Starting phenix.real_space_refine on Fri Aug 7 22:35:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9siu_54932/08_2026/9siu_54932.cif Found real_map, /net/cci-nas-00/data/ceres_data/9siu_54932/08_2026/9siu_54932.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9siu_54932/08_2026/9siu_54932.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9siu_54932/08_2026/9siu_54932.map" model { file = "/net/cci-nas-00/data/ceres_data/9siu_54932/08_2026/9siu_54932.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9siu_54932/08_2026/9siu_54932.cif" } resolution = 2.64 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= 0.002 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 110 5.49 5 S 116 5.16 5 C 14877 2.51 5 N 4024 2.21 5 O 4796 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 82 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23923 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2650 Classifications: {'peptide': 334} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 5} Link IDs: {'PTRANS': 17, 'TRANS': 316} Chain breaks: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 1986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1986 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 8, 'TRANS': 243} Chain: "I" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1417 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 169} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 251 Classifications: {'DNA': 12} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 11} Chain: "D" Number of atoms: 2621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2621 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 15, 'TRANS': 306} Chain: "E" Number of atoms: 2630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2630 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 15, 'TRANS': 307} Chain: "F" Number of atoms: 2617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2617 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 306} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 2630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2630 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 15, 'TRANS': 307} Chain: "G" Number of atoms: 2637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2637 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 15, 'TRANS': 308} Chain: "H" Number of atoms: 2386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2386 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 11, 'TRANS': 280} Chain breaks: 2 Chain: "K" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 810 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain: "J" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1288 Classifications: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 17, 'rna2p_pyr': 10, 'rna3p_pur': 20, 'rna3p_pyr': 13} Link IDs: {'rna2p': 27, 'rna3p': 32} Time building chain proxies: 5.87, per 1000 atoms: 0.25 Number of scatterers: 23923 At special positions: 0 Unit cell: (111.65, 144.275, 161.675, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 116 16.00 P 110 15.00 O 4796 8.00 N 4024 7.00 C 14877 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.13 Conformation dependent library (CDL) restraints added in 1.2 seconds 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5078 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 36 sheets defined 33.8% alpha, 9.6% beta 37 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 3.49 Creating SS restraints... Processing helix chain 'A' and resid 3 through 10 removed outlier: 3.969A pdb=" N LEU A 7 " --> pdb=" O ARG A 3 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A 8 " --> pdb=" O ASN A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 32 removed outlier: 4.659A pdb=" N ASP A 32 " --> pdb=" O PHE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 83 through 86 Processing helix chain 'A' and resid 87 through 95 Processing helix chain 'A' and resid 111 through 117 Processing helix chain 'A' and resid 124 through 134 Processing helix chain 'A' and resid 166 through 179 removed outlier: 3.736A pdb=" N ARG A 179 " --> pdb=" O ASP A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 199 removed outlier: 3.660A pdb=" N GLY A 199 " --> pdb=" O ALA A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 206 Processing helix chain 'A' and resid 217 through 221 Processing helix chain 'A' and resid 223 through 231 removed outlier: 4.138A pdb=" N GLU A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 265 removed outlier: 4.634A pdb=" N LEU A 258 " --> pdb=" O ALA A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 277 removed outlier: 3.771A pdb=" N ARG A 277 " --> pdb=" O ARG A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 293 removed outlier: 3.557A pdb=" N VAL A 285 " --> pdb=" O LYS A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 340 Processing helix chain 'B' and resid 28 through 46 removed outlier: 3.644A pdb=" N PHE B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 130 removed outlier: 4.008A pdb=" N GLU B 130 " --> pdb=" O LYS B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 170 Processing helix chain 'B' and resid 174 through 186 Processing helix chain 'B' and resid 235 through 240 removed outlier: 3.642A pdb=" N LEU B 240 " --> pdb=" O ASN B 237 " (cutoff:3.500A) Processing helix chain 'I' and resid 15 through 23 Processing helix chain 'I' and resid 23 through 35 removed outlier: 3.751A pdb=" N VAL I 27 " --> pdb=" O ASP I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 119 Processing helix chain 'I' and resid 124 through 139 removed outlier: 3.955A pdb=" N HIS I 130 " --> pdb=" O PRO I 126 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS I 132 " --> pdb=" O GLU I 128 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LYS I 133 " --> pdb=" O MET I 129 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS I 134 " --> pdb=" O HIS I 130 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN I 135 " --> pdb=" O ILE I 131 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N GLN I 137 " --> pdb=" O LYS I 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 71 removed outlier: 3.815A pdb=" N LYS D 69 " --> pdb=" O ASP D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 104 No H-bonds generated for 'chain 'D' and resid 102 through 104' Processing helix chain 'D' and resid 111 through 129 Processing helix chain 'D' and resid 131 through 144 Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 186 through 201 Processing helix chain 'D' and resid 250 through 260 Processing helix chain 'D' and resid 267 through 272 Processing helix chain 'D' and resid 296 through 306 Processing helix chain 'D' and resid 312 through 326 Processing helix chain 'E' and resid 63 through 70 removed outlier: 3.873A pdb=" N LYS E 69 " --> pdb=" O ASP E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 104 No H-bonds generated for 'chain 'E' and resid 102 through 104' Processing helix chain 'E' and resid 111 through 129 Processing helix chain 'E' and resid 131 through 144 Processing helix chain 'E' and resid 175 through 177 No H-bonds generated for 'chain 'E' and resid 175 through 177' Processing helix chain 'E' and resid 186 through 201 Processing helix chain 'E' and resid 250 through 259 Processing helix chain 'E' and resid 267 through 272 Processing helix chain 'E' and resid 296 through 306 Processing helix chain 'E' and resid 312 through 326 Processing helix chain 'F' and resid 63 through 71 removed outlier: 3.844A pdb=" N LYS F 69 " --> pdb=" O ASP F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 104 No H-bonds generated for 'chain 'F' and resid 102 through 104' Processing helix chain 'F' and resid 111 through 129 Processing helix chain 'F' and resid 131 through 145 Processing helix chain 'F' and resid 175 through 177 No H-bonds generated for 'chain 'F' and resid 175 through 177' Processing helix chain 'F' and resid 186 through 201 removed outlier: 3.526A pdb=" N GLN F 195 " --> pdb=" O GLU F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 259 Processing helix chain 'F' and resid 267 through 272 removed outlier: 3.576A pdb=" N TYR F 271 " --> pdb=" O