Starting phenix.real_space_refine on Thu Feb 5 10:57:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mtk_48612/02_2026/9mtk_48612.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mtk_48612/02_2026/9mtk_48612.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mtk_48612/02_2026/9mtk_48612.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mtk_48612/02_2026/9mtk_48612.map" model { file = "/net/cci-nas-00/data/ceres_data/9mtk_48612/02_2026/9mtk_48612.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mtk_48612/02_2026/9mtk_48612.cif" } resolution = 2.54 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= 0.001 sd= 0.018 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 72 5.16 5 C 10516 2.51 5 N 2847 2.21 5 O 3214 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16649 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2474 Classifications: {'peptide': 315} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 295} Chain breaks: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 2479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2479 Classifications: {'peptide': 315} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 295} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 2484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2484 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 19, 'TRANS': 298} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "H" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 908 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 908 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "J" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 809 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 10, 'TRANS': 100} Chain: "L" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 809 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 10, 'TRANS': 100} Chain: "M" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 912 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "N" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 809 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 10, 'TRANS': 100} Chain: "B" Number of atoms: 1361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1361 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 167} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "D" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1369 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 1, 'TRANS': 167} Chain: "F" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1327 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 1, 'TRANS': 162} Chain breaks: 1 Time building chain proxies: 3.65, per 1000 atoms: 0.22 Number of scatterers: 16649 At special positions: 0 Unit cell: (146.004, 134.366, 148.12, 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 72 16.00 O 3214 8.00 N 2847 7.00 C 10516 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.06 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.01 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS D 137 " distance=2.02 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS F 137 " distance=2.05 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 277 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.03 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " 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 Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 655.9 milliseconds 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3920 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 46 sheets defined 21.0% alpha, 29.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 77 removed outlier: 4.019A pdb=" N GLU A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 122 through 127 removed outlier: 4.482A pdb=" N TRP A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 77 removed outlier: 4.139A pdb=" N GLU C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 113 Processing helix chain 'C' and resid 122 through 127 removed outlier: 4.436A pdb=" N TRP C 127 " --> pdb=" O LYS C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.984A pdb=" N GLY E 55 " --> pdb=" O LYS E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 73 through 80 removed outlier: 4.091A pdb=" N GLU E 77 " --> pdb=" O PRO E 74 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N SER E 78 " --> pdb=" O GLU E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 114 removed outlier: 4.159A pdb=" N SER E 114 " --> pdb=" O GLU E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 196 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.813A pdb=" N THR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.637A pdb=" N THR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'L' and resid 28 through 32 removed outlier: 3.575A pdb=" N TYR L 32 " --> pdb=" O THR L 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.747A pdb=" N THR M 32 " --> pdb=" O PHE M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 64 removed outlier: 3.619A pdb=" N LYS M 64 " --> pdb=" O VAL M 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 61 through 64' Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.568A pdb=" N TYR N 32 " --> pdb=" O THR N 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 57 Processing helix chain 'B' and resid 74 through 127 removed outlier: 3.578A pdb=" N GLU B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 155 Processing helix chain 'B' and resid 158 through 170 removed outlier: 3.755A pdb=" N TYR B 162 " --> pdb=" O ASP B 158 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLU B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N GLU B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN B 169 " --> pdb=" O GLU B 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 57 Processing helix chain 'D' and resid 74 through 127 Processing helix chain 'D' and resid 145 through 155 Processing helix chain 'D' and resid 158 through 170 removed outlier: 3.794A pdb=" N TYR D 162 " --> pdb=" O ASP D 158 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLU D 164 " --> pdb=" O PRO D 160 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N GLU D 165 " --> pdb=" O LYS D 161 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU D 168 " --> pdb=" O GLU D 164 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN D 169 " --> pdb=" O GLU D 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 59 removed outlier: 3.908A pdb=" N MET F 59 " --> pdb=" O VAL F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 127 removed outlier: 3.635A pdb=" N GLU F 105 " --> pdb=" O LEU F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 155 Processing helix chain 'F' and resid 158 through 