) cc_final: 0.7957 (tm-30) REVERT: B 866 THR cc_start: 0.9405 (p) cc_final: 0.9051 (p) REVERT: B 900 MET cc_start: 0.7776 (mmt) cc_final: 0.6845 (mmt) REVERT: B 990 GLU cc_start: 0.8099 (pt0) cc_final: 0.7776 (pp20) REVERT: I 27 PHE cc_start: 0.8494 (p90) cc_final: 0.8200 (p90) REVERT: I 30 LYS cc_start: 0.9216 (tmmt) cc_final: 0.8762 (ttmm) REVERT: I 31 ASP cc_start: 0.8894 (p0) cc_final: 0.7854 (p0) REVERT: I 152 ASP cc_start: 0.9348 (m-30) cc_final: 0.8769 (t70) REVERT: I 179 GLN cc_start: 0.9488 (pt0) cc_final: 0.8974 (mp10) REVERT: J 47 LYS cc_start: 0.9004 (tmtt) cc_final: 0.8708 (tptp) REVERT: J 52 GLU cc_start: 0.8332 (tp30) cc_final: 0.8115 (tp30) REVERT: J 100 ILE cc_start: 0.8635 (mp) cc_final: 0.8401 (mm) REVERT: J 181 TYR cc_start: 0.8183 (m-80) cc_final: 0.7421 (m-10) REVERT: C 869 MET cc_start: 0.9158 (ttp) cc_final: 0.8796 (ttp) REVERT: C 900 MET cc_start: 0.7353 (mmt) cc_final: 0.6687 (mmt) REVERT: C 986 LYS cc_start: 0.8856 (tppt) cc_final: 0.8508 (tppp) REVERT: K 31 ASP cc_start: 0.8887 (p0) cc_final: 0.7851 (p0) REVERT: K 54 ASP cc_start: 0.9235 (p0) cc_final: 0.8756 (p0) outliers start: 1 outliers final: 0 residues processed: 358 average time/residue: 0.1887 time to fit residues: 96.3729 Evaluate side-chains 281 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 137 optimal weight: 4.9990 chunk 244 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 117 optimal weight: 0.0870 chunk 29 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 146 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 166 optimal weight: 9.9990 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A1002 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 179 GLN B 872 GLN ** B 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 ASN B 957 GLN B 965 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 172 HIS ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 179 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.079636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.055957 restraints weight = 121855.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.057750 restraints weight = 78625.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.058792 restraints weight = 60198.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.059382 restraints weight = 51406.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.059725 restraints weight = 47027.568| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.5681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 20013 Z= 0.337 Angle : 0.769 9.044 27246 Z= 0.401 Chirality : 0.047 0.215 3174 Planarity : 0.006 0.069 3474 Dihedral : 5.718 54.604 2967 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 22.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer: Outliers : 0.14 % Allowed : 3.90 % Favored : 95.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.16), residues: 2529 helix: 1.56 (0.19), residues: 684 sheet: -1.40 (0.20), residues: 621 loop : -2.61 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 905 TYR 0.026 0.003 TYR B 873 PHE 0.021 0.002 PHE I 108 TRP 0.014 0.002 TRP L 152 HIS 0.010 0.002 HIS A1101 Details of bonding type rmsd covalent geometry : bond 0.00716 (19974) covalent geometry : angle 0.75873 (27156) SS BOND : bond 0.01101 ( 27) SS BOND : angle 1.99839 ( 54) hydrogen bonds : bond 0.04786 ( 789) hydrogen bonds : angle 5.17493 ( 2292) link_NAG-ASN : bond 0.00648 ( 12) link_NAG-ASN : angle 2.81017 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5058 Ramachandran restraints generated. 2529 Oldfield, 0 Emsley, 2529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5058 Ramachandran restraints generated. 