ASP F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 306 removed outlier: 3.540A pdb=" N ARG F 303 " --> pdb=" O LYS F 299 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 326 Processing helix chain 'C' and resid 36 through 40 Processing helix chain 'C' and resid 63 through 71 removed outlier: 3.769A pdb=" N LYS C 69 " --> pdb=" O ASP C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 106 Processing helix chain 'C' and resid 111 through 129 Processing helix chain 'C' and resid 131 through 144 Processing helix chain 'C' and resid 175 through 177 No H-bonds generated for 'chain 'C' and resid 175 through 177' Processing helix chain 'C' and resid 186 through 201 Processing helix chain 'C' and resid 250 through 259 Processing helix chain 'C' and resid 267 through 272 removed outlier: 3.624A pdb=" N TYR C 271 " --> pdb=" O ASP C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 306 Processing helix chain 'C' and resid 312 through 326 Processing helix chain 'G' and resid 36 through 40 Processing helix chain 'G' and resid 63 through 68 removed outlier: 4.042A pdb=" N GLU G 68 " --> pdb=" O PRO G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 104 No H-bonds generated for 'chain 'G' and resid 102 through 104' Processing helix chain 'G' and resid 111 through 129 Processing helix chain 'G' and resid 131 through 144 Processing helix chain 'G' and resid 175 through 177 No H-bonds generated for 'chain 'G' and resid 175 through 177' Processing helix chain 'G' and resid 186 through 201 Processing helix chain 'G' and resid 250 through 259 Processing helix chain 'G' and resid 267 through 272 removed outlier: 3.761A pdb=" N TYR G 271 " --> pdb=" O ASP G 267 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 306 Processing helix chain 'G' and resid 312 through 326 removed outlier: 3.740A pdb=" N ILE G 324 " --> pdb=" O MET G 320 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 40 Processing helix chain 'H' and resid 111 through 129 Processing helix chain 'H' and resid 131 through 144 Processing helix chain 'H' and resid 145 through 153 removed outlier: 6.212A pdb=" N ARG H 150 " --> pdb=" O PHE H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 186 through 202 Processing helix chain 'H' and resid 250 through 259 Processing helix chain 'H' and resid 267 through 272 Processing helix chain 'H' and resid 292 through 295 Processing helix chain 'H' and resid 296 through 306 Processing helix chain 'H' and resid 312 through 326 removed outlier: 3.790A pdb=" N TYR H 318 " --> pdb=" O GLU H 314 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 40 Processing sheet with id=AA3, first strand: chain 'A' and resid 148 through 153 removed outlier: 4.269A pdb=" N LYS A 148 " --> pdb=" O ILE A 163 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 158 through 163 current: chain 'B' and resid 101 through 112 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 101 through 112 current: chain 'B' and resid 137 through 141 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 137 through 141 current: chain 'B' and resid 214 through 229 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 214 through 229 current: chain 'B' and resid 249 through 253 Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 186 removed outlier: 8.439A pdb=" N VAL B 24 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N PHE A 212 " --> pdb=" O VAL B 24 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 249 through 250 removed outlier: 4.675A pdb=" N SER A 324 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 66 through 68 Processing sheet with id=AA7, first strand: chain 'I' and resid 2 through 8 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 2 through 8 current: chain 'I' and resid 57 through 62 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'I' and resid 47 through 48 removed outlier: 4.018A pdb=" N HIS I 53 " --> pdb=" O SER I 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 99 through 100 removed outlier: 3.650A pdb=" N ALA I 160 " --> pdb=" O LYS I 100 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA I 142 " --> pdb=" O LEU I 159 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 106 through 109 Processing sheet with id=AB2, first strand: chain 'D' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 25 through 27 current: chain 'D' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 45 through 46 current: chain 'D' and resid 172 through 173 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 172 through 173 current: chain 'D' and resid 246 through 249 No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 50 through 51 removed outlier: 4.255A pdb=" N CYS D 82 " --> pdb=" O VAL D 223 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 54 through 57 Processing sheet with id=AB5, first strand: chain 'D' and resid 282 through 283 removed outlier: 3.801A pdb=" N ALA D 283 " --> pdb=" O ILE D 288 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE D 288 " --> pdb=" O ALA D 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'E' and resid 106 through 109 Processing sheet with id=AB7, first strand: chain 'E' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 25 through 27 current: chain 'E' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 45 through 46 current: chain 'E' and resid 167 through 168 No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'E' and resid 50 through 57 removed outlier: 4.019A pdb=" N CYS E 82 " --> pdb=" O VAL E 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 242 through 243 Processing sheet with id=AC1, first strand: chain 'E' and resid 282 through 283 Processing sheet with id=AC2, first strand: chain 'F' and resid 19 through 21 Processing sheet with id=AC3, first strand: chain 'F' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 25 through 27 current: chain 'F' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 45 through 46 current: chain 'F' and resid 167 through 168 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 167 through 168 current: chain 'F' and resid 246 through 249 No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'F' and resid 50 through 57 removed outlier: 4.323A pdb=" N CYS F 82 " --> pdb=" O VAL F 223 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 260 through 262 Processing sheet with id=AC6, first strand: chain 'F' and resid 282 through 283 Processing sheet with id=AC7, first strand: chain 'C' and resid 108 through 109 Processing sheet with id=AC8, first strand: chain 'C' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 25 through 27 current: chain 'C' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 45 through 46 current: chain 'C' and resid 167 through 168 No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'C' and resid 50 through 57 removed outlier: 4.158A pdb=" N CYS C 82 " --> pdb=" O VAL C 223 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 242 through 243 Processing sheet with id=AD2, first strand: chain 'G' and resid 106 through 109 Processing sheet with id=AD3, first strand: chain 'G' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 25 through 27 current: chain 'G' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 45 through 46 current: chain 'G' and resid 167 through 168 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 167 through 168 current: chain 'G' and resid 246 through 249 No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'G' and resid 50 through 57 removed outlier: 3.980A pdb=" N CYS G 82 " --> pdb=" O VAL G 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 260 through 262 Processing sheet with id=AD6, first strand: chain 'G' and resid 282 through 283 removed outlier: 3.665A pdb=" N ILE G 288 " --> pdb=" O ALA G 283 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 106 through 109 Processing sheet with id=AD8, first strand: chain 'H' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 25 through 27 current: chain 'H' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 45 through 46 current: chain 'H' and resid 172 through 173 No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'H' and resid 260 through 262 645 hydrogen bonds defined for protein. 