169 removed outlier: 3.785A pdb=" N TYR F 162 " --> pdb=" O ASP F 158 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLU F 164 " --> pdb=" O PRO F 160 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N GLU F 165 " --> pdb=" O LYS F 161 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU F 168 " --> pdb=" O GLU F 164 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN F 169 " --> pdb=" O GLU F 165 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 36 removed outlier: 3.844A pdb=" N ASN B 28 " --> pdb=" O GLY B 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 53A removed outlier: 6.405A pdb=" N LEU A 51 " --> pdb=" O HIS A 275 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N CYS A 277 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.445A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE A 87 " --> pdb=" O ILE A 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 115 through 121A removed outlier: 6.338A pdb=" N GLU A 260A" --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE A 118 " --> pdb=" O THR A 259 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N THR A 259 " --> pdb=" O PHE A 118 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ARG A 120 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA A 257 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 115 through 121A removed outlier: 6.338A pdb=" N GLU A 260A" --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE A 118 " --> pdb=" O THR A 259 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N THR A 259 " --> pdb=" O PHE A 118 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ARG A 120 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA A 257 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.682A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB2, first strand: chain 'D' and resid 32 through 36 Processing sheet with id=AB3, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AB4, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AB5, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AB6, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.544A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE C 87 " --> pdb=" O ILE C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 117 through 121A removed outlier: 6.718A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 136 through 141 removed outlier: 4.716A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 151 through 153 Processing sheet with id=AC1, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AC2, first strand: chain 'F' and resid 33 through 36 Processing sheet with id=AC3, first strand: chain 'E' and resid 25 through 26 Processing sheet with id=AC4, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AC5, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AC6, first strand: chain 'E' and resid 59 through 60 removed outlier: 6.584A pdb=" N LEU E 59 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE E 87 " --> pdb=" O ILE E 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 119 through 121 removed outlier: 3.664A pdb=" N GLU E 175 " --> pdb=" O MET E 260 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N LEU E 179 " --> pdb=" O PRO E 254 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 119 through 121 removed outlier: 3.664A pdb=" N GLU E 175 " --> pdb=" O MET E 260 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 136 through 141 removed outlier: 4.747A pdb=" N CYS E 139 " --> pdb=" O SER E 146 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AD2, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AD3, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.628A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.628A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AD6, first strand: chain 'I' and resid 57 through 59 removed outlier: 6.597A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ALA I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE I 34 " --> pdb=" O ALA I 50 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 57 through 59 removed outlier: 6.597A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ALA I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE I 34 " --> pdb=" O ALA I 50 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 3 through 5 Processing sheet with id=AD9, first strand: chain 'J' and resid 11 through 13 removed outlier: 6.818A pdb=" N MET J 11 " --> pdb=" O THR J 105 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 11 through 13 removed outlier: 6.818A pdb=" N MET J 11 " --> pdb=" O THR J 105 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 3 through 5 Processing sheet with id=AE3, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.983A pdb=" N MET L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.983A pdb=" N MET L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 4 through 6 Processing sheet with id=AE6, first strand: chain 'M' and resid 57 through 59 removed outlier: 6.595A pdb=" N TRP M 36 " --> pdb=" O LEU M 48 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA M 50 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE M 34 " --> pdb=" O ALA M 50 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 57 through 59 removed outlier: 6.595A pdb=" N TRP M 36 " --> pdb=" O LEU M 48 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA M 50 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE M 34 " --> pdb=" O ALA M 50 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 3 through 5 Processing sheet with id=AE9, first strand: chain 'N' and resid 11 through 13 removed outlier: 7.136A pdb=" N MET N 11 " --> pdb=" O THR N 105 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'N' and resid 11 through 13 removed outlier: 7.136A pdb=" N MET N 11 " --> pdb=" O THR N 105 " (cutoff:3.500A) 690 hydrogen bonds defined for protein. 