2529 Oldfield, 0 Emsley, 2529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 350 time to evaluate : 0.749 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 765 ARG cc_start: 0.8769 (ptp90) cc_final: 0.8319 (ptp90) REVERT: A 900 MET cc_start: 0.7173 (mmt) cc_final: 0.6260 (mmt) REVERT: A 1038 LYS cc_start: 0.9098 (mppt) cc_final: 0.8885 (mppt) REVERT: A 1068 VAL cc_start: 0.8749 (p) cc_final: 0.8510 (p) REVERT: G 30 LYS cc_start: 0.8870 (tptm) cc_final: 0.8490 (mmmm) REVERT: G 31 ASP cc_start: 0.8971 (p0) cc_final: 0.8159 (p0) REVERT: G 54 ASP cc_start: 0.9202 (p0) cc_final: 0.8689 (p0) REVERT: G 69 ILE cc_start: 0.8756 (mm) cc_final: 0.8502 (tp) REVERT: G 151 LYS cc_start: 0.9199 (ptpp) cc_final: 0.8958 (pttt) REVERT: H 38 TYR cc_start: 0.6329 (m-80) cc_final: 0.6033 (m-80) REVERT: H 100 ILE cc_start: 0.8947 (mp) cc_final: 0.8676 (mm) REVERT: H 139 LEU cc_start: 0.7221 (mt) cc_final: 0.6897 (mt) REVERT: H 176 TYR cc_start: 0.8404 (m-80) cc_final: 0.8151 (m-80) REVERT: B 819 GLU cc_start: 0.6942 (pp20) cc_final: 0.6670 (tm-30) REVERT: B 900 MET cc_start: 0.7814 (mmt) cc_final: 0.6932 (mmt) REVERT: B 902 MET cc_start: 0.9134 (mtm) cc_final: 0.8870 (mtt) REVERT: B 1031 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7740 (tm-30) REVERT: B 1041 ASP cc_start: 0.8186 (t70) cc_final: 0.7964 (t0) REVERT: I 27 PHE cc_start: 0.8546 (p90) cc_final: 0.8306 (p90) REVERT: I 30 LYS cc_start: 0.9120 (tmmt) cc_final: 0.8548 (tptp) REVERT: I 152 ASP cc_start: 0.9331 (m-30) cc_final: 0.8854 (t70) REVERT: J 29 ILE cc_start: 0.9103 (mt) cc_final: 0.8859 (mp) REVERT: J 47 LYS cc_start: 0.9008 (tmtt) cc_final: 0.8760 (tmtt) REVERT: J 100 ILE cc_start: 0.8852 (mp) cc_final: 0.8577 (mm) REVERT: J 181 TYR cc_start: 0.8369 (m-80) cc_final: 0.7774 (m-10) REVERT: C 865 LEU cc_start: 0.8458 (mp) cc_final: 0.7858 (mp) REVERT: C 869 MET cc_start: 0.9190 (ttp) cc_final: 0.8933 (ttm) REVERT: C 872 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8699 (pm20) REVERT: C 900 MET cc_start: 0.7475 (mmt) cc_final: 0.6621 (mmt) REVERT: C 902 MET cc_start: 0.9310 (mtm) cc_final: 0.9085 (mtm) REVERT: C 986 LYS cc_start: 0.8869 (tppt) cc_final: 0.8373 (tppp) REVERT: K 30 LYS cc_start: 0.9170 (tmmt) cc_final: 0.8741 (ttmm) REVERT: K 54 ASP cc_start: 0.9273 (p0) cc_final: 0.8875 (p0) REVERT: K 68 PHE cc_start: 0.7939 (m-80) cc_final: 0.7671 (m-80) REVERT: L 44 LYS cc_start: 0.9228 (mppt) cc_final: 0.9020 (mmtm) REVERT: L 96 ARG cc_start: 0.8635 (ptp90) cc_final: 0.8321 (ptp90) REVERT: L 142 ASP cc_start: 0.9311 (t0) cc_final: 0.8867 (p0) REVERT: L 181 TYR cc_start: 0.8680 (m-10) cc_final: 0.8352 (m-10) outliers start: 3 outliers final: 0 residues processed: 353 average time/residue: 0.1898 time to fit residues: 94.4326 Evaluate side-chains 281 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 280 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 108 optimal weight: 0.6980 chunk 154 optimal weight: 6.9990 chunk 220 optimal weight: 0.9980 chunk 181 optimal weight: 0.9980 chunk 207 optimal weight: 0.9980 chunk 194 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 52 optimal weight: 0.0670 chunk 177 optimal weight: 0.1980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 179 GLN G 207 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 172 HIS ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.083533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.060315 restraints weight = 121028.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.062493 restraints weight = 84935.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.063141 restraints weight = 60186.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.063481 restraints weight = 56143.