1806 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 90 hydrogen bonds 176 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 56 stacking parallelities Total time for adding SS restraints: 4.89 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 6929 1.33 - 1.45: 4702 1.45 - 1.57: 12635 1.57 - 1.69: 219 1.69 - 1.81: 185 Bond restraints: 24670 Sorted by residual: bond pdb=" C3' DT K 45 " pdb=" C2' DT K 45 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.31e+01 bond pdb=" C3' DA L 12 " pdb=" C2' DA L 12 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" N VAL I 146 " pdb=" CA VAL I 146 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.22e-02 6.72e+03 9.44e+00 bond pdb=" C3' DA K 27 " pdb=" C2' DA K 27 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.11e+00 bond pdb=" N MET A 97 " pdb=" CA MET A 97 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.18e-02 7.18e+03 8.77e+00 ... (remaining 24665 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 32814 1.79 - 3.58: 922 3.58 - 5.37: 66 5.37 - 7.16: 12 7.16 - 8.95: 2 Bond angle restraints: 33816 Sorted by residual: angle pdb=" O4' DC K 38 " pdb=" C4' DC K 38 " pdb=" C3' DC K 38 " ideal model delta sigma weight residual 106.00 102.75 3.25 6.00e-01 2.78e+00 2.93e+01 angle pdb=" O4' DC K 14 " pdb=" C4' DC K 14 " pdb=" C3' DC K 14 " ideal model delta sigma weight residual 106.00 102.79 3.21 6.00e-01 2.78e+00 2.86e+01 angle pdb=" O4' DT K 26 " pdb=" C4' DT K 26 " pdb=" C3' DT K 26 " ideal model delta sigma weight residual 106.00 103.11 2.89 6.00e-01 2.78e+00 2.33e+01 angle pdb=" O4' DT K 37 " pdb=" C4' DT K 37 " pdb=" C3' DT K 37 " ideal model delta sigma weight residual 106.00 103.24 2.76 6.00e-01 2.78e+00 2.11e+01 angle pdb=" C TYR A 232 " pdb=" CA TYR A 232 " pdb=" CB TYR A 232 " ideal model delta sigma weight residual 110.42 119.37 -8.95 1.99e+00 2.53e-01 2.02e+01 ... (remaining 33811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.97: 13852 33.97 - 67.94: 961 67.94 - 101.91: 80 101.91 - 135.88: 0 135.88 - 169.85: 1 Dihedral angle restraints: 14894 sinusoidal: 7035 harmonic: 7859 Sorted by residual: dihedral pdb=" CA ASP A 246 " pdb=" C ASP A 246 " pdb=" N ASN A 247 " pdb=" CA ASN A 247 " ideal model delta harmonic sigma weight residual 180.00 153.74 26.26 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA MET A 104 " pdb=" C MET A 104 " pdb=" N GLU A 105 " pdb=" CA GLU A 105 " ideal model delta harmonic sigma weight residual 180.00 154.08 25.92 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" O4' U J 44 " pdb=" C1' U J 44 " pdb=" N1 U J 44 " pdb=" C2 U J 44 " ideal model delta sinusoidal sigma weight residual -128.00 -57.39 -70.61 1 1.70e+01 3.46e-03 2.22e+01 ... (remaining 14891 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 3600 0.107 - 0.215: 148 0.215 - 0.322: 0 0.322 - 0.429: 0 0.429 - 0.536: 1 Chirality restraints: 3749 Sorted by residual: chirality pdb=" P DA L 2 " pdb=" OP1 DA L 2 " pdb=" OP2 DA L 2 " pdb=" O5' DA L 2 " both_signs ideal model delta sigma weight residual True 2.34 -2.87 -0.54 2.00e-01 2.50e+01 7.19e+00 chirality pdb=" C1' C J 28 " pdb=" O4' C J 28 " pdb=" C2' C J 28 " pdb=" N1 C J 28 " both_signs ideal model delta sigma weight residual False 2.47 2.28 0.19 2.00e-01 2.50e+01 9.43e-01 chirality pdb=" CB ILE I 58 " pdb=" CA ILE I 58 " pdb=" CG1 ILE I 58 " pdb=" CG2 ILE I 58 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.39e-01 ... (remaining 3746 not shown) Planarity restraints: 3932 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 105 " -0.013 2.00e-02 2.50e+03 2.70e-02 7.26e+00 pdb=" C GLU A 105 " 0.047 2.00e-02 2.50e+03 pdb=" O GLU A 105 " -0.018 2.00e-02 2.50e+03 pdb=" N HIS A 106 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU G 309 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.76e+00 pdb=" C GLU G 309 " 0.045 2.00e-02 2.50e+03 pdb=" O GLU G 309 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP G 310 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR G 265 " -0.033 5.00e-02 4.00e+02 5.07e-02 4.11e+00 pdb=" N PRO G 266 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO G 266 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO G 266 " -0.028 5.00e-02 4.00e+02 ... (remaining 3929 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2354 2.74 - 3.28: 23352 3.28 - 3.82: 42863 3.82 - 4.36: 54258 4.36 - 4.90: 87468 Nonbonded interactions: 210295 Sorted by model distance: nonbonded pdb=" OE1 GLU F 61 " pdb=" NH2 ARG G 15 " model vdw 2.204 3.120 nonbonded pdb=" O GLU C 278 " pdb=" OH TYR C 318 " model vdw 2.224 3.040 nonbonded pdb=" O LEU C 311 " pdb=" NZ LYS C 316 " model vdw 2.225 3.120 nonbonded pdb=" OG SER E 57 " pdb=" OE1 GLU F 278 " model vdw 2.227 3.040 nonbonded pdb=" O GLY A 26 " pdb=" OG SER A 30 " model vdw 2.227 3.040 ... (remaining 210290 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 'C' and (resid 12 through 51 or resid 79 through 231 or resid 237 through \ 333)) selection = (chain 'D' and (resid 12 through 51 or resid 79 through 231 or resid 237 through \ 333)) selection = (chain 'E' and (resid 12 through 51 or resid 79 through 231 or resid 237 through \ 333)) selection = (chain 'F' and (resid 12 through 51 or resid 79 through 231 or resid 237 through \ 333)) selection = (chain 'G' and (resid 12 through 51 or resid 79 through 231 or resid 237 through \ 333)) selection = (chain 'H' and resid 12 through 333) } 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: 5.100 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: 0.030 Extract box with map and model: 0.590 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 27.020 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 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 : 0.004 0.043 24670 Z= 0.243 Angle : 0.638 8.952 33816 Z= 0.445 Chirality : 0.047 0.536 3749 Planarity : 0.004 0.051 3932 Dihedral : 20.496 169.852 9816 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.79 % Favored : 96.10 % Rotamer: Outliers : 2.28 % Allowed : 25.51 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.16), residues: 2638 helix: 0.94 (0.19), residues: 759 sheet: 0.45 (0.26), residues: 439 loop : -1.14 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 325 TYR 0.018 0.001 TYR G 224 PHE 0.032 0.001 PHE D 273 TRP 0.007 0.001 TRP G 33 HIS 0.007 0.001 HIS I 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.24 (24670) covalent geometry : angle 0.63841 / 0.45 (33816) hydrogen bonds : bond 0.15192 / 9.87 ( 735) hydrogen bonds : angle 6.34230 / 4.46 ( 1982) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 627 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.6671 (tp-100) cc_final: 0.6389 (tp-100) REVERT: A 264 LYS cc_start: 0.7046 (mttt) cc_final: 0.6778 (mttt) REVERT: A 283 GLU cc_start: 0.6539 (tm-30) cc_final: 0.6288 (tm-30) REVERT: I 115 MET cc_start: 0.5799 (mpm) cc_final: 0.5531 (mpm) REVERT: E 227 GLN cc_start: 0.7968 (tt0) cc_final: 0.7748 (tt0) REVERT: E 244 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7710 (mt-10) REVERT: F 72 MET cc_start: 0.7751 (mmm) cc_final: 0.7413 (mmm) REVERT: C 169 TYR cc_start: 0.8136 (m-80) cc_final: 0.7646 (m-80) REVERT: C 231 PHE cc_start: 0.5969 (m-80) cc_final: 0.5595 (m-80) REVERT: G 29 GLU cc_start: 0.6841 (mp0) cc_final: 0.6617 (mp0) REVERT: G 303 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7653 (mtm-85) REVERT: G 309 GLU cc_start: 0.5814 (mt-10) cc_final: 0.5565 (mt-10) outliers start: 54 outliers final: 35 residues processed: 660 average time/residue: 0.6835 time to fit residues: 515.1902 Evaluate side-chains 620 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 584 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 25 PHE Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 56 ASN Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 94 ASP Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 102 ILE Chi-restraints excluded: chain I residue 104 GLU Chi-restraints excluded: chain I residue 117 LYS Chi-restraints excluded: chain I residue 144 ILE Chi-restraints excluded: chain I residue 145 LYS Chi-restraints excluded: chain I residue 155 TYR Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain G residue 303 ARG Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 305 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.2980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.0370 chunk 155 optimal weight: 0.0980 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 0.0050 chunk 111 optimal weight: 2.9990 overall best weight: 0.2272 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 ASN A 159 HIS A 319 ASN B 105 ASN B 208 GLN D 227 GLN D 256 ASN ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 GLN C 80 GLN C 195 GLN G 77 GLN G 178 ASN G 195 GLN H 256 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.132368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.110379 restraints weight = 34237.095| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.55 r_work: 0.3385 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.0901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24670 Z= 0.126 Angle : 0.557 7.355 33816 Z= 0.308 Chirality : 0.042 0.251 3749 Planarity : 0.004 0.049 3932 Dihedral : 18.154 173.534 4458 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.83 % Favored : 96.06 % Rotamer: Outliers : 3.97 % Allowed : 26.31 % Favored : 69.72 % 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: -0.21 (0.16), residues: 2638 helix: 1.11 (0.19), residues: 767 sheet: 0.59 (0.26), residues: 446 loop : -1.11 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 142 TYR 0.014 0.001 TYR D 268 PHE 0.019 0.001 PHE F 273 TRP 0.005 0.001 TRP G 149 HIS 0.007 0.001 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.13 (24670) covalent geometry : angle 0.55656 / 0.31 (33816) hydrogen bonds : bond 0.04831 / 3.27 ( 735) hydrogen bonds : angle 5.45078 / 3.89 ( 1982) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 600 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.7132 (tp-100) cc_final: 0.6775 (tp-100) REVERT: A 283 GLU cc_start: 0.7022 (tm-30) cc_final: 0.6689 (tm-30) REVERT: I 66 GLU cc_start: 0.6117 (OUTLIER) cc_final: 0.5847 (tm-30) REVERT: I 115 MET cc_start: 0.5839 (OUTLIER) cc_final: 0.5537 (mpm) REVERT: D 66 LYS cc_start: 0.8041 (mtpp) cc_final: 0.7490 (mtpp) REVERT: D 68 GLU cc_start: 0.7622 (tm-30) cc_final: 0.7404 (tm-30) REVERT: D 70 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7450 (mt-10) REVERT: D 123 ASP cc_start: 0.7715 (m-30) cc_final: 0.7424 (m-30) REVERT: D 272 GLU cc_start: 0.7975 (pt0) cc_final: 0.7731 (mt-10) REVERT: E 244 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8143 (mt-10) REVERT: F 12 LEU cc_start: 0.7685 (mp) cc_final: 0.7283 (mt) REVERT: F 66 LYS cc_start: 0.7869 (mttt) cc_final: 0.7591 (mttm) REVERT: F 72 MET cc_start: 0.8478 (mmm) cc_final: 0.8259 (mmm) REVERT: C 169 TYR cc_start: 0.8332 (m-80) cc_final: 0.8131 (m-80) REVERT: C 302 ASP cc_start: 0.8100 (m-30) cc_final: 0.7860 (m-30) REVERT: G 29 GLU cc_start: 0.8130 (mp0) cc_final: 0.7827 (mp0) REVERT: G 124 GLU cc_start: 0.7292 (tp30) cc_final: 0.7087 (tp30) REVERT: G 184 GLU cc_start: 0.7035 (pm20) cc_final: 0.6821 (pm20) outliers start: 94 outliers final: 42 residues processed: 655 average time/residue: 0.5930 time to fit residues: 445.5823 Evaluate side-chains 615 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 571 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 66 GLU Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 102 ILE Chi-restraints excluded: chain I residue 103 ARG Chi-restraints excluded: chain I residue 104 GLU Chi-restraints excluded: chain I residue 115 MET Chi-restraints excluded: chain I residue 117 LYS Chi-restraints excluded: chain I residue 129 MET Chi-restraints excluded: chain I residue 137 GLN Chi-restraints excluded: chain I residue 144 ILE Chi-restraints excluded: chain I residue 145 LYS Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain F residue 242 LYS Chi-restraints excluded: chain F residue 330 SER Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 82 CYS Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 296 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 161 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 chunk 71 optimal weight: 7.9990 chunk 139 optimal weight: 0.4980 chunk 116 optimal weight: 0.0870 chunk 135 optimal weight: 2.9990 chunk 150 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 153 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 ASN A 159 HIS A 319 ASN ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 GLN ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 ASN ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 GLN F 227 GLN C 80 GLN G 77 GLN G 178 ASN ** H 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 279 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.131090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.109127 restraints weight = 34222.527| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.55 r_work: 0.3375 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24670 Z= 0.153 Angle : 0.546 7.527 33816 Z= 0.301 Chirality : 0.042 0.236 3749 Planarity : 0.004 0.051 3932 Dihedral : 18.032 174.425 4416 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.56 % Favored : 96.36 % Rotamer: Outliers : 3.63 % Allowed : 26.90 % Favored : 69.47 % 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 (0.16), residues: 2638 helix: 1.18 (0.19), residues: 765 sheet: 0.77 (0.26), residues: 422 loop : -1.15 (0.15), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 325 TYR 0.018 0.001 TYR A 23 PHE 0.012 0.001 PHE H 37 TRP 0.005 0.001 TRP A 74 HIS 0.006 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (24670) covalent geometry : angle 0.54622 / 0.30 (33816) hydrogen bonds : bond 0.04686 / 3.20 ( 735) hydrogen bonds : angle 5.30990 / 3.80 ( 1982) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 574 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.7300 (mtt180) REVERT: A 142 ARG cc_start: 0.5617 (OUTLIER) cc_final: 0.4940 (ttt90) REVERT: A 205 LYS cc_start: 0.8700 (mttt) cc_final: 0.8385 (mtpp) REVERT: A 283 GLU cc_start: 0.7059 (tm-30) cc_final: 0.6820 (tm-30) REVERT: I 115 MET cc_start: 0.5672 (OUTLIER) cc_final: 0.5341 (mpm) REVERT: D 68 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7408 (tm-30) REVERT: D 70 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7760 (mt-10) REVERT: D 123 ASP cc_start: 0.7710 (m-30) cc_final: 0.7474 (m-30) REVERT: E 191 GLU cc_start: 0.7309 (mm-30) cc_final: 0.7101 (mm-30) REVERT: E 244 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8157 (mt-10) REVERT: F 12 LEU cc_start: 0.7723 (mp) cc_final: 0.7330 (mt) REVERT: F 66 LYS cc_start: 0.7897 (mttt) cc_final: 0.7651 (mttm) REVERT: F 278 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7591 (mm-30) REVERT: G 29 GLU cc_start: 0.8085 (mp0) cc_final: 0.7825 (mp0) REVERT: G 184 GLU cc_start: 0.6973 (pm20) cc_final: 0.6739 (pm20) REVERT: G 304 MET cc_start: 0.8055 (ttt) cc_final: 0.7693 (ttt) REVERT: H 262 ASP cc_start: 0.8638 (t0) cc_final: 0.8333 (t70) REVERT: H 267 ASP cc_start: 0.7439 (p0) cc_final: 0.7179 (p0) REVERT: H 270 THR cc_start: 0.7833 (OUTLIER) cc_final: 0.7623 (p) outliers start: 86 outliers final: 46 residues processed: 623 average time/residue: 0.6357 time to fit residues: 453.2139 Evaluate side-chains 598 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 548 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ARG Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 25 PHE Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 102 ILE Chi-restraints excluded: chain I residue 104 GLU Chi-restraints excluded: chain I residue 115 MET Chi-restraints excluded: chain I residue 117 LYS Chi-restraints excluded: chain I residue 137 GLN Chi-restraints excluded: chain I residue 144 ILE Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 256 ASN Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 171 SER Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 82 CYS Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 270 THR Chi-restraints excluded: chain H residue 272 GLU Chi-restraints excluded: chain H residue 285 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 19 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 219 optimal weight: 0.0030 chunk 255 optimal weight: 2.9990 chunk 264 optimal weight: 3.9990 chunk 239 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 211 optimal weight: 0.6980 chunk 136 optimal weight: 0.7980 chunk 88 optimal weight: 0.5980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 HIS A 319 ASN ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 GLN ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 GLN F 308 ASN C 80 GLN G 77 GLN G 178 ASN ** H 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.131431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.109443 restraints weight = 34112.785| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.56 r_work: 0.3381 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24670 Z= 0.139 Angle : 0.531 9.458 33816 Z= 0.293 Chirality : 0.042 0.237 3749 Planarity : 0.004 0.051 3932 Dihedral : 17.984 174.188 4407 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.64 % Favored : 96.25 % Rotamer: Outliers : 3.93 % Allowed : 27.03 % Favored : 69.