Starting phenix.real_space_refine on Sun Jul 5 00:15:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9siu_54932/07_2026/9siu_54932.cif Found real_map, /net/cci-nas-00/data/ceres_data/9siu_54932/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9siu_54932/07_2026/9siu_54932.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9siu_54932/07_2026/9siu_54932.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9siu_54932/07_2026/9siu_54932.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9siu_54932/07_2026/9siu_54932.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 5.36, per 1000 atoms: 0.22 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: 1.98 Conformation dependent library (CDL) restraints added in 945.1 milliseconds 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: 2.94 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: 3.74 Time building geometry restraints manager: 2.66 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: 32938 1.79 - 3.58: 798 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: 3634 0.107 - 0.215: 114 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=" 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 chirality pdb=" CB VAL C 162 " pdb=" CA VAL C 162 " pdb=" CG1 VAL C 162 " pdb=" CG2 VAL C 162 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.32e-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: 5.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 23.080 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.490 ------------------------------------------------------------------------------- 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= 0.240 Angle : 0.619 8.952 33816 Z= 0.420 Chirality : 0.044 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 0.00376 / 0.24 (24670) covalent geometry : angle 0.61856 / 0.42 (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 : 0.743 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: 0.6289 (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: 0.7764 (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: 0.6518 time to fit residues: 491.0548 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 : 0.854 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.132351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.110398 restraints weight = 34266.355| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.55 r_work: 0.3386 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.0891 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= 0.129 Angle : 0.552 7.642 33816 Z= 0.308 Chirality : 0.042 0.241 3749 Planarity : 0.004 0.051 3932 Dihedral : 18.197 176.232 4458 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.90 % Favored : 95.98 % Rotamer: Outliers : 3.80 % Allowed : 26.52 % Favored : 69.68 % 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: -0.20 (0.16), residues: 2638 helix: 1.13 (0.19), residues: 767 sheet: 0.57 (0.25), residues: 449 loop : -1.12 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 142 TYR 0.014 0.001 TYR A 292 PHE 0.018 0.001 PHE F 273 TRP 0.006 0.001 TRP G 149 HIS 0.007 0.001 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (24670) covalent geometry : angle 0.55198 / 0.31 (33816) hydrogen bonds : bond 0.04851 / 3.28 ( 735) hydrogen bonds : angle 5.44934 / 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 693 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 603 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.7143 (tp-100) cc_final: 0.6787 (tp-100) REVERT: A 205 LYS cc_start: 0.8703 (mttt) cc_final: 0.8382 (mtpp) REVERT: A 283 GLU cc_start: 0.7027 (tm-30) cc_final: 0.6714 (tm-30) REVERT: I 66 GLU cc_start: 0.6110 (OUTLIER) cc_final: 0.5841 (tm-30) REVERT: I 115 MET cc_start: 0.5833 (OUTLIER) cc_final: 0.5530 (mpm) REVERT: D 66 LYS cc_start: 0.8038 (mtpp) cc_final: 0.7491 (mtpp) REVERT: D 68 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7404 (tm-30) REVERT: D 70 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7454 (mt-10) REVERT: D 123 ASP cc_start: 0.7710 (m-30) cc_final: 0.7409 (m-30) REVERT: D 272 GLU cc_start: 0.7984 (pt0) cc_final: 0.7750 (mt-10) REVERT: E 244 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8152 (mt-10) REVERT: F 12 LEU cc_start: 0.7687 (mp) cc_final: 0.7288 (mt) REVERT: F 66 LYS cc_start: 0.7875 (mttt) cc_final: 0.7607 (mttm) REVERT: C 169 TYR cc_start: 0.8350 (m-80) cc_final: 0.8123 (m-80) REVERT: C 302 ASP cc_start: 0.8100 (m-30) cc_final: 0.7867 (m-30) REVERT: G 29 GLU cc_start: 0.8125 (mp0) cc_final: 0.7821 (mp0) REVERT: G 124 GLU cc_start: 0.7296 (tp30) cc_final: 0.7095 (tp30) REVERT: G 184 GLU cc_start: 0.7050 (pm20) cc_final: 0.6832 (pm20) outliers