1854 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: 3.17 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5409 1.34 - 1.46: 4049 1.46 - 1.59: 7484 1.59 - 1.71: 0 1.71 - 1.84: 96 Bond restraints: 17038 Sorted by residual: bond pdb=" C ARG C 315 " pdb=" N LEU C 316 " ideal model delta sigma weight residual 1.330 1.212 0.118 1.46e-02 4.69e+03 6.49e+01 bond pdb=" C GLN B 125 " pdb=" N LEU B 126 " ideal model delta sigma weight residual 1.335 1.430 -0.095 1.38e-02 5.25e+03 4.73e+01 bond pdb=" C LEU C 314 " pdb=" N ARG C 315 " ideal model delta sigma weight residual 1.330 1.236 0.094 1.46e-02 4.69e+03 4.17e+01 bond pdb=" C PHE E 102 " pdb=" N ILE E 103 " ideal model delta sigma weight residual 1.333 1.282 0.051 1.20e-02 6.94e+03 1.80e+01 bond pdb=" C GLU D 105 " pdb=" N ARG D 106 " ideal model delta sigma weight residual 1.335 1.279 0.056 1.38e-02 5.25e+03 1.66e+01 ... (remaining 17033 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 22564 2.37 - 4.73: 508 4.73 - 7.10: 63 7.10 - 9.47: 6 9.47 - 11.83: 2 Bond angle restraints: 23143 Sorted by residual: angle pdb=" CA PHE D 9 " pdb=" CB PHE D 9 " pdb=" CG PHE D 9 " ideal model delta sigma weight residual 113.80 125.63 -11.83 1.00e+00 1.00e+00 1.40e+02 angle pdb=" N LYS D 58 " pdb=" CA LYS D 58 " pdb=" C LYS D 58 " ideal model delta sigma weight residual 114.31 104.43 9.88 1.29e+00 6.01e-01 5.86e+01 angle pdb=" CA LEU C 314 " pdb=" C LEU C 314 " pdb=" N ARG C 315 " ideal model delta sigma weight residual 115.92 123.89 -7.97 1.28e+00 6.10e-01 3.87e+01 angle pdb=" N THR E 280 " pdb=" CA THR E 280 " pdb=" C THR E 280 " ideal model delta sigma weight residual 114.56 106.82 7.74 1.27e+00 6.20e-01 3.72e+01 angle pdb=" C GLN B 125 " pdb=" N LEU B 126 " pdb=" CA LEU B 126 " ideal model delta sigma weight residual 120.31 111.85 8.46 1.52e+00 4.33e-01 3.09e+01 ... (remaining 23138 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 8876 18.00 - 35.99: 916 35.99 - 53.99: 246 53.99 - 71.98: 46 71.98 - 89.98: 21 Dihedral angle restraints: 10105 sinusoidal: 3958 harmonic: 6147 Sorted by residual: dihedral pdb=" CB CYS E 52 " pdb=" SG CYS E 52 " pdb=" SG CYS E 277 " pdb=" CB CYS E 277 " ideal model delta sinusoidal sigma weight residual 93.00 5.30 87.70 1 1.00e+01 1.00e-02 9.21e+01 dihedral pdb=" CB CYS E 64 " pdb=" SG CYS E 64 " pdb=" SG CYS E 76 " pdb=" CB CYS E 76 " ideal model delta sinusoidal sigma weight residual 93.00 164.76 -71.76 1 1.00e+01 1.00e-02 6.60e+01 dihedral pdb=" CB CYS C 52 " pdb=" SG CYS C 52 " pdb=" SG CYS C 277 " pdb=" CB CYS C 277 " ideal model delta sinusoidal sigma weight residual -86.00 -20.52 -65.48 1 1.00e+01 1.00e-02 5.62e+01 ... (remaining 10102 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2090 0.059 - 0.117: 386 0.117 - 0.176: 48 0.176 - 0.235: 8 0.235 - 0.293: 4 Chirality restraints: 2536 Sorted by residual: chirality pdb=" CA PHE B 138 " pdb=" N PHE B 138 " pdb=" C PHE B 138 " pdb=" CB PHE B 138 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA PHE D 9 " pdb=" N PHE D 9 " pdb=" C PHE D 9 " pdb=" CB PHE D 9 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA CYS A 277 " pdb=" N CYS A 277 " pdb=" C CYS A 277 " pdb=" CB CYS A 277 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 2533 not shown) Planarity restraints: 2997 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 83 " 0.597 9.50e-02 1.11e+02 2.68e-01 4.37e+01 pdb=" NE ARG H 83 " -0.035 2.00e-02 2.50e+03 pdb=" CZ ARG H 83 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG H 83 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG H 83 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 106 " -0.548 9.50e-02 1.11e+02 2.46e-01 3.69e+01 pdb=" NE ARG D 106 " 0.033 2.00e-02 2.50e+03 pdb=" CZ ARG D 106 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG D 106 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG D 106 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 315 " -0.449 9.50e-02 1.11e+02 2.01e-01 2.49e+01 pdb=" NE ARG C 315 " 0.027 2.00e-02 2.50e+03 pdb=" CZ ARG C 315 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG C 315 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 315 " -0.015 2.00e-02 2.50e+03 ... (remaining 2994 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2230 2.75 - 3.29: 14834 3.29 - 3.83: 27364 3.83 - 4.36: 33228 4.36 - 4.90: 58583 Nonbonded interactions: 136239 Sorted by model distance: nonbonded pdb=" NZ LYS C 163 " pdb=" OE2 GLU C 246 " model vdw 2.216 3.120 nonbonded pdb=" NH1 ARG E 208 " pdb=" OE2 GLU E 238 " model vdw 2.245 3.120 nonbonded pdb=" O SER I 30 " pdb=" OG SER I 52A" model vdw 2.251 3.040 nonbonded pdb=" OD1 ASN B 128 " pdb=" OH TYR B 159 " model vdw 2.258 3.040 nonbonded pdb=" O SER E 85 " pdb=" N SER E 265 " model vdw 2.258 3.120 ... (remaining 136234 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 53A or (resid 54 and (name N or name CA or name \ C or name O or name CB )) or resid 55 through 62 or (resid 63 and (name N or na \ me CA or name C or name O or name CB )) or resid 64 through 309 or (resid 310 an \ d (name N or name CA or name C or name O or name CB )) or resid 311 through 324) \ ) selection = (chain 'C' and (resid 11 through 53A or (resid 54 and (name N or name CA or name \ C or name O or name CB )) or resid 55 through 81A or (resid 82 and (name N or n \ ame CA or name C or name O or name CB )) or resid 83 through 277 or (resid 278 a \ nd (name N or name CA or name C or name O or name CB )) or resid 279 through 309 \ or (resid 310 and (name N or name CA or name C or name O or name CB )) or resid \ 311 through 324)) selection = (chain 'E' and (resid 11 through 78 or resid 81A through 277 or (resid 278 and ( \ name N or name CA or name C or name O or name CB )) or resid 279 through 324)) } ncs_group { reference = (chain 'B' and (resid 2 through 59 or resid 65 through 170)) selection = (chain 'D' and (resid 2 through 38 or (resid 39 and (name N or name CA or name C \ or name O or name CB )) or resid 40 through 59 or resid 65 through 142 or (resi \ d 143 and (name N or name CA or name C or name O or name CB )) or resid 144 thro \ ugh 170)) selection = (chain 'F' and (resid 2 through 38 or (resid 39 and (name N or name CA or name C \ or name O or name CB )) or resid 40 through 142 or (resid 143 and (name N or na \ me CA or name C or name O or name CB )) or resid 144 through 170)) } ncs_group { reference = chain 'H' selection = chain 'I' selection = (chain 'M' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 109)) } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'N' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 15.850 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 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:7.