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.16), residues: 2638 helix: 1.24 (0.19), residues: 767 sheet: 0.81 (0.26), residues: 422 loop : -1.12 (0.15), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 303 TYR 0.020 0.001 TYR A 292 PHE 0.018 0.001 PHE F 273 TRP 0.005 0.001 TRP G 149 HIS 0.007 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (24670) covalent geometry : angle 0.53105 / 0.29 (33816) hydrogen bonds : bond 0.04437 / 3.02 ( 735) hydrogen bonds : angle 5.18217 / 3.73 ( 1982) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 571 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7281 (mtt180) REVERT: A 205 LYS cc_start: 0.8690 (mttt) cc_final: 0.8424 (mtpp) REVERT: A 264 LYS cc_start: 0.7488 (mttt) cc_final: 0.6960 (tttt) REVERT: A 283 GLU cc_start: 0.7066 (tm-30) cc_final: 0.6831 (tm-30) REVERT: B 175 MET cc_start: 0.6784 (OUTLIER) cc_final: 0.6557 (tpp) REVERT: I 115 MET cc_start: 0.5545 (OUTLIER) cc_final: 0.5249 (mpm) REVERT: I 132 LYS cc_start: 0.7670 (mmmt) cc_final: 0.7467 (mmmt) REVERT: D 68 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7418 (tm-30) REVERT: D 70 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7718 (mt-10) REVERT: D 123 ASP cc_start: 0.7698 (m-30) cc_final: 0.7446 (m-30) REVERT: E 191 GLU cc_start: 0.7301 (mm-30) cc_final: 0.7038 (mm-30) REVERT: E 244 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8170 (mt-10) REVERT: E 303 ARG cc_start: 0.8320 (mtp85) cc_final: 0.8089 (mtp85) REVERT: F 12 LEU cc_start: 0.7731 (mp) cc_final: 0.7341 (mt) REVERT: F 29 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7781 (mm-30) REVERT: F 66 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7662 (mttm) REVERT: F 120 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7168 (tm130) REVERT: F 124 GLU cc_start: 0.7871 (pt0) cc_final: 0.7538 (pt0) REVERT: F 278 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7580 (mm-30) REVERT: C 81 SER cc_start: 0.8619 (m) cc_final: 0.8321 (p) REVERT: G 29 GLU cc_start: 0.8064 (mp0) cc_final: 0.7808 (mp0) REVERT: G 69 LYS cc_start: 0.8067 (mptm) cc_final: 0.7837 (mptm) REVERT: G 184 GLU cc_start: 0.6964 (pm20) cc_final: 0.6737 (pm20) REVERT: H 262 ASP cc_start: 0.8642 (t0) cc_final: 0.8349 (t70) REVERT: H 267 ASP cc_start: 0.7440 (p0) cc_final: 0.7141 (p0) outliers start: 93 outliers final: 47 residues processed: 614 average time/residue: 0.6796 time to fit residues: 477.6052 Evaluate side-chains 619 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 566 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ARG Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 102 ILE Chi-restraints excluded: chain I residue 104 GLU Chi-restraints excluded: chain I residue 115 MET Chi-restraints excluded: chain I residue 117 LYS Chi-restraints excluded: chain I residue 128 GLU Chi-restraints excluded: chain I residue 129 MET Chi-restraints excluded: chain I residue 137 GLN Chi-restraints excluded: chain I residue 144 ILE Chi-restraints excluded: chain I residue 145 LYS Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 256 ASN Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 66 LYS Chi-restraints excluded: chain F residue 120 GLN Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 272 GLU Chi-restraints excluded: chain H residue 285 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 45 optimal weight: 1.9990 chunk 215 optimal weight: 0.3980 chunk 239 optimal weight: 1.9990 chunk 108 optimal weight: 0.0470 chunk 146 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 57 optimal weight: 0.0980 chunk 44 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 HIS A 319 ASN B 208 GLN D 227 GLN ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 ASN F 195 GLN G 178 ASN H 151 ASN ** H 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 279 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.132184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.110105 restraints weight = 33787.577| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.54 r_work: 0.3389 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24670 Z= 0.130 Angle : 0.522 9.929 33816 Z= 0.287 Chirality : 0.041 0.241 3749 Planarity : 0.004 0.050 3932 Dihedral : 17.937 174.086 4407 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.56 % Favored : 96.32 % Rotamer: Outliers : 3.80 % Allowed : 26.77 % Favored : 69.43 % 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: -0.04 (0.16), residues: 2638 helix: 1.35 (0.19), residues: 761 sheet: 0.89 (0.27), residues: 421 loop : -1.10 (0.15), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 303 TYR 0.023 0.001 TYR A 292 PHE 0.010 0.001 PHE A 212 TRP 0.005 0.001 TRP G 149 HIS 0.007 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (24670) covalent geometry : angle 0.52186 / 0.29 (33816) hydrogen bonds : bond 0.04253 / 2.90 ( 735) hydrogen bonds : angle 5.06768 / 3.64 ( 1982) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 581 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.7124 (mtt180) REVERT: A 142 ARG cc_start: 0.5483 (OUTLIER) cc_final: 0.4579 (ttt90) REVERT: A 205 LYS cc_start: 0.8721 (mttt) cc_final: 0.8435 (mtpp) REVERT: A 264 LYS cc_start: 0.7350 (mttt) cc_final: 0.7042 (tttt) REVERT: A 283 GLU cc_start: 0.7058 (tm-30) cc_final: 0.6852 (tm-30) REVERT: A 322 MET cc_start: 0.3907 (OUTLIER) cc_final: 0.3644 (ttp) REVERT: B 175 MET cc_start: 0.6742 (OUTLIER) cc_final: 0.6517 (tpp) REVERT: I 88 LYS cc_start: 0.7974 (mmtm) cc_final: 0.7676 (mmtm) REVERT: I 115 MET cc_start: 0.5406 (OUTLIER) cc_final: 0.5147 (mpm) REVERT: I 132 LYS cc_start: 0.7679 (mmmt) cc_final: 0.7469 (mmmt) REVERT: I 145 LYS cc_start: 0.6777 (OUTLIER) cc_final: 0.6075 (tmmm) REVERT: D 70 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7741 (mt-10) REVERT: D 123 ASP cc_start: 0.7680 (m-30) cc_final: 0.7437 (m-30) REVERT: E 191 GLU cc_start: 0.7328 (mm-30) cc_final: 0.7092 (mm-30) REVERT: E 244 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8158 (mt-10) REVERT: E 303 ARG cc_start: 0.8309 (mtp85) cc_final: 0.8090 (mtp85) REVERT: F 12 LEU cc_start: 0.7731 (mp) cc_final: 0.7342 (mt) REVERT: F 66 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7679 (mttm) REVERT: F 278 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7629 (mm-30) REVERT: C 81 SER cc_start: 0.8623 (m) cc_final: 0.8336 (p) REVERT: C 307 LYS cc_start: 0.8666 (mtpp) cc_final: 0.8426 (mtmm) REVERT: G 29 GLU cc_start: 0.8097 (mp0) cc_final: 0.7826 (mp0) REVERT: G 69 LYS cc_start: 0.8053 (mptm) cc_final: 0.7818 (mptm) REVERT: G 184 GLU cc_start: 0.6948 (pm20) cc_final: 0.6718 (pm20) REVERT: H 262 ASP cc_start: 0.8653 (t0) cc_final: 0.8323 (t70) outliers start: 90 outliers final: 56 residues processed: 626 average time/residue: 0.6702 time to fit residues: 480.8073 Evaluate side-chains 626 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 563 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 88 ARG Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 25 PHE Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 102 ILE Chi-restraints excluded: chain I residue 104 GLU Chi-restraints excluded: chain I residue 115 MET Chi-restraints excluded: chain I residue 117 LYS