start: 90 outliers final: 40 residues processed: 657 average time/residue: 0.6657 time to fit residues: 501.1755 Evaluate side-chains 611 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 569 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL 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 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 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 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 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: 6.9990 chunk 139 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 135 optimal weight: 0.0870 chunk 150 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 overall best weight: 0.9962 ------------------------------------------------------------------------------- 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 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** H 279 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.129829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.107712 restraints weight = 34167.523| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.55 r_work: 0.3354 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 24670 Z= 0.197 Angle : 0.566 7.564 33816 Z= 0.313 Chirality : 0.044 0.248 3749 Planarity : 0.005 0.051 3932 Dihedral : 18.097 177.273 4414 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.68 % Favored : 96.25 % Rotamer: Outliers : 3.93 % Allowed : 26.86 % Favored : 69.21 % 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: -0.24 (0.16), residues: 2638 helix: 1.14 (0.19), residues: 765 sheet: 0.73 (0.26), residues: 423 loop : -1.19 (0.15), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 291 TYR 0.018 0.002 TYR A 23 PHE 0.014 0.002 PHE C 273 TRP 0.008 0.001 TRP A 74 HIS 0.007 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.20 (24670) covalent geometry : angle 0.56598 / 0.31 (33816) hydrogen bonds : bond 0.05007 / 3.42 ( 735) hydrogen bonds : angle 5.40807 / 3.87 ( 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 663 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 570 time to evaluate : 0.882 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: 0.7791 (OUTLIER) cc_final: 0.7197 (mtt90) REVERT: A 142 ARG cc_start: 0.5707 (OUTLIER) cc_final: 0.4789 (ttt90) REVERT: A 205 LYS cc_start: 0.8696 (mttt) cc_final: 0.8426 (mtpp) REVERT: A 283 GLU cc_start: 0.7080 (tm-30) cc_final: 0.6804 (tm-30) REVERT: A 322 MET cc_start: 0.4172 (OUTLIER) cc_final: 0.3724 (ttp) REVERT: I 115 MET cc_start: 0.5690 (OUTLIER) cc_final: 0.5350 (mpm) REVERT: D 68 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7421 (tm-30) REVERT: D 70 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7754 (mt-10) REVERT: D 123 ASP cc_start: 0.7725 (m-30) cc_final: 0.7479 (m-30) REVERT: D 272 GLU cc_start: 0.8041 (pt0) cc_final: 0.7830 (mt-10) REVERT: E 191 GLU cc_start: 0.7290 (mm-30) cc_final: 0.7083 (mm-30) REVERT: E 309 GLU cc_start: 0.7433 (mt-10) cc_final: 0.7172 (tt0) REVERT: F 12 LEU cc_start: 0.7732 (mp) cc_final: 0.7338 (mt) REVERT: F 66 LYS cc_start: 0.7878 (mttt) cc_final: 0.7635 (mttm) REVERT: F 72 MET cc_start: 0.8515 (mmm) cc_final: 0.8282 (mmm) REVERT: F 278 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7577 (mm-30) REVERT: G 29 GLU cc_start: 0.8108 (mp0) cc_final: 0.7866 (mp0) REVERT: G 184 GLU cc_start: 0.7014 (pm20) cc_final: 0.6777 (pm20) REVERT: G 244 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8189 (mt-10) REVERT: G 302 ASP cc_start: 0.7558 (m-30) cc_final: 0.7086 (m-30) REVERT: G 304 MET cc_start: 0.8056 (ttt) cc_final: 0.7706 (ttt) REVERT: H 262 ASP cc_start: 0.8655 (t0) cc_final: 0.8353 (t70) REVERT: H 267 ASP cc_start: 0.7469 (p0) cc_final: 0.7216 (p0) REVERT: H 270 THR cc_start: 0.7833 (OUTLIER) cc_final: 0.7617 (p) outliers start: 93 outliers final: 48 residues processed: 619 average time/residue: 0.6716 time to fit residues: 475.7890 Evaluate side-chains 610 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 557 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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 166 SER 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 A residue 322 MET 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 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 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 120 GLN Chi-restraints excluded: chain E residue 181 THR 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 G residue 229 MET Chi-restraints excluded: chain G residue 269 THR 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: 6.9990 chunk 49 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 219 optimal