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.063469 restraints weight = 49165.158| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.5515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20013 Z= 0.139 Angle : 0.656 9.042 27246 Z= 0.335 Chirality : 0.045 0.218 3174 Planarity : 0.006 0.183 3474 Dihedral : 5.176 56.234 2967 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.39 % Favored : 92.57 % Rotamer: Outliers : 0.05 % Allowed : 2.43 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.17), residues: 2529 helix: 1.83 (0.20), residues: 717 sheet: -0.95 (0.22), residues: 510 loop : -2.68 (0.16), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 87 TYR 0.033 0.002 TYR A 873 PHE 0.024 0.002 PHE A1062 TRP 0.015 0.001 TRP L 37 HIS 0.007 0.001 HIS H 201 Details of bonding type rmsd covalent geometry : bond 0.00308 (19974) covalent geometry : angle 0.64866 (27156) SS BOND : bond 0.00402 ( 27) SS BOND : angle 1.17558 ( 54) hydrogen bonds : bond 0.03852 ( 789) hydrogen bonds : angle 4.67855 ( 2292) link_NAG-ASN : bond 0.00471 ( 12) link_NAG-ASN : angle 2.54896 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5058 Ramachandran restraints generated. 2529 Oldfield, 0 Emsley, 2529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5058 Ramachandran restraints generated. 2529 Oldfield, 0 Emsley, 2529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 355 time to evaluate : 0.767 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: 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: symmetry clash REVERT: A 844 ILE cc_start: 0.7665 (mm) cc_final: 0.7416 (mp) REVERT: A 900 MET cc_start: 0.7113 (mmt) cc_final: 0.6255 (mmt) REVERT: A 902 MET cc_start: 0.9366 (mtm) cc_final: 0.8999 (mtm) REVERT: A 1052 PHE cc_start: 0.8097 (m-80) cc_final: 0.7802 (m-10) REVERT: A 1068 VAL cc_start: 0.8539 (p) cc_final: 0.8217 (p) REVERT: G 30 LYS cc_start: 0.8712 (tptm) cc_final: 0.7897 (mmmm) REVERT: G 31 ASP cc_start: 0.9018 (p0) cc_final: 0.8267 (p0) REVERT: G 54 ASP cc_start: 0.9040 (p0) cc_final: 0.8506 (p0) REVERT: G 69 ILE cc_start: 0.8543 (mm) cc_final: 0.8277 (tp) REVERT: G 107 ASP cc_start: 0.8247 (m-30) cc_final: 0.7278 (m-30) REVERT: G 151 LYS cc_start: 0.9203 (ptpp) cc_final: 0.8949 (pttt) REVERT: H 100 ILE cc_start: 0.8646 (mp) cc_final: 0.8247 (mm) REVERT: H 139 LEU cc_start: 0.7196 (mt) cc_final: 0.6870 (mt) REVERT: H 190 LYS cc_start: 0.9471 (mmpt) cc_final: 0.9250 (mmmt) REVERT: B 900 MET cc_start: 0.7730 (mmt) cc_final: 0.6821 (mmt) REVERT: B 902 MET cc_start: 0.9090 (mtm) cc_final: 0.8824 (mtt) REVERT: I 27 PHE cc_start: 0.8059 (p90) cc_final: 0.7777 (p90) REVERT: I 54 ASP cc_start: 0.9127 (p0) cc_final: 0.8664 (p0) REVERT: I 107 ASP cc_start: 0.7767 (m-30) cc_final: 0.7395 (m-30) REVERT: I 152 ASP cc_start: 0.9242 (m-30) cc_final: 0.8723 (t70) REVERT: J 100 ILE cc_start: 0.8670 (mp) cc_final: 0.8453 (mm) REVERT: J 181 TYR cc_start: 0.8167 (m-80) cc_final: 0.7563 (m-10) REVERT: C 900 MET cc_start: 0.7308 (mmt) cc_final: 0.6654 (mmt) REVERT: K 54 ASP cc_start: 0.9087 (p0) cc_final: 0.8667 (p0) REVERT: K 152 ASP cc_start: 0.8873 (t70) cc_final: 0.8619 (t70) REVERT: K 184 TYR cc_start: 0.9252 (m-80) cc_final: 0.8887 (m-80) REVERT: L 142 ASP cc_start: 0.9268 (t0) cc_final: 0.8883 (p0) outliers start: 1 outliers final: 0 residues processed: 356 average time/residue: 0.1970 time to fit residues: 97.3848 Evaluate side-chains 277 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 30 optimal weight: 3.9990 chunk 77 optimal weight: 0.3980 chunk 220 optimal weight: 7.9990 chunk 239 optimal weight: 5.9990 chunk 244 optimal weight: 6.9990 chunk 180 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 200 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 188 GLN ** B 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN I 13 GLN I 179 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.079111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.056046 restraints weight = 122402.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.057511 restraints weight = 85675.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.058454 restraints weight = 62501.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.058408 restraints weight = 65344.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.058459 restraints weight = 55235.110| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.6148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 20013 Z= 0.312 Angle : 0.796 8.992 27246 Z= 0.415 Chirality : 0.048 0.233 3174 Planarity : 0.007 0.228 3474 Dihedral : 5.841 55.311 2967 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 23.