Chi-restraints excluded: chain I residue 128 GLU Chi-restraints excluded: chain I residue 129 MET Chi-restraints excluded: chain I residue 137 GLN Chi-restraints excluded: chain I residue 144 ILE Chi-restraints excluded: chain I residue 145 LYS Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 256 ASN Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain F residue 66 LYS Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 308 ASN Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 272 GLU Chi-restraints excluded: chain H residue 285 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 49 optimal weight: 0.9990 chunk 205 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 240 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 chunk 273 optimal weight: 9.9990 chunk 73 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 ASN ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 GLN D 227 GLN ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 178 ASN F 195 GLN C 80 GLN G 77 GLN G 178 ASN H 227 GLN ** H 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.128532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.106380 restraints weight = 33887.491| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.55 r_work: 0.3334 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 24670 Z= 0.254 Angle : 0.607 10.161 33816 Z= 0.328 Chirality : 0.045 0.238 3749 Planarity : 0.005 0.056 3932 Dihedral : 17.982 174.442 4407 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.94 % Favored : 95.98 % Rotamer: Outliers : 4.56 % Allowed : 26.65 % Favored : 68.79 % 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: -0.23 (0.16), residues: 2638 helix: 1.22 (0.19), residues: 765 sheet: 0.73 (0.26), residues: 434 loop : -1.25 (0.15), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 325 TYR 0.022 0.002 TYR A 23 PHE 0.017 0.002 PHE G 273 TRP 0.015 0.002 TRP A 74 HIS 0.010 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00593 / 0.25 (24670) covalent geometry : angle 0.60708 / 0.33 (33816) hydrogen bonds : bond 0.05106 / 3.48 ( 735) hydrogen bonds : angle 5.34471 / 3.83 ( 1982) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 591 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7178 (mtt90) REVERT: A 205 LYS cc_start: 0.8718 (mttt) cc_final: 0.8456 (mtpp) REVERT: A 264 LYS cc_start: 0.7471 (mttt) cc_final: 0.7110 (tttt) REVERT: A 283 GLU cc_start: 0.7110 (tm-30) cc_final: 0.6877 (tm-30) REVERT: B 180 ILE cc_start: 0.7814 (mm) cc_final: 0.7562 (mp) REVERT: I 14 ILE cc_start: 0.7534 (OUTLIER) cc_final: 0.7229 (mt) REVERT: I 88 LYS cc_start: 0.8040 (mmtm) cc_final: 0.7749 (mmtm) REVERT: I 115 MET cc_start: 0.5451 (OUTLIER) cc_final: 0.5175 (mpm) REVERT: D 70 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7744 (mt-10) REVERT: D 123 ASP cc_start: 0.7743 (m-30) cc_final: 0.7477 (m-30) REVERT: E 191 GLU cc_start: 0.7384 (mm-30) cc_final: 0.7165 (mm-30) REVERT: E 244 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8225 (mt-10) REVERT: E 302 ASP cc_start: 0.7646 (m-30) cc_final: 0.7226 (m-30) REVERT: E 303 ARG cc_start: 0.8340 (mtp85) cc_final: 0.8071 (mtp85) REVERT: F 12 LEU cc_start: 0.7772 (mp) cc_final: 0.7393 (mt) REVERT: F 66 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7673 (mttm) REVERT: F 120 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7637 (tm130) REVERT: C 81 SER cc_start: 0.8817 (m) cc_final: 0.8590 (p) REVERT: C 87 GLU cc_start: 0.6914 (pm20) cc_final: 0.6690 (mp0) REVERT: C 204 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7516 (mtp85) REVERT: C 244 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7741 (mt-10) REVERT: C 259 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7609 (ptt90) REVERT: G 29 GLU cc_start: 0.8102 (mp0) cc_final: 0.7895 (mp0) REVERT: G 69 LYS cc_start: 0.8147 (mptm) cc_final: 0.7892 (mptm) REVERT: G 184 GLU cc_start: 0.7037 (pm20) cc_final: 0.6795 (pm20) REVERT: G 302 ASP cc_start: 0.7568 (m-30) cc_final: 0.7047 (m-30) REVERT: H 244 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7490 (mt-10) REVERT: H 262 ASP cc_start: 0.8650 (t0) cc_final: 0.8347 (t70) outliers start: 108 outliers final: 59 residues processed: 648 average time/residue: 0.6750 time to fit residues: 501.3132 Evaluate side-chains 636 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 568 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 88 ARG Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 102 ILE Chi-restraints excluded: chain I residue 104 GLU Chi-restraints excluded: chain I residue 115 MET Chi-restraints excluded: chain I residue 117 LYS Chi-restraints excluded: chain I residue 128 GLU Chi-restraints excluded: chain I residue 129 MET Chi-restraints excluded: chain I residue 137 GLN Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 256 ASN Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 120 GLN Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain F residue 66 LYS Chi-restraints excluded: chain F residue 120 GLN Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain F residue 242 LYS Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 204 ARG Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 259 ARG Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 171 SER Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 82 CYS Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 244 GLU Chi-restraints excluded: chain H residue 272 GLU Chi-restraints excluded: chain H residue 296 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 6 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 224 optimal weight: 0.6980 chunk 69 optimal weight: 8.9990 chunk 88 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 chunk 140 optimal weight: 2.9990 chunk 59 optimal weight: 0.0050 chunk 28 optimal weight: 0.7980 chunk 134 optimal weight: 0.2980 chunk 197 optimal weight: 0.4980 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 HIS A 275 HIS A 319 ASN B 166 ASN ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 GLN ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 GLN G 77 GLN G 178 ASN ** H 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 279 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.131260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.109206 restraints weight = 33844.258| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.55 r_work: 0.3374 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24670 Z= 0.129 Angle : 0.543 11.139 33816 Z= 0.297 Chirality : 0.042 0.260 3749 Planarity : 0.004 0.050 3932 Dihedral : 17.945 174.175 4405 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.53 % Favored : 96.40 % Rotamer: Outliers : 3.89 % Allowed : 28.34 % Favored : 67.78 % 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: -0.13 (0.16), residues: 2638 helix: 1.31 (0.19), residues: 767 sheet: 0.91 (0.27), residues: 418 loop : -1.21 (0.15), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 142 TYR 0.022 0.001 TYR A 292 PHE 0.018 0.001 PHE F 273 TRP 0.005 0.001 TRP F 33 HIS 0.006 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (24670) covalent geometry : angle 0.54264 / 0.30 (33816) hydrogen bonds : bond 0.04275 / 2.89 ( 735) hydrogen bonds : angle 5.12388 / 3.68 ( 1982) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 563 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7216 (mtt180) REVERT: A 205 LYS cc_start: 0.8748 (mttt) cc_final: 0.8476 (mtpp) REVERT: A 264 LYS cc_start: 0.7396 (mttt) cc_final: 0.7062 (tttt) REVERT: A 283 GLU cc_start: 0.7106 (tm-30) cc_final: 0.6898 (tm-30) REVERT: B 68 LYS cc_start: 0.8342 (mtpp) cc_final: 0.8078 (mtpp) REVERT: I 14 ILE cc_start: 0.7505 (OUTLIER) cc_final: 0.7253 (mt) REVERT: I 66 GLU cc_start: 0.6177 (OUTLIER) cc_final: 0.5885 (tm-30) REVERT: I 115 MET cc_start: 0.5305 (OUTLIER) cc_final: 0.5055 (mpm) REVERT: I 145 LYS cc_start: 0.6882 (OUTLIER) cc_final: 0.6161 (ptmm) REVERT: D 70 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7718 (mt-10) REVERT: D 123 ASP cc_start: 0.7724 (m-30) cc_final: 0.7488 (m-30) REVERT: E 191 GLU cc_start: 0.7399 (mm-30) cc_final: 0.7168 (mm-30) REVERT: E 244 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8176 (mt-10) REVERT: E 