weight: 0.9980 chunk 255 optimal weight: 0.7980 chunk 264 optimal weight: 2.9990 chunk 239 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 211 optimal weight: 0.9990 chunk 136 optimal weight: 0.8980 chunk 88 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 18 ASN ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 GLN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.130210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.107994 restraints weight = 33816.819| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.54 r_work: 0.3355 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24670 Z= 0.177 Angle : 0.549 10.232 33816 Z= 0.304 Chirality : 0.043 0.239 3749 Planarity : 0.004 0.050 3932 Dihedral : 18.065 177.034 4405 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.83 % Favored : 96.10 % Rotamer: Outliers : 4.01 % Allowed : 26.60 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.18 (0.19), residues: 765 sheet: 0.75 (0.26), residues: 423 loop : -1.18 (0.15), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 303 TYR 0.023 0.001 TYR A 292 PHE 0.018 0.001 PHE F 273 TRP 0.007 0.001 TRP A 74 HIS 0.007 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 (24670) covalent geometry : angle 0.54866 / 0.30 (33816) hydrogen bonds : bond 0.04704 / 3.20 ( 735) hydrogen bonds : angle 5.33080 / 3.83 ( 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 665 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 570 time to evaluate : 0.895 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: 0.7789 (OUTLIER) cc_final: 0.7322 (mtt180) REVERT: A 142 ARG cc_start: 0.5739 (OUTLIER) cc_final: 0.4822 (ttt90) REVERT: A 205 LYS cc_start: 0.8728 (mttt) cc_final: 0.8412 (mtpp) REVERT: A 264 LYS cc_start: 0.7517 (mttt) cc_final: 0.6993 (mttt) REVERT: A 283 GLU cc_start: 0.7096 (tm-30) cc_final: 0.6844 (tm-30) REVERT: A 322 MET cc_start: 0.4137 (OUTLIER) cc_final: 0.3711 (ttp) REVERT: B 175 MET cc_start: 0.6808 (OUTLIER) cc_final: 0.6562 (tpp) REVERT: I 115 MET cc_start: 0.5590 (OUTLIER) cc_final: 0.5292 (mpm) REVERT: D 70 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7785 (mt-10) REVERT: D 123 ASP cc_start: 0.7686 (m-30) cc_final: 0.7441 (m-30) REVERT: E 191 GLU cc_start: 0.7319 (mm-30) cc_final: 0.7060 (mm-30) REVERT: E 244 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8194 (mt-10) REVERT: E 303 ARG cc_start: 0.8358 (mtp85) cc_final: 0.8082 (mtp85) REVERT: F 12 LEU cc_start: 0.7741 (mp) cc_final: 0.7335 (mt) REVERT: F 29 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7750 (mm-30) REVERT: F 66 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7715 (mttm) REVERT: F 278 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7634 (mm-30) REVERT: C 81 SER cc_start: 0.8710 (m) cc_final: 0.8451 (p) REVERT: G 29 GLU cc_start: 0.8113 (mp0) cc_final: 0.7878 (mp0) REVERT: G 69 LYS cc_start: 0.8087 (mptm) cc_final: 0.7838 (mptm) REVERT: G 184 GLU cc_start: 0.7000 (pm20) cc_final: 0.6767 (pm20) REVERT: G 244 GLU cc_start: 0.8406 (mt-10) cc_final: 0.8183 (mt-10) REVERT: G 302 ASP cc_start: 0.7546 (m-30) cc_final: 0.7074 (m-30) REVERT: G 304 MET cc_start: 0.8147 (ttt) cc_final: 0.7923 (ttt) REVERT: H 244 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7540 (mt-10) REVERT: H 262 ASP cc_start: 0.8653 (t0) cc_final: 0.8357 (t70) REVERT: H 267 ASP cc_start: 0.7477 (p0) cc_final: 0.7168 (p0) outliers start: 95 outliers final: 56 residues processed: 618 average time/residue: 0.6634 time to fit residues: 468.3373 Evaluate side-chains 621 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 557 time to evaluate : 0.881 ------------------------------------------------------------------------------- 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 275 HIS 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 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 7 ILE 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 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 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 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 120 GLN 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 104 GLU Chi-restraints excluded: chain F residue 140 ASN 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 269 THR Chi-restraints excluded: chain C residue 270 THR 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 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 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 244 GLU 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: 0.2980 chunk 215 optimal weight: 0.8980 chunk 239 optimal weight: 1.9990 chunk 108 optimal weight: 0.0060 chunk 146 optimal