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.16), residues: 2529 helix: 1.30 (0.19), residues: 714 sheet: -1.31 (0.20), residues: 624 loop : -2.83 (0.16), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 905 TYR 0.040 0.003 TYR A 873 PHE 0.021 0.002 PHE G 108 TRP 0.018 0.002 TRP H 152 HIS 0.013 0.002 HIS A1101 Details of bonding type rmsd covalent geometry : bond 0.00670 (19974) covalent geometry : angle 0.78714 (27156) SS BOND : bond 0.00726 ( 27) SS BOND : angle 1.75217 ( 54) hydrogen bonds : bond 0.04835 ( 789) hydrogen bonds : angle 5.13059 ( 2292) link_NAG-ASN : bond 0.00505 ( 12) link_NAG-ASN : angle 2.66451 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5058 Ramachandran restraints generated. 2529 Oldfield, 0 Emsley, 2529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5058 Ramachandran restraints generated. 2529 Oldfield, 0 Emsley, 2529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 0.701 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: 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: symmetry clash revert: symmetry clash REVERT: A 844 ILE cc_start: 0.8140 (mm) cc_final: 0.7869 (mm) REVERT: A 867 ASP cc_start: 0.9223 (t70) cc_final: 0.9013 (p0) REVERT: A 900 MET cc_start: 0.7248 (mmt) cc_final: 0.6399 (mmt) REVERT: A 1039 ARG cc_start: 0.8261 (ptm-80) cc_final: 0.7902 (ptm160) REVERT: A 1068 VAL cc_start: 0.8813 (p) cc_final: 0.8543 (p) REVERT: G 31 ASP cc_start: 0.9022 (p0) cc_final: 0.7580 (p0) REVERT: G 32 TYR cc_start: 0.7905 (m-10) cc_final: 0.7561 (m-10) REVERT: G 54 ASP cc_start: 0.9211 (p0) cc_final: 0.8688 (p0) REVERT: G 151 LYS cc_start: 0.9222 (ptpp) cc_final: 0.8985 (pttt) REVERT: H 52 GLU cc_start: 0.8224 (tp30) cc_final: 0.7953 (tp30) REVERT: H 100 ILE cc_start: 0.8873 (mp) cc_final: 0.8556 (mm) REVERT: H 139 LEU cc_start: 0.7287 (mt) cc_final: 0.6948 (mt) REVERT: H 142 ASP cc_start: 0.9530 (t0) cc_final: 0.9133 (p0) REVERT: H 176 TYR cc_start: 0.8524 (m-80) cc_final: 0.8283 (m-80) REVERT: H 190 LYS cc_start: 0.9515 (mmpt) cc_final: 0.9275 (mmmt) REVERT: B 828 LEU cc_start: 0.8409 (tp) cc_final: 0.8204 (tp) REVERT: B 900 MET cc_start: 0.7808 (mmt) cc_final: 0.6952 (mmt) REVERT: B 902 MET cc_start: 0.9220 (mtm) cc_final: 0.8958 (mtt) REVERT: B 1031 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7916 (tm-30) REVERT: I 20 LEU cc_start: 0.9214 (tp) cc_final: 0.8901 (tt) REVERT: I 27 PHE cc_start: 0.8490 (p90) cc_final: 0.8222 (p90) REVERT: I 54 ASP cc_start: 0.9288 (p0) cc_final: 0.8794 (p0) REVERT: I 107 ASP cc_start: 0.8162 (m-30) cc_final: 0.7842 (m-30) REVERT: I 152 ASP cc_start: 0.9278 (m-30) cc_final: 0.8742 (t70) REVERT: I 184 TYR cc_start: 0.9144 (m-80) cc_final: 0.8468 (m-80) REVERT: J 29 ILE cc_start: 0.9109 (mt) cc_final: 0.8876 (mp) REVERT: J 100 ILE cc_start: 0.8917 (mp) cc_final: 0.8646 (mm) REVERT: J 181 TYR cc_start: 0.8311 (m-80) cc_final: 0.8061 (m-80) REVERT: C 725 GLU cc_start: 0.8234 (tm-30) cc_final: 0.8025 (tm-30) REVERT: C 865 LEU cc_start: 0.8357 (mm) cc_final: 0.8157 (mp) REVERT: C 866 THR cc_start: 0.9530 (p) cc_final: 0.9152 (p) REVERT: C 900 MET cc_start: 0.7350 (mmt) cc_final: 0.6377 (mmt) REVERT: K 6 GLU cc_start: 0.8092 (pp20) cc_final: 0.7092 (pm20) REVERT: K 30 LYS cc_start: 0.9131 (tmmt) cc_final: 0.8636 (ttmm) REVERT: K 54 ASP cc_start: 0.9278 (p0) cc_final: 0.8897 (p0) REVERT: K 152 ASP cc_start: 0.8936 (t70) cc_final: 0.8696 (t70) REVERT: L 47 LYS cc_start: 0.9078 (tmtt) cc_final: 0.8544 (tptp) REVERT: L 52 GLU cc_start: 0.8085 (tp30) cc_final: 0.7672 (tp30) REVERT: L 142 ASP cc_start: 0.9416 (t0) cc_final: 0.9056 (p0) REVERT: L 181 TYR cc_start: 0.8637 (m-10) cc_final: 0.8379 (m-10) outliers start: 0 outliers final: 0 residues processed: 347 average time/residue: 0.1927 time to fit residues: 94.1994 