302 ASP cc_start: 0.7639 (m-30) cc_final: 0.7221 (m-30) REVERT: E 303 ARG cc_start: 0.8320 (mtp85) cc_final: 0.8095 (mtp85) REVERT: F 12 LEU cc_start: 0.7772 (mp) cc_final: 0.7387 (mt) REVERT: F 66 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7711 (mttm) REVERT: F 120 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7517 (tm130) REVERT: F 259 ARG cc_start: 0.7656 (mtm-85) cc_final: 0.7345 (mtp180) REVERT: F 278 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7581 (mm-30) REVERT: C 81 SER cc_start: 0.8744 (m) cc_final: 0.8457 (p) REVERT: C 244 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7740 (mt-10) REVERT: C 303 ARG cc_start: 0.8319 (mtm110) cc_final: 0.8116 (mtm110) REVERT: G 29 GLU cc_start: 0.8095 (mp0) cc_final: 0.7855 (mp0) REVERT: G 69 LYS cc_start: 0.8105 (mptm) cc_final: 0.7871 (mptm) REVERT: G 184 GLU cc_start: 0.7032 (pm20) cc_final: 0.6784 (pm20) REVERT: G 304 MET cc_start: 0.8096 (ttt) cc_final: 0.7824 (ttt) REVERT: H 262 ASP cc_start: 0.8663 (t0) cc_final: 0.8369 (t70) outliers start: 92 outliers final: 49 residues processed: 610 average time/residue: 0.6804 time to fit residues: 475.6017 Evaluate side-chains 624 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 567 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ARG Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 66 GLU Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 102 ILE Chi-restraints excluded: chain I residue 104 GLU Chi-restraints excluded: chain I residue 115 MET Chi-restraints excluded: chain I residue 117 LYS Chi-restraints excluded: chain I residue 128 GLU Chi-restraints excluded: chain I residue 129 MET Chi-restraints excluded: chain I residue 145 LYS Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain F residue 66 LYS Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 120 GLN Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain F residue 242 LYS Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 219 CYS Chi-restraints excluded: chain G residue 226 SER Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 272 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 266 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 149 optimal weight: 0.9980 chunk 214 optimal weight: 1.9990 chunk 166 optimal weight: 0.0980 chunk 258 optimal weight: 0.9990 chunk 136 optimal weight: 0.5980 chunk 29 optimal weight: 8.9990 chunk 96 optimal weight: 0.6980 chunk 13 optimal weight: 0.0000 chunk 122 optimal weight: 0.6980 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 HIS A 319 ASN B 166 ASN ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 GLN ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 178 ASN F 195 GLN F 333 GLN C 80 GLN G 77 GLN G 178 ASN ** H 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 279 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.131418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.109593 restraints weight = 33676.569| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.53 r_work: 0.3384 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24670 Z= 0.129 Angle : 0.536 11.937 33816 Z= 0.294 Chirality : 0.041 0.259 3749 Planarity : 0.004 0.051 3932 Dihedral : 17.898 174.331 4405 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.64 % Favored : 96.29 % Rotamer: Outliers : 3.80 % Allowed : 28.63 % Favored : 67.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.09 (0.16), residues: 2638 helix: 1.35 (0.19), residues: 767 sheet: 0.94 (0.27), residues: 414 loop : -1.19 (0.15), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 325 TYR 0.019 0.001 TYR A 292 PHE 0.013 0.001 PHE I 25 TRP 0.006 0.001 TRP G 264 HIS 0.039 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (24670) covalent geometry : angle 0.53619 / 0.29 (33816) hydrogen bonds : bond 0.04197 / 2.85 ( 735) hydrogen bonds : angle 5.05104 / 3.62 ( 1982) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 573 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 LYS cc_start: 0.8705 (mttt) cc_final: 0.8407 (mtpp) REVERT: A 264 LYS cc_start: 0.7402 (mttt) cc_final: 0.7055 (tttt) REVERT: A 283 GLU cc_start: 0.7086 (tm-30) cc_final: 0.6867 (tm-30) REVERT: B 48 ILE cc_start: 0.8742 (mt) cc_final: 0.8517 (mt) REVERT: B 68 LYS cc_start: 0.8327 (mtpp) cc_final: 0.8059 (mtpp) REVERT: I 66 GLU cc_start: 0.6090 (OUTLIER) cc_final: 0.5812 (tm-30) REVERT: I 115 MET cc_start: 0.5243 (OUTLIER) cc_final: 0.5006 (mpm) REVERT: I 145 LYS cc_start: 0.6837 (OUTLIER) cc_final: 0.6068 (tmmm) REVERT: D 70 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7706 (mt-10) REVERT: D 123 ASP cc_start: 0.7674 (m-30) cc_final: 0.7449 (m-30) REVERT: E 191 GLU cc_start: 0.7391 (mm-30) cc_final: 0.7142 (mm-30) REVERT: F 12 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7384 (mt) REVERT: F 66 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7667 (mttm) REVERT: C 81 SER cc_start: 0.8697 (m) cc_final: 0.8487 (p) REVERT: C 302 ASP cc_start: 0.8189 (m-30) cc_final: 0.7934 (m-30) REVERT: G 29 GLU cc_start: 0.8054 (mp0) cc_final: 0.7809 (mp0) REVERT: G 69 LYS cc_start: 0.8092 (mptm) cc_final: 0.7892 (mptm) REVERT: G 184 GLU cc_start: 0.7051 (pm20) cc_final: 0.6797 (pm20) REVERT: H 262 ASP cc_start: 0.8646 (t0) cc_final: 0.8353 (t70) outliers start: 90 outliers final: 60 residues processed: 621 average time/residue: 0.6828 time to fit residues: 485.8645 Evaluate side-chains 628 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 563 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 88 ARG Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 25 PHE Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 66 GLU Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 102 ILE Chi-restraints excluded: chain I residue 104 GLU Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain I residue 115 MET Chi-restraints excluded: chain I residue 117 LYS Chi-restraints excluded: chain I residue 128 GLU Chi-restraints excluded: chain I residue 129 MET Chi-restraints excluded: chain I residue 137 GLN Chi-restraints excluded: chain I residue 145 LYS Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 256 ASN Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 66 LYS Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain F residue 242 LYS Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 219 CYS Chi-restraints excluded: chain G residue 226 SER Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 82 CYS Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 239 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 106 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 274 optimal weight: 20.0000 chunk 184 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 HIS A 319 ASN B 166 ASN ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 GLN ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 178 ASN F 195 GLN F 227 GLN F 333 GLN G 178 ASN ** H 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 279 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.130017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.108087 restraints weight = 33915.064| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.54 r_work: 0.3360 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24670 Z= 0.191 Angle : 0.572 13.189 33816 Z= 0.309 Chirality : 0.043 0.253 3749 Planarity : 0.004 0.050 3932 Dihedral : 17.895 174.432 4405 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.75 % Favored : 96.17 % Rotamer: Outliers : 3.12 % Allowed : 29.18 % Favored : 67.69 % 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 (0.16), residues: 2638 helix: 1.33 (0.19), residues: 766 sheet: 0.82 (0.26), residues: 431 loop : -1.23 (0.15), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 325 TYR 0.018 0.001 TYR A 292 PHE 0.017 0.002 PHE F 273 TRP 0.010 0.001 TRP A 74 HIS 0.005 0.001 HIS F 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.19 (24670) covalent geometry : angle 0.57189 / 0.31 (33816) hydrogen bonds : bond 0.04490 / 3.06 ( 735) hydrogen bonds : angle 5.11495 / 3.66 ( 1982) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 569 time to evaluate : 0.892 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 205 LYS cc_start: 0.8733 (mttt) cc_final: 0.8439 (mtpp) REVERT: A 264 LYS cc_start: 0.7449 (mttt) cc_final: 0.7096 (tttt) REVERT: A 283 GLU cc_start: 0.7127 (tm-30) cc_final: 0.6894 (tm-30) REVERT: B 68 LYS cc_start: 0.8346 (mtpp) cc_final: 0.8072 (mtpp) REVERT: B 180 ILE cc_start: 0.7806 (mm) cc_final: 0.7535 (mp) REVERT: I 66 GLU cc_start: 0.6103 (OUTLIER) cc_final: 0.5817 (tm-30) REVERT: I 115 MET cc_start: 0.5164 (OUTLIER) cc_final: 0.4940 (mpm) REVERT: D 70 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7702 (mt-10) REVERT: D 123 ASP cc_start: 0.7698 (m-30) cc_final: 0.7450 (m-30) REVERT: E 191 GLU cc_start: 0.7390 (mm-30) cc_final: 0.7135 (mm-30) REVERT: F 12 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7403 (mt) REVERT: F 66 LYS cc_start: 0.7895 (OUTLIER) cc_final: 0.7665 (mttm) REVERT: C 81 SER cc_start: 0.8742 (m) cc_final: 0.8462 (p) REVERT: C 302 ASP cc_start: 0.8233 (m-30) cc_final: 0.7972 (m-30) REVERT: G 29 GLU cc_start: 0.8059 (mp0) cc_final: 0.7851 (mp0) REVERT: G 184 GLU cc_start: 0.7081 (pm20) cc_final: 0.6820 (pm20) REVERT: G 304 MET cc_start: 0.8100 (ttt) cc_final: 0.7898 (ttt) REVERT: H 262 ASP cc_start: 0.8645 (t0) cc_final: 0.8347 (t70) outliers start: 74 outliers final: 56 residues processed: 611 average time/residue: 0.6616 time to fit residues: 463.9077 Evaluate side-chains 624 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 564 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 88 ARG Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 66 GLU Chi-restraints excluded: chain I residue 102 ILE Chi-restraints excluded: chain I residue 104 GLU Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain I residue 115 MET Chi-restraints excluded: chain I residue 117 LYS Chi-restraints excluded: chain I residue 128 GLU Chi-restraints excluded: chain I residue 129 MET Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 256 ASN Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 120 GLN Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 66 LYS Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain F residue 242 LYS Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 171 SER Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 219 CYS Chi-restraints excluded: chain G residue 226 SER Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 82 CYS Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 239 LYS Chi-restraints excluded: chain H residue 305 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 30 optimal weight: 0.9980 chunk 231 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 165 optimal weight: 0.5980 chunk 187 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 176 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 133 optimal weight: 0.5980 chunk 93 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 HIS A 319 ASN ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 GLN ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 ASN F 195 GLN F 333 GLN G 178 ASN ** H 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 279 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.130164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.108627 restraints weight = 34234.472| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.54 r_work: 0.3369 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 24670 Z= 0.158 Angle : 0.560 14.063 33816 Z= 0.303 Chirality : 0.042 0.251 3749 Planarity : 0.004 0.050 3932 Dihedral : 17.860 174.435 4403 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.68 % Favored : 96.25 % Rotamer: Outliers : 2.91 % Allowed : 29.35 % Favored : 67.74 % 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 (0.16), residues: 2638 helix: 1.38 (0.19), residues: 762 sheet: 0.91 (0.26), residues: 425 loop : -1.21 (0.15), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 325 TYR 0.018 0.001 TYR A 23 PHE 0.014 0.001 PHE H 177 TRP 0.007 0.001 TRP G 264 HIS 0.004 0.001 HIS F 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (24670) covalent geometry : angle 0.56009 / 0.30 (33816) hydrogen bonds : bond 0.04327 / 2.94 ( 735) hydrogen bonds : angle 5.08701 / 3.64 ( 1982) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 567 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 LYS cc_start: 0.8709 (mttt) cc_final: 0.8427 (mtpp) REVERT: A 264 LYS cc_start: 0.7414 (mttt) cc_final: 0.7077 (tttt) REVERT: A 283 GLU cc_start: 0.7114 (tm-30) cc_final: 0.6882 (tm-30) REVERT: B 68 LYS cc_start: 0.8354 (mtpp) cc_final: 0.8078 (mtpp) REVERT: I 66 GLU cc_start: 0.6033 (OUTLIER) cc_final: 0.5761 (tm-30) REVERT: I 115 MET cc_start: 0.5083 (OUTLIER) cc_final: 0.4862 (mpm) REVERT: I 145 LYS cc_start: 0.6861 (OUTLIER) cc_final: 0.6134 (tmmm) REVERT: D 70 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7710 (mt-10) REVERT: D 123 ASP cc_start: 0.7694 (m-30) cc_final: 0.7465 (m-30) REVERT: E 191 GLU cc_start: 0.7396 (mm-30) cc_final: 0.7143 (mm-30) REVERT: F 12 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7408 (mt) REVERT: C 81 SER cc_start: 0.8693 (m) cc_final: 0.8418 (p) REVERT: C 87 GLU cc_start: 0.6933 (pm20) cc_final: 0.6535 (pm20) REVERT: C 302 ASP cc_start: 0.8216 (m-30) cc_final: 0.7979 (m-30) REVERT: G 29 GLU cc_start: 0.7994 (mp0) cc_final: 0.7785 (mp0) REVERT: G 184 GLU cc_start: 0.7005 (pm20) cc_final: 0.6762 (pm20) REVERT: H 262 ASP cc_start: 0.8594 (t0) cc_final: 0.8274 (t70) outliers start: 69 outliers final: 56 residues processed: 607 average time/residue: 0.6399 time to fit residues: 445.6510 Evaluate side-chains 622 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 562 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain I residue 25 PHE Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 66 GLU Chi-restraints excluded: chain I residue 102 ILE Chi-restraints excluded: chain I residue 104 GLU Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain I residue 115 MET Chi-restraints excluded: chain I residue 117 LYS Chi-restraints excluded: chain I residue 128 GLU Chi-restraints excluded: chain I residue 129 MET Chi-restraints excluded: chain I residue 145 LYS Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 256 ASN Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain F residue 242 LYS Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 171 SER Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 219 CYS Chi-restraints excluded: chain G residue 226 SER Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 82 CYS Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 239 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 130 optimal weight: 2.9990 chunk 228 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 chunk 262 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 152 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 HIS A 275 HIS A 319 ASN ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 GLN ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 GLN F 333 GLN G 77 GLN G 178 ASN ** H 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 279 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.129884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.108079 restraints weight = 33837.124| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.54 r_work: 0.3356 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24670 Z= 0.180 Angle : 0.577 15.507 33816 Z= 0.310 Chirality : 0.043 0.254 3749 Planarity : 0.004 0.051 3932 Dihedral : 17.849 174.586 4403 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.87 % Favored : 96.06 % Rotamer: Outliers : 3.08 % Allowed : 29.35 % Favored : 67.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.12 (0.16), residues: 2638 helix: 1.38 (0.19), residues: 760 sheet: 0.90 (0.26), residues: 424 loop : -1.24 (0.15), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG F 325 TYR 0.019 0.001 TYR A 23 PHE 0.019 0.002 PHE F 273 TRP 0.009 0.001 TRP A 74 HIS 0.005 0.001 HIS F 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (24670) covalent geometry : angle 0.57662 / 0.31 (33816) hydrogen bonds : bond 0.04468 / 3.04 ( 735) hydrogen bonds : angle 5.12241 / 3.66 ( 1982) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10951.49 seconds wall clock time: 187 minutes 12.03 seconds (11232.03 seconds total)