weight: 0.0370 chunk 12 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 31 optimal weight: 0.4980 chunk 93 optimal weight: 0.6980 overall best weight: 0.3074 ------------------------------------------------------------------------------- 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** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.132190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.110101 restraints weight = 33754.153| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.55 r_work: 0.3389 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 24670 Z= 0.118 Angle : 0.518 9.799 33816 Z= 0.288 Chirality : 0.041 0.209 3749 Planarity : 0.004 0.050 3932 Dihedral : 18.026 176.212 4405 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.60 % Favored : 96.29 % Rotamer: Outliers : 3.72 % Allowed : 27.15 % Favored : 69.13 % 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: -0.11 (0.16), residues: 2638 helix: 1.28 (0.19), residues: 767 sheet: 0.84 (0.27), residues: 419 loop : -1.14 (0.15), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 303 TYR 0.022 0.001 TYR A 292 PHE 0.011 0.001 PHE H 37 TRP 0.005 0.001 TRP F 33 HIS 0.007 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (24670) covalent geometry : angle 0.51826 / 0.29 (33816) hydrogen bonds : bond 0.04211 / 2.87 ( 735) hydrogen bonds : angle 5.10617 / 3.68 ( 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 648 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 560 time to evaluate : 1.084 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: 0.7765 (OUTLIER) cc_final: 0.7268 (mtt180) REVERT: A 205 LYS cc_start: 0.8712 (mttt) cc_final: 0.8397 (mtpp) REVERT: A 264 LYS cc_start: 0.7366 (mttt) cc_final: 0.7086 (tttt) REVERT: A 283 GLU cc_start: 0.7082 (tm-30) cc_final: 0.6869 (tm-30) REVERT: I 115 MET cc_start: 0.5409 (OUTLIER) cc_final: 0.5140 (mpm) REVERT: I 145 LYS cc_start: 0.6782 (OUTLIER) cc_final: 0.6066 (tmmm) REVERT: D 70 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7732 (mt-10) REVERT: D 123 ASP cc_start: 0.7683 (m-30) cc_final: 0.7433 (m-30) REVERT: E 191 GLU cc_start: 0.7327 (mm-30) cc_final: 0.7089 (mm-30) REVERT: E 303 ARG cc_start: 0.8311 (mtp85) cc_final: 0.7540 (mtp85) REVERT: E 309 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7118 (tt0) REVERT: F 12 LEU cc_start: 0.7737 (mp) cc_final: 0.7345 (mt) REVERT: F 66 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7693 (mttm) REVERT: F 278 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7536 (mm-30) REVERT: C 81 SER cc_start: 0.8659 (m) cc_final: 0.8321 (t) REVERT: G 29 GLU cc_start: 0.8104 (mp0) cc_final: 0.7834 (mp0) REVERT: G 69 LYS cc_start: 0.8045 (mptm) cc_final: 0.7827 (mptm) REVERT: G 184 GLU cc_start: 0.6967 (pm20) cc_final: 0.6739 (pm20) REVERT: H 262 ASP cc_start: 0.8648 (t0) cc_final: 0.8329 (t70) outliers start: 88 outliers final: 48 residues processed: 604 average time/residue: 0.6487 time to fit residues: 448.5563 Evaluate side-chains 606 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 554 time to evaluate : 0.782 ------------------------------------------------------------------------------- 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 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 153 ASP Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain I residue 6 LEU 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 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 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 166 ASP 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 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 270 THR Chi-restraints excluded: chain C residue 301 ILE 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 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: 0.5980 chunk 205 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 240 optimal weight: 5.9990 chunk 171 optimal weight: 2.9990 chunk 193 optimal weight: 2.9990 chunk 273 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 ASN ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 = 0.3699 r_free = 0.3699 target = 0.127143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.104993 restraints weight = 33887.323| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.55 r_work: 0.3311 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 24670 Z= 0.328 Angle : 0.649 10.021 33816 Z= 0.351 Chirality : 0.048 0.294 3749 Planarity : 0.005 0.064 3932 Dihedral : 18.078 176.813 4405 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.09 % Favored : 95.83 % Rotamer: Outliers : 4.48 % Allowed : 27.20 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.16), residues: 2