Evaluate side-chains 284 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 40 optimal weight: 4.9990 chunk 212 optimal weight: 0.8980 chunk 191 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 220 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 183 optimal weight: 0.9980 chunk 241 optimal weight: 0.0030 chunk 155 optimal weight: 0.0870 chunk 207 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 overall best weight: 0.4968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 953 ASN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 172 HIS I 179 GLN ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 949 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.082787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.059499 restraints weight = 121614.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.061237 restraints weight = 79079.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.062255 restraints weight = 61162.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.062836 restraints weight = 52631.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.063128 restraints weight = 48286.062| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.5953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20013 Z= 0.142 Angle : 0.681 9.032 27246 Z= 0.347 Chirality : 0.046 0.230 3174 Planarity : 0.006 0.196 3474 Dihedral : 5.398 56.856 2967 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.16), residues: 2529 helix: 1.74 (0.20), residues: 717 sheet: -0.97 (0.22), residues: 510 loop : -2.75 (0.15), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 765 TYR 0.045 0.002 TYR C 873 PHE 0.018 0.002 PHE J 122 TRP 0.047 0.002 TRP J 152 HIS 0.008 0.001 HIS I 208 Details of bonding type rmsd covalent geometry : bond 0.00317 (19974) covalent geometry : angle 0.67372 (27156) SS BOND : bond 0.00399 ( 27) SS BOND : angle 1.41076 ( 54) hydrogen bonds : bond 0.03900 ( 789) hydrogen bonds : angle 4.65773 ( 2292) link_NAG-ASN : bond 0.00413 ( 12) link_NAG-ASN : angle 2.43702 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5058 Ramachandran restraints generated. 2529 Oldfield, 0 Emsley, 2529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5058 Ramachandran restraints generated. 2529 Oldfield, 0 Emsley, 2529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 0.767 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 765 ARG cc_start: 0.8731 (ptp90) cc_final: 0.8316 (ptp-170) REVERT: A 844 ILE cc_start: 0.7615 (mm) cc_final: 0.7380 (mp) REVERT: A 900 MET cc_start: 0.7095 (mmt) cc_final: 0.6263 (mmt) REVERT: A 902 MET cc_start: 0.9363 (mtm) cc_final: 0.8963 (mtm) REVERT: G 6 GLU cc_start: 0.7833 (pp20) cc_final: 0.7479 (pp20) REVERT: G 31 ASP cc_start: 0.9007 (p0) cc_final: 0.7701 (p0) REVERT: G 54 ASP cc_start: 0.9173 (p0) cc_final: 0.8633 (p0) REVERT: G 69 ILE cc_start: 0.8639 (mm) cc_final: 0.8383 (tp) REVERT: G 151 LYS cc_start: 0.9244 (ptpp) cc_final: 0.9004 (pttt) REVERT: H 52 GLU cc_start: 0.7933 (tp30) cc_final: 0.7383 (tp30) REVERT: H 100 ILE cc_start: 0.8739 (mp) cc_final: 0.8369 (mm) REVERT: H 139 LEU cc_start: 0.7209 (mt) cc_final: 0.6899 (mt) REVERT: H 176 TYR cc_start: 0.8345 (m-80) cc_final: 0.7965 (m-80) REVERT: H 190 LYS cc_start: 0.9524 (mmpt) cc_final: 0.9297 (mmmt) REVERT: H 197 CYS cc_start: 0.4199 (p) cc_final: 0.3887 (p) REVERT: B 900 MET cc_start: 0.7696 (mmt) cc_final: 0.6852 (mmt) REVERT: B 902 MET cc_start: 0.9134 (mtm) cc_final: 0.8906 (mtt) REVERT: B 986 LYS cc_start: 0.8744 (tppt) cc_final: 0.8510 (tppp) REVERT: B 1031 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7776 (tm-30) REVERT: B 1054 GLN cc_start: 0.6543 (mp10) cc_final: 0.6249 (mp10) REVERT: I 20 LEU cc_start: 0.9289 (tp) cc_final: 0.8975 (tt) REVERT: I 27 PHE cc_start: 0.8178 (p90) cc_final: 0.7826 (p90) REVERT: I 54 ASP cc_start: 0.9224 (p0) cc_final: 0.8813 (p0) REVERT: I 107 ASP cc_start: 0.7944 (m-30) cc_final: 0.7631 (m-30) REVERT: I 152 ASP