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 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 : 0.005 0.118 17061 Z= 0.303 Angle : 0.794 11.832 23189 Z= 0.492 Chirality : 0.048 0.293 2536 Planarity : 0.009 0.268 2997 Dihedral : 15.926 89.981 6116 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.57 % Favored : 95.34 % Rotamer: Outliers : 2.05 % Allowed : 18.09 % Favored : 79.87 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.18), residues: 2101 helix: 2.06 (0.27), residues: 359 sheet: 0.85 (0.24), residues: 482 loop : -1.09 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 224 TYR 0.017 0.001 TYR E 201 PHE 0.038 0.002 PHE D 9 TRP 0.014 0.001 TRP H 103 HIS 0.007 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00526 (17038) covalent geometry : angle 0.78895 (23143) SS BOND : bond 0.01000 ( 23) SS BOND : angle 2.12288 ( 46) hydrogen bonds : bond 0.11088 ( 641) hydrogen bonds : angle 6.52295 ( 1854) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 1819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 400 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8352 (ptpt) cc_final: 0.8144 (ptpp) REVERT: A 75 GLU cc_start: 0.6625 (mt-10) cc_final: 0.6235 (mt-10) REVERT: A 315 ARG cc_start: 0.8924 (ttm-80) cc_final: 0.8671 (ttm-80) REVERT: C 133 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8099 (mtpm) REVERT: C 282 GLN cc_start: 0.7659 (mm-40) cc_final: 0.7289 (tm-30) REVERT: E 119 GLU cc_start: 0.7314 (tm-30) cc_final: 0.6900 (tm-30) REVERT: E 282 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.7367 (mm-40) REVERT: E 283 THR cc_start: 0.8608 (OUTLIER) cc_final: 0.8319 (m) REVERT: H 38 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.8340 (ptt180) REVERT: B 120 GLU cc_start: 0.7859 (mp0) cc_final: 0.7558 (mp0) REVERT: F 116 LYS cc_start: 0.8400 (tptp) cc_final: 0.7994 (tptm) outliers start: 37 outliers final: 15 residues processed: 422 average time/residue: 0.7627 time to fit residues: 349.6849 Evaluate side-chains 408 residues out of total 1819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 389 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 282 GLN Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 67 SER Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 22 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.3980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 322 ASN E 159 ASN E 166 GLN E 282 GLN H 39 GLN L 38 GLN M 39 GLN N 38 GLN B 27 GLN B 30 GLN D 50 ASN F 28 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.115684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.105960 restraints weight = 23967.307| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.64 r_work: 0.3418 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.0786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 17061 Z= 0.214 Angle : 0.576 6.971 23189 Z= 0.300 Chirality : 0.044 0.181 2536 Planarity : 0.004 0.053 2997 Dihedral : 5.473 56.010 2338 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.95 % Favored : 96.00 % Rotamer: Outliers : 4.26 % Allowed : 16.81 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.18), residues: 2101 helix: 2.29 (0.26), residues: 359 sheet: 0.90 (0.24), residues: 482 loop : -1.16 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 224 TYR 0.015 0.002 TYR B 34 PHE 0.020 0.002 PHE F 9 TRP 0.011 0.001 TRP M 103 HIS 0.007 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00506 (17038) covalent geometry : angle 0.57269 (23143) SS BOND : bond 0.00437 ( 23) SS BOND : angle 1.51735 ( 46) hydrogen bonds : bond 0.04342 ( 641) hydrogen bonds : angle 5.06568 ( 1854) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 1819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 387 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8593 (ptpt) cc_final: 0.8348 (ptpp) REVERT: A 75 GLU cc_start: 0.6657 (mt-10) cc_final: 0.6210 (mt-10) REVERT: A 109 ARG cc_start: 0.8630 (mtp85) cc_final: 0.8399 (mtp85) REVERT: A 295 GLN cc_start: 0.8301 (pp30) cc_final: 0.8073 (pp30) REVERT: A 315 ARG cc_start: 0.8924 (ttm-80) cc_final: 0.8717 (ttm-80) REVERT: C 133 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8247 (mtpm) REVERT: C 163 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8160 (tttp) REVERT: C 282 GLN cc_start: 0.7771 (mm-40) cc_final: 0.7412 (tm-30) REVERT: C 315 ARG cc_start: 0.8807 (ttm-80) cc_final: 0.8449 (ttt180) REVERT: E 119 GLU cc_start: 0.7279 (tm-30) cc_final: 0.6906 (tm-30) REVERT: E 282 GLN cc_start: 0.7971 (OUTLIER) cc_final: 0.7710 (mm-40) REVERT: E 283 THR cc_start: 0.8368 (OUTLIER) cc_final: 0.8132 (p) REVERT: N 79 GLN cc_start: 0.7830 (mp10) cc_final: 0.7567 (mp10) REVERT: B 103 GLU cc_start: 0.7515 (mp0) cc_final: 0.7268 (mp0) REVERT: B 120 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7642 (mp0) REVERT: D 2 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.7143 (tm) REVERT: D 108 LEU cc_start: 0.8446 (mt) cc_final: 0.8174 (mp) REVERT: F 152 VAL cc_start: 0.8598 (p) cc_final: 0.8387 (t) outliers start: 77 outliers final: 30 residues processed: 423 average time/residue: 0.7226 time to fit residues: 334.2373 Evaluate side-chains 415 residues out of total 1819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 379 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 238 GLU Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 282 GLN Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 43 ASN Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain F residue 22 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 160 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 105 optimal weight: 4.9990 chunk 140 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 chunk 157 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 111 GLN E 159 ASN E 166 GLN D 50 ASN D 125 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.115478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.105730 restraints weight = 24147.044| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.64 r_work: 0.3414 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 17061 Z= 0.212 Angle : 0.563 7.335 23189 Z= 0.292 Chirality : 0.044 0.184 2536 Planarity : 0.004 0.054 2997 Dihedral : 5.176 52.815 2321 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.95 % Favored : 96.00 % Rotamer: Outliers : 4.70 % Allowed : 16.87 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.18), residues: 2101 helix: 2.30 (0.26), residues: 357 sheet: 0.92 (0.24), residues: 482 loop : -1.15 (0.16), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG N 97 TYR 0.016 0.002 TYR B 34 PHE 0.021 0.002 PHE D 9 TRP 0.011 0.001 TRP H 47 HIS 0.007 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00502 (17038) covalent geometry : angle 0.55883 (23143) SS BOND : bond 0.00375 ( 23) SS BOND : angle 1.63582 ( 46) hydrogen bonds : bond 0.04265 ( 641) hydrogen bonds : angle 4.85776 ( 1854) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 1819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 390 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ARG cc_start: 0.8615 (mtp85) cc_final: 0.8341 (mtp85) REVERT: A 295 GLN cc_start: 0.8314 (pp30) cc_final: 0.8041 (pp30) REVERT: A 315 ARG cc_start: 0.8938 (ttm-80) cc_final: 0.8732 (ttm-80) REVERT: C 133 LYS cc_start: 0.8551 (mtmt) cc_final: 0.8269 (mtpm) REVERT: C 282 GLN cc_start: 0.7792 (mm-40) cc_final: 0.7488 (tm-30) REVERT: C 315 ARG cc_start: 0.8833 (ttm-80) cc_final: 0.8507 (ttt180) REVERT: E 119 GLU cc_start: 0.7305 (tm-30) cc_final: 0.6922 (tm-30) REVERT: E 282 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7848 (mm-40) REVERT: E 283 THR cc_start: 0.8428 (OUTLIER) cc_final: 0.8186 (p) REVERT: N 79 GLN cc_start: 0.7792 (mp10) cc_final: 0.7481 (mp10) REVERT: B 103 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7315 (mp0) REVERT: B 120 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7665 (mp0) REVERT: B 125 GLN cc_start: 0.8415 (mt0) cc_final: 0.8192 (tt0) REVERT: D 2 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.7113 (tm) REVERT: D 22 TYR cc_start: 0.8723 (OUTLIER) cc_final: 0.8175 (m-80) REVERT: D 108 LEU cc_start: 0.8471 (mt) cc_final: 0.8159 (mp) REVERT: F 152 VAL cc_start: 0.8599 (p) cc_final: 0.8367 (t) outliers start: 85 outliers final: 41 residues processed: 434 average time/residue: 0.6640 time to fit residues: 315.5301 Evaluate side-chains 443 residues out of total 1819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 396 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 307 LYS Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 282 GLN Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain J residue 11 MET Chi-restraints excluded: chain J residue 92 LYS Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 158 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 163 optimal weight: 0.0030 chunk 90 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 chunk 95 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 chunk 192 optimal weight: 0.5980 chunk 184 optimal weight: 1.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 159 ASN E 166 GLN D 50 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.116286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.106619 restraints weight = 23997.541| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.63 r_work: 0.3416 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 17061 Z= 0.148 Angle : 0.531 11.045 23189 Z= 0.276 Chirality : 0.042 0.209 2536 Planarity : 0.004 0.060 2997 Dihedral : 4.828 51.319 2315 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.47 % Favored : 96.48 % Rotamer: Outliers : 4.37 % Allowed : 18.20 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.18), residues: 2101 helix: 2.32 (0.27), residues: 363 sheet: 1.01 (0.24), residues: 482 loop : -1.12 (0.16), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 97 TYR 0.012 0.001 TYR B 34 PHE 0.016 0.001 PHE D 9 TRP 0.009 0.001 TRP M 47 HIS 0.005 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00347 (17038) covalent geometry : angle 0.52579 (23143) SS BOND : bond 0.00415 ( 23) SS BOND : angle 1.76536 ( 46) hydrogen bonds : bond 0.03917 ( 641) hydrogen bonds : angle 4.67548 ( 1854) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 1819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 398 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 ARG cc_start: 0.8915 (ttm-80) cc_final: 0.8674 (ttm-80) REVERT: C 133 LYS cc_start: 0.8530 (mtmt) cc_final: 0.8267 (mtpm) REVERT: C 315 ARG cc_start: 0.8813 (ttm-80) cc_final: 0.8497 (ttt180) REVERT: E 119 GLU cc_start: 0.7276 (tm-30) cc_final: 0.6910 (tm-30) REVERT: E 282 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7818 (mm-40) REVERT: N 79 GLN cc_start: 0.7811 (mp10) cc_final: 0.7608 (mp10) REVERT: N 90 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8452 (mp) REVERT: B 103 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7312 (mp0) REVERT: B 120 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7663 (mp0) REVERT: D 2 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.7079 (tm) REVERT: D 22 TYR cc_start: 0.8717 (OUTLIER) cc_final: 0.8182 (m-80) REVERT: D 108 LEU cc_start: 0.8436 (mt) cc_final: 0.8129 (mp) REVERT: F 152 VAL cc_start: 0.8598 (p) cc_final: 0.8362 (t) outliers start: 79 outliers final: 35 residues processed: 437 average time/residue: 0.6560 time to fit residues: 313.7400 Evaluate side-chains 430 residues out of total 1819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 389 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 282 GLN Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 92 LYS Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 90 LEU Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 158 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 24 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 168 optimal weight: 0.0050 chunk 206 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 89 optimal weight: 0.4980 chunk 172 optimal weight: 0.9980 chunk 183 optimal weight: 0.9980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 111 GLN E 159 ASN E 166 GLN B 125 GLN D 50 ASN ** F 28 ASN ** 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 = 0.3660 r_free = 0.3660 target = 0.116357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.106707 restraints weight = 23986.978| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.63 r_work: 0.3425 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17061 Z= 0.151 Angle : 0.525 10.249 23189 Z= 0.272 Chirality : 0.042 0.177 2536 Planarity : 0.004 0.051 2997 Dihedral : 4.604 51.348 2312 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.57 % Favored : 96.38 % Rotamer: Outliers : 4.87 % Allowed : 18.53 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.18), residues: 2101 helix: 2.34 (0.27), residues: 365 sheet: 1.07 (0.24), residues: 482 loop : -1.11 (0.16), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 97 TYR 0.013 0.001 TYR E 201 PHE 0.015 0.001 PHE D 9 TRP 0.009 0.001 TRP M 47 HIS 0.004 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00357 (17038) covalent geometry : angle 0.52100 (23143) SS BOND : bond 0.00431 ( 23) SS BOND : angle 1.51242 ( 46) hydrogen bonds : bond 0.03888 ( 641) hydrogen bonds : angle 4.59909 ( 1854) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 1819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 390 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ARG cc_start: 0.8652 (mtp85) cc_final: 0.8435 (mtp85) REVERT: A 275 HIS cc_start: 0.8123 (m90) cc_final: 0.7839 (m90) REVERT: A 295 GLN cc_start: 0.8425 (pp30) cc_final: 0.8016 (pp30) REVERT: A 315 ARG cc_start: 0.8920 (ttm-80) cc_final: 0.8664 (ttm-80) REVERT: C 133 LYS cc_start: 0.8572 (mtmt) cc_final: 0.8313 (mtpm) REVERT: C 163 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8146 (tttp) REVERT: C 315 ARG cc_start: 0.8817 (ttm-80) cc_final: 0.8469 (ttt180) REVERT: E 119 GLU cc_start: 0.7257 (tm-30) cc_final: 0.6896 (tm-30) REVERT: E 282 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7774 (mm-40) REVERT: N 79 GLN cc_start: 0.7802 (mp10) cc_final: 0.7580 (mp10) REVERT: N 90 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8499 (mp) REVERT: B 103 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7326 (mp0) REVERT: B 120 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7663 (mp0) REVERT: D 2 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.7062 (tm) REVERT: D 22 TYR cc_start: 0.8723 (OUTLIER) cc_final: 0.8189 (m-80) REVERT: D 164 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7717 (mm-30) REVERT: F 152 VAL cc_start: 0.8597 (p) cc_final: 0.8370 (t) outliers start: 88 outliers final: 48 residues processed: 435 average time/residue: 0.6559 time to fit residues: 311.1658 Evaluate side-chains 444 residues out of total 1819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 389 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 214 LYS Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 282 GLN Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain J residue 11 MET Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 92 LYS Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain N residue 11 MET Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 90 LEU Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 43 ASN Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 158 ASP Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 168 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 41 optimal weight: 0.7980 chunk 128 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 0.0170 chunk 124 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 159 ASN E 166 GLN B 125 GLN D 50 ASN D 125 GLN ** F 28 ASN ** 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 = 0.3656 r_free = 0.3656 target = 0.116047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.106376 restraints weight = 24019.060| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.64 r_work: 0.3421 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17061 Z= 0.167 Angle : 0.529 9.726 23189 Z= 0.274 Chirality : 0.042 0.176 2536 Planarity : 0.004 0.052 2997 Dihedral : 4.559 52.987 2311 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.66 % Favored : 96.29 % Rotamer: Outliers : 4.37 % Allowed : 19.03 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.18), residues: 2101 helix: 2.33 (0.27), residues: 363 sheet: 1.08 (0.24), residues: 482 loop : -1.10 (0.16), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 97 TYR 0.013 0.001 TYR B 34 PHE 0.015 0.001 PHE D 9 TRP 0.010 0.001 TRP M 47 HIS 0.004 0.001 HIS D 111 Details of bonding type rmsd covalent geometry : bond 0.00397 (17038) covalent geometry : angle 0.52512 (23143) SS BOND : bond 0.00426 ( 23) SS BOND : angle 1.49004 ( 46) hydrogen bonds : bond 0.03913 ( 641) hydrogen bonds : angle 4.58500 ( 1854) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 383 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ARG cc_start: 0.8672 (mtp85) cc_final: 0.8360 (mtp85) REVERT: A 275 HIS cc_start: 0.8130 (m90) cc_final: 0.7892 (m90) REVERT: A 295 GLN cc_start: 0.8422 (pp30) cc_final: 0.8123 (pp30) REVERT: A 315 ARG cc_start: 0.8924 (ttm-80) cc_final: 0.8676 (ttm-80) REVERT: C 133 LYS cc_start: 0.8553 (mtmt) cc_final: 0.8294 (mtpm) REVERT: C 315 ARG cc_start: 0.8814 (ttm-80) cc_final: 0.8471 (ttt180) REVERT: E 119 GLU cc_start: 0.7259 (tm-30) cc_final: 0.6935 (tm-30) REVERT: E 282 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7790 (mm-40) REVERT: N 79 GLN cc_start: 0.7816 (mp10) cc_final: 0.7563 (mp10) REVERT: N 90 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8482 (mp) REVERT: B 103 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7360 (mp0) REVERT: B 120 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7682 (mp0) REVERT: D 2 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.7061 (tm) REVERT: D 22 TYR cc_start: 0.8741 (OUTLIER) cc_final: 0.8125 (m-80) REVERT: D 164 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7735 (mm-30) REVERT: F 152 VAL cc_start: 0.8592 (p) cc_final: 0.8369 (t) outliers start: 79 outliers final: 47 residues processed: 425 average time/residue: 0.6949 time to fit residues: 321.2029 Evaluate side-chains 435 residues out of total 1819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 382 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 214 LYS Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 282 GLN Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain J residue 11 MET Chi-restraints excluded: chain J residue 92 LYS Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 90 LEU Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 43 ASN Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 168 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 13 optimal weight: 0.0050 chunk 208 optimal weight: 0.7980 chunk 108 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 155 optimal weight: 0.2980 chunk 48 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 159 ASN E 166 GLN B 125 GLN D 50 ASN D 125 GLN ** F 28 ASN ** 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 = 0.3658 r_free = 0.3658 target = 0.116141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.106504 restraints weight = 23893.325| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.63 r_work: 0.3424 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17061 Z= 0.159 Angle : 0.529 9.235 23189 Z= 0.273 Chirality : 0.042 0.169 2536 Planarity : 0.004 0.052 2997 Dihedral : 4.581 52.850 2311 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.62 % Favored : 96.34 % Rotamer: Outliers : 4.09 % Allowed : 19.63 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.18), residues: 2101 helix: 2.33 (0.27), residues: 363 sheet: 1.06 (0.24), residues: 502 loop : -1.08 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 97 TYR 0.012 0.001 TYR B 34 PHE 0.015 0.001 PHE D 9 TRP 0.009 0.001 TRP M 47 HIS 0.003 0.001 HIS F 26 Details of bonding type rmsd covalent geometry : bond 0.00376 (17038) covalent geometry : angle 0.52459 (23143) SS BOND : bond 0.00423 ( 23) SS BOND : angle 1.55914 ( 46) hydrogen bonds : bond 0.03862 ( 641) hydrogen bonds : angle 4.56714 ( 1854) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 385 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8156 (m-30) cc_final: 0.7945 (m-30) REVERT: A 275 HIS cc_start: 0.8142 (m90) cc_final: 0.7899 (m90) REVERT: A 295 GLN cc_start: 0.8437 (pp30) cc_final: 0.8111 (pp30) REVERT: A 315 ARG cc_start: 0.8925 (ttm-80) cc_final: 0.8669 (ttm-80) REVERT: C 133 LYS cc_start: 0.8562 (mtmt) cc_final: 0.8295 (mtpp) REVERT: C 315 ARG cc_start: 0.8811 (ttm-80) cc_final: 0.8472 (ttt180) REVERT: E 119 GLU cc_start: 0.7254 (tm-30) cc_final: 0.6934 (tm-30) REVERT: E 282 