cc_start: 0.9280 (m-30) cc_final: 0.8743 (t70) REVERT: J 100 ILE cc_start: 0.8712 (mp) cc_final: 0.8440 (mm) REVERT: J 181 TYR cc_start: 0.8349 (m-80) cc_final: 0.8139 (m-80) REVERT: C 865 LEU cc_start: 0.8174 (mm) cc_final: 0.7874 (mm) REVERT: C 900 MET cc_start: 0.7179 (mmt) cc_final: 0.6172 (mmt) REVERT: K 6 GLU cc_start: 0.7712 (pp20) cc_final: 0.6691 (pm20) REVERT: K 54 ASP cc_start: 0.9179 (p0) cc_final: 0.8773 (p0) REVERT: K 152 ASP cc_start: 0.8946 (t70) cc_final: 0.8706 (t70) REVERT: K 184 TYR cc_start: 0.9195 (m-80) cc_final: 0.8933 (m-80) REVERT: L 181 TYR cc_start: 0.8477 (m-10) cc_final: 0.8269 (m-10) outliers start: 0 outliers final: 0 residues processed: 351 average time/residue: 0.1975 time to fit residues: 96.9546 Evaluate side-chains 274 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 155 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 153 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 213 optimal weight: 4.9990 chunk 239 optimal weight: 4.9990 chunk 204 optimal weight: 3.9990 chunk 49 optimal weight: 0.3980 chunk 180 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 172 HIS I 179 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.080785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.057502 restraints weight = 121179.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.059779 restraints weight = 83966.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.059898 restraints weight = 56625.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.060304 restraints weight = 56413.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.060385 restraints weight = 51812.473| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.6173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 20013 Z= 0.209 Angle : 0.726 13.914 27246 Z= 0.376 Chirality : 0.047 0.235 3174 Planarity : 0.006 0.179 3474 Dihedral : 5.575 56.379 2967 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.17), residues: 2529 helix: 1.53 (0.19), residues: 723 sheet: -1.24 (0.20), residues: 615 loop : -2.72 (0.16), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C1091 TYR 0.040 0.002 TYR A 873 PHE 0.017 0.002 PHE L 143 TRP 0.023 0.002 TRP J 152 HIS 0.009 0.002 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00459 (19974) covalent geometry : angle 0.71828 (27156) SS BOND : bond 0.00549 ( 27) SS BOND : angle 1.58113 ( 54) hydrogen bonds : bond 0.04274 ( 789) hydrogen bonds : angle 4.77554 ( 2292) link_NAG-ASN : bond 0.00375 ( 12) link_NAG-ASN : angle 2.46193 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5058 Ramachandran restraints generated. 2529 Oldfield, 0 Emsley, 2529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5058 Ramachandran restraints generated. 2529 Oldfield, 0 Emsley, 2529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 335 time to evaluate : 0.781 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: 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: symmetry clash revert: symmetry clash REVERT: A 765 ARG cc_start: 0.8763 (ptp90) cc_final: 0.8376 (ptp-170) REVERT: A 844 ILE cc_start: 0.7866 (mm) cc_final: 0.7559 (mm) REVERT: A 900 MET cc_start: 0.7154 (mmt) cc_final: 0.6265 (mmt) REVERT: A 1089 PHE cc_start: 0.6793 (p90) cc_final: 0.6406 (p90) REVERT: G 31 ASP cc_start: 0.9077 (p0) cc_final: 0.7690 (p0) REVERT: G 54 ASP cc_start: 0.9185 (p0) cc_final: 0.8686 (p0) REVERT: G 69 ILE cc_start: 0.8693 (mm) cc_final: 0.8416 (tp) REVERT: G 151 LYS cc_start: 0.9247 (ptpp) cc_final: 0.9025 (pttt) REVERT: H 52 GLU cc_start: 0.7959 (tp30) cc_final: 0.7430 (tp30) REVERT: H 100 ILE cc_start: 0.8778 (mp) cc_final: 0.8473 (mm) REVERT: H 139 LEU cc_start: 0.7118 (mt) cc_final: 0.6837 (mt) REVERT: H 142 ASP cc_start: 0.9495 (t0) cc_final: 0.9079 (p0) REVERT: H 190 LYS cc_start: 0.9523 (mmpt) cc_final: 0.9291 (mmmt) REVERT: H 197 CYS cc_start: 0.4464 (p) cc_final: 0.4149 (p) REVERT: B 900 MET cc_start: 0.7750 (mmt) cc_final: 0.6916 (mmt) REVERT: B 902 MET cc_start: 0.9198 (mtm) cc_final: 0.8971 (mtt) REVERT: B 1054 GLN cc_start: 0.6736 (mp10) cc_final: 0.6511 (mp10) REVERT: I 20 LEU cc_start: 0.9235 (tp) cc_final: 0.8904 (tt) REVERT: I 27 PHE cc_start: 0.8381 (p90) cc_final: 0.8029 (p90) REVERT: I 54 ASP cc_start: 0.9271 (p0) cc_final: 0.8783 (p0) REVERT: I 107 ASP cc_start: 0.7990 (m-30) cc_final: 0.7734 (m-30) REVERT: I 152 ASP cc_start: 0.9279 (m-30) cc_final: 0.8811 (t70) REVERT: J 47 LYS cc_start: 0.9130 (tmtt) cc_final: 0.8895 (tptp) REVERT: J 100 ILE cc_start: 0.8795 (mp) cc_final: 0.8511 (mm) REVERT: C 900 MET cc_start: 0.7292 (mmt) cc_final: 0.6331 (mmt) REVERT: K 54 ASP cc_start: 0.9223 (p0) cc_final: 0.8864 (p0) REVERT: K 152 ASP cc_start: 0.8963 (t70) cc_final: 0.8724 (t70) REVERT: K 184 TYR cc_start: 0.9208 (m-80) cc_final: 0.8944 (m-80) REVERT: L 47 LYS cc_start: 0.8970 (tmtt) cc_final: 0.8372 (tptp) REVERT: L 139 LEU cc_start: 0.6922 (mt) cc_final: 0.6632 (mt) REVERT: L 197 CYS cc_start: 0.4595 (p) cc_final: 0.4378 (p) outliers start: 0 outliers final: 0 residues processed: 335 average time/residue: 0.1901 time to fit residues: 89.4567 Evaluate side-chains 274 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 7 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 202 optimal weight: 0.0270 chunk 225 optimal weight: 6.9990 chunk 121 optimal weight: 0.9980 chunk 213 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 203 optimal weight: 1.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 172 HIS ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.083020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.059645 restraints weight = 121692.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.061443 restraints weight = 79837.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.062491 restraints weight = 61771.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.063058 restraints weight = 53023.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.063396 restraints weight = 48724.848| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.6105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20013 Z= 0.144 Angle : 0.703 9.615 27246 Z= 0.359 Chirality : 0.046 0.238 3174 Planarity : 0.006 0.155 3474 Dihedral : 5.370 57.259 2967 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.17), residues: 2529 helix: 1.76 (0.20), residues: 717 sheet: -1.24 (0.21), residues: 609 loop : -2.65 (0.16), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 39 TYR 0.022 0.002 TYR J 93 PHE 0.043 0.002 PHE L 143 TRP 0.019 0.002 TRP J 152 HIS 0.006 0.001 HIS H 201 Details of bonding type rmsd covalent geometry : bond 0.00319 (19974) covalent geometry : angle 0.69666 (27156) SS BOND : bond 0.00389 ( 27) SS BOND : angle 1.37314 ( 54) hydrogen bonds : bond 0.03885 ( 789) hydrogen bonds : angle 4.55594 ( 2292) link_NAG-ASN : bond 0.00348 ( 12) link_NAG-ASN : angle 2.31045 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5058 Ramachandran restraints generated. 2529 Oldfield, 0 Emsley, 2529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5058 Ramachandran restraints generated. 2529 Oldfield, 0 Emsley, 2529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 0.758 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: 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: A 765 ARG cc_start: 0.8738 (ptp90) cc_final: 0.8332 (ptp-170) REVERT: A 844 ILE cc_start: 0.7470 (mm) cc_final: 0.7092 (mp) REVERT: A 900 MET cc_start: 0.7114 (mmt) cc_final: 0.6239 (mmt) REVERT: A 902 MET cc_start: 0.9329 (mtm) cc_final: 0.8907 (mtm) REVERT: G 31 ASP cc_start: 0.9071 (p0) cc_final: 0.7472 (p0) REVERT: G 54 ASP cc_start: 0.9143 (p0) cc_final: 0.8643 (p0) REVERT: G 69 ILE cc_start: 0.8609 (mm) cc_final: 0.8345 (tp) REVERT: G 107 ASP cc_start: 0.8049 (m-30) cc_final: 0.7600 (m-30) REVERT: G 151 LYS cc_start: 0.9230 (ptpp) cc_final: 0.8999 (pttt) REVERT: G 174 PHE cc_start: 0.7765 (m-80) cc_final: 0.7551 (m-80) REVERT: H 52 GLU cc_start: 0.7974 (tp30) cc_final: 0.7641 (tp30) REVERT: H 100 ILE cc_start: 0.8669 (mp) cc_final: 0.8389 (mm) REVERT: H 139 LEU cc_start: 0.7089 (mt) cc_final: 0.6787 (mt) REVERT: H 142 ASP cc_start: 0.9468 (t0) cc_final: 0.9065 (p0) REVERT: H 176 TYR cc_start: 0.8309 (m-80) cc_final: 0.7972 (m-80) REVERT: H 190 LYS cc_start: 0.9553 (mmpt) cc_final: 0.9333 (mmmt) REVERT: H 197 CYS cc_start: 0.4113 (p) cc_final: 0.3825 (p) REVERT: B 900 MET cc_start: 0.7642 (mmt) cc_final: 0.6755 (mmt) REVERT: B 1031 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7652 (tm-30) REVERT: B 1041 ASP cc_start: 0.8200 (t0) cc_final: 0.7975 (t70) REVERT: I 27 PHE cc_start: 0.8263 (p90) cc_final: 0.7922 (p90) REVERT: I 46 GLU cc_start: 0.8280 (mp0) cc_final: 0.8076 (mp0) REVERT: I 54 ASP cc_start: 0.9251 (p0) cc_final: 0.8823 (p0) REVERT: I 107 ASP cc_start: 0.7961 (m-30) cc_final: 0.7389 (m-30) REVERT: I 152 ASP cc_start: 0.9317 (m-30) cc_final: 0.8797 (t70) REVERT: J 100 ILE cc_start: 0.8690 (mp) cc_final: 0.8371 (mm) REVERT: J 190 LYS cc_start: 0.9423 (mmpt) cc_final: 0.8950 (mmtm) REVERT: C 900 MET cc_start: 0.7200 (mmt) cc_final: 0.6221 (mmt) REVERT: K 6 GLU cc_start: 0.7753 (pp20) cc_final: 0.6761 (pm20) REVERT: K 46 GLU cc_start: 0.8636 (mp0) cc_final: 0.8324 (mp0) REVERT: K 54 ASP cc_start: 0.9187 (p0) cc_final: 0.8773 (p0) REVERT: K 152 ASP cc_start: 0.8931 (t70) cc_final: 0.8688 (t70) REVERT: K 184 TYR cc_start: 0.9199 (m-80) cc_final: 0.8936 (m-80) REVERT: L 139 LEU cc_start: 0.6735 (mt) cc_final: 0.6522 (mt) REVERT: L 153 LYS cc_start: 0.8815 (tptt) cc_final: 0.8607 (tppt) REVERT: L 190 LYS cc_start: 0.8824 (mmpt) cc_final: 0.8576 (mmmt) REVERT: L 197 CYS cc_start: 0.4694 (p) cc_final: 0.4461 (p) outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.1962 time to fit residues: 94.3344 Evaluate side-chains 274 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 54 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 207 optimal weight: 6.9990 chunk 50 optimal weight: 0.2980 chunk 98 optimal weight: 0.0070 chunk 205 optimal weight: 7.9990 chunk 70 optimal weight: 0.2980 chunk 51 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 182 optimal weight: 0.8980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1048 HIS A1101 HIS ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 172 HIS ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 16 GLN ** 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 = 0.3958 r_free = 0.3958 target = 0.084019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.061811 restraints weight = 120534.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.063195 restraints weight = 84756.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.063885 restraints weight = 68733.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.064468 restraints weight = 61297.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.064706 restraints weight = 56978.011| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.6066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20013 Z= 0.136 Angle : 0.685 9.142 27246 Z= 0.350 Chirality : 0.046 0.237 3174 Planarity : 0.006 0.130 3474 Dihedral : 5.180 57.563 2967 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.17), residues: 2529 helix: 1.89 (0.20), residues: 720 sheet: -1.08 (0.21), residues: 615 loop : -2.61 (0.16), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 39 TYR 0.046 0.002 TYR A 873 PHE 0.035 0.002 PHE L 143 TRP 0.013 0.001 TRP J 152 HIS 0.006 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00303 (19974) covalent geometry : angle 0.67887 (27156) SS BOND : bond 0.00376 ( 27) SS BOND : angle 1.29473 ( 54) hydrogen bonds : bond 0.03860 ( 789) hydrogen bonds : angle 4.38050 ( 2292) link_NAG-ASN : bond 0.00303 ( 12) link_NAG-ASN : angle 2.24406 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4894.37 seconds wall clock time: 85 minutes 16.42 seconds (5116.42 seconds total)