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7787 (mm-40) REVERT: I 69 VAL cc_start: 0.8951 (t) cc_final: 0.8712 (m) REVERT: N 79 GLN cc_start: 0.7826 (mp10) cc_final: 0.7579 (mp10) REVERT: N 90 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8478 (mp) REVERT: B 120 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7674 (mp0) REVERT: D 2 LEU cc_start: 0.7278 (OUTLIER) cc_final: 0.7054 (tm) REVERT: D 22 TYR cc_start: 0.8728 (OUTLIER) cc_final: 0.8196 (m-80) REVERT: D 164 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7755 (mm-30) REVERT: F 152 VAL cc_start: 0.8590 (p) cc_final: 0.8362 (t) outliers start: 74 outliers final: 51 residues processed: 427 average time/residue: 0.6511 time to fit residues: 302.6541 Evaluate side-chains 436 residues out of total 1819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 380 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 214 LYS Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 282 GLN Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain J residue 11 MET Chi-restraints excluded: chain J residue 92 LYS Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 90 LEU Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 43 ASN Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 154 ASN Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 168 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 55 optimal weight: 0.6980 chunk 193 optimal weight: 0.3980 chunk 15 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 27 optimal weight: 0.0470 chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 ASN E 111 GLN E 159 ASN E 166 GLN B 125 GLN D 50 ASN D 125 GLN ** F 28 ASN ** 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 = 0.3662 r_free = 0.3662 target = 0.116413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.106748 restraints weight = 24032.890| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.64 r_work: 0.3427 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17061 Z= 0.145 Angle : 0.521 8.796 23189 Z= 0.270 Chirality : 0.042 0.167 2536 Planarity : 0.004 0.052 2997 Dihedral : 4.556 52.647 2311 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.71 % Favored : 96.24 % Rotamer: Outliers : 3.76 % Allowed : 19.75 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.18), residues: 2101 helix: 2.38 (0.27), residues: 363 sheet: 1.07 (0.24), residues: 502 loop : -1.07 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 97 TYR 0.012 0.001 TYR M 91 PHE 0.015 0.001 PHE D 9 TRP 0.009 0.001 TRP M 47 HIS 0.003 0.001 HIS F 26 Details of bonding type rmsd covalent geometry : bond 0.00343 (17038) covalent geometry : angle 0.51667 (23143) SS BOND : bond 0.00402 ( 23) SS BOND : angle 1.61036 ( 46) hydrogen bonds : bond 0.03777 ( 641) hydrogen bonds : angle 4.52846 ( 1854) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 382 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 HIS cc_start: 0.8122 (m90) cc_final: 0.7877 (m90) REVERT: A 295 GLN cc_start: 0.8439 (pp30) cc_final: 0.8095 (pp30) REVERT: A 315 ARG cc_start: 0.8928 (ttm-80) cc_final: 0.8654 (ttm-80) REVERT: C 133 LYS cc_start: 0.8551 (mtmt) cc_final: 0.8301 (mtpm) REVERT: C 315 ARG cc_start: 0.8808 (ttm-80) cc_final: 0.8471 (ttt180) REVERT: E 119 GLU cc_start: 0.7258 (tm-30) cc_final: 0.6938 (tm-30) REVERT: E 282 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7779 (mm-40) REVERT: I 69 VAL cc_start: 0.8953 (t) cc_final: 0.8713 (m) REVERT: N 79 GLN cc_start: 0.7822 (mp10) cc_final: 0.7578 (mp10) REVERT: N 90 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8507 (mp) REVERT: B 103 GLU cc_start: 0.7525 (mp0) cc_final: 0.7267 (mp0) REVERT: B 120 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7672 (mp0) REVERT: D 2 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.7002 (tm) REVERT: D 22 TYR cc_start: 0.8731 (OUTLIER) cc_final: 0.8203 (m-80) REVERT: D 164 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7763 (mm-30) REVERT: F 152 VAL cc_start: 0.8593 (p) cc_final: 0.8377 (t) outliers start: 68 outliers final: 44 residues processed: 423 average time/residue: 0.6946 time to fit residues: 320.1261 Evaluate side-chains 430 residues out of total 1819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 381 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 282 GLN Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain J residue 11 MET Chi-restraints excluded: chain J residue 92 LYS Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 90 LEU Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 43 ASN Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 168 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 65 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 187 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 175 optimal weight: 0.0670 chunk 120 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 180 optimal weight: 0.6980 chunk 205 optimal weight: 0.5980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 ASN E 159 ASN E 166 GLN B 125 GLN D 50 ASN D 125 GLN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.116394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.106734 restraints weight = 24080.200| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.64 r_work: 0.3428 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17061 Z= 0.150 Angle : 0.528 8.712 23189 Z= 0.273 Chirality : 0.042 0.170 2536 Planarity : 0.004 0.051 2997 Dihedral : 4.550 52.412 2311 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.52 % Favored : 96.43 % Rotamer: Outliers : 3.10 % Allowed : 20.80 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.18), residues: 2101 helix: 2.41 (0.27), residues: 363 sheet: 1.08 (0.24), residues: 502 loop : -1.06 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 97 TYR 0.012 0.001 TYR M 91 PHE 0.015 0.001 PHE D 9 TRP 0.009 0.001 TRP M 47 HIS 0.003 0.001 HIS F 26 Details of bonding type rmsd covalent geometry : bond 0.00356 (17038) covalent geometry : angle 0.52393 (23143) SS BOND : bond 0.00405 ( 23) SS BOND : angle 1.58075 ( 46) hydrogen bonds : bond 0.03781 ( 641) hydrogen bonds : angle 4.52691 ( 1854) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 386 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ARG cc_start: 0.8628 (mtp85) cc_final: 0.8304 (mtp85) REVERT: A 275 HIS cc_start: 0.8122 (m90) cc_final: 0.7868 (m90) REVERT: A 295 GLN cc_start: 0.8448 (pp30) cc_final: 0.8131 (pp30) REVERT: A 315 ARG cc_start: 0.8927 (ttm-80) cc_final: 0.8655 (ttm-80) REVERT: C 133 LYS cc_start: 0.8563 (mtmt) cc_final: 0.8295 (mtpp) REVERT: C 315 ARG cc_start: 0.8810 (ttm-80) cc_final: 0.8478 (ttt180) REVERT: E 119 GLU cc_start: 0.7253 (tm-30) cc_final: 0.6936 (tm-30) REVERT: E 282 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7781 (mm-40) REVERT: I 69 VAL cc_start: 0.8950 (t) cc_final: 0.8710 (m) REVERT: N 79 GLN cc_start: 0.7825 (mp10) cc_final: 0.7578 (mp10) REVERT: N 90 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8498 (mp) REVERT: B 69 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.6921 (pt0) REVERT: B 120 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7667 (mp0) REVERT: D 2 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.7018 (tm) REVERT: D 22 TYR cc_start: 0.8726 (OUTLIER) cc_final: 0.8197 (m-80) REVERT: D 164 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7766 (mm-30) REVERT: F 152 VAL cc_start: 0.8587 (p) cc_final: 0.8371 (t) outliers start: 56 outliers final: 43 residues processed: 418 average time/residue: 0.7357 time to fit residues: 334.7209 Evaluate side-chains 433 residues out of total 1819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 384 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 214 LYS Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 282 GLN Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain J residue 11 MET Chi-restraints excluded: chain J residue 92 LYS Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 90 LEU Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 43 ASN Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 168 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 209 optimal weight: 0.0770 chunk 167 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 202 optimal weight: 0.9990 chunk 159 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 142 optimal weight: 1.9990 chunk 174 optimal weight: 0.8980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 159 ASN E 166 GLN B 125 GLN D 50 ASN D 125 GLN ** F 28 ASN ** 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 = 0.3661 r_free = 0.3661 target = 0.116334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.106661 restraints weight = 23975.222| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.64 r_work: 0.3427 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17061 Z= 0.158 Angle : 0.532 8.704 23189 Z= 0.275 Chirality : 0.042 0.170 2536 Planarity : 0.004 0.052 2997 Dihedral : 4.560 52.742 2311 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.66 % Favored : 96.29 % Rotamer: Outliers : 3.15 % Allowed : 20.91 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.18), residues: 2101 helix: 2.40 (0.27), residues: 363 sheet: 1.04 (0.24), residues: 502 loop : -1.07 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 97 TYR 0.012 0.001 TYR B 34 PHE 0.015 0.001 PHE D 9 TRP 0.009 0.001 TRP M 47 HIS 0.005 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00374 (17038) covalent geometry : angle 0.52829 (23143) SS BOND : bond 0.00409 ( 23) SS BOND : angle 1.57251 ( 46) hydrogen bonds : bond 0.03799 ( 641) hydrogen bonds : angle 4.52457 ( 1854) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4202 Ramachandran restraints generated. 2101 Oldfield, 0 Emsley, 2101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 1819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 391 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.8162 (pttm) cc_final: 0.7920 (ptpp) REVERT: A 172 LYS cc_start: 0.8434 (mmtt) cc_final: 0.8203 (mmtp) REVERT: A 226 GLN cc_start: 0.8291 (mm110) cc_final: 0.8040 (mm-40) REVERT: A 275 HIS cc_start: 0.8125 (m90) cc_final: 0.7876 (m90) REVERT: A 295 GLN cc_start: 0.8447 (pp30) cc_final: 0.8124 (pp30) REVERT: A 315 ARG cc_start: 0.8933 (ttm-80) cc_final: 0.8663 (ttm-80) REVERT: C 133 LYS cc_start: 0.8563 (mtmt) cc_final: 0.8291 (mtpp) REVERT: C 315 ARG cc_start: 0.8807 (ttm-80) cc_final: 0.8476 (ttt180) REVERT: E 119 GLU cc_start: 0.7259 (tm-30) cc_final: 0.6934 (tm-30) REVERT: E 282 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7773 (mm-40) REVERT: I 69 VAL cc_start: 0.8950 (t) cc_final: 0.8713 (m) REVERT: N 79 GLN cc_start: 0.7828 (mp10) cc_final: 0.7544 (mp10) REVERT: N 90 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8460 (mp) REVERT: B 103 GLU cc_start: 0.7485 (mp0) cc_final: 0.7263 (mp0) REVERT: B 120 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7655 (mp0) REVERT: D 2 LEU cc_start: 0.7210 (OUTLIER) cc_final: 0.6990 (tm) REVERT: D 22 TYR cc_start: 0.8726 (OUTLIER) cc_final: 0.8180 (m-80) REVERT: D 164 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7744 (mm-30) REVERT: F 152 VAL cc_start: 0.8583 (p) cc_final: 0.8365 (t) outliers start: 57 outliers final: 45 residues processed: 423 average time/residue: 0.7141 time to fit residues: 328.8291 Evaluate side-chains 429 residues out of total 1819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 379 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 214 LYS Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 282 GLN Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain J residue 11 MET Chi-restraints excluded: chain J residue 92 LYS Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 90 LEU Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 43 ASN Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 168 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 41 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 122 optimal weight: 0.0000 chunk 84 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 121 optimal weight: 0.1980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 322 ASN E 159 ASN E 166 GLN B 125 GLN D 50 ASN D 125 GLN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.116143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.106434 restraints weight = 23957.883| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.63 r_work: 0.3429 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17061 Z= 0.156 Angle : 0.541 8.638 23189 Z= 0.278 Chirality : 0.042 0.171 2536 Planarity : 0.004 0.051 2997 Dihedral : 4.574 52.703 2311 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.52 % Favored : 96.43 % Rotamer: Outliers : 3.15 % Allowed : 20.96 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.18), residues: 2101 helix: 2.37 (0.27), residues: 363 sheet: 1.02 (0.23), residues: 502 loop : -1.07 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 97 TYR 0.012 0.001 TYR M 91 PHE 0.015 0.001 PHE D 9 TRP 0.010 0.001 TRP D 21 HIS 0.004 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00371 (17038) covalent geometry : angle 0.53633 (23143) SS BOND : bond 0.00398 ( 23) SS BOND : angle 1.64994 ( 46) hydrogen bonds : bond 0.03780 ( 641) hydrogen bonds : angle 4.52736 ( 1854) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7637.41 seconds wall clock time: 130 minutes 18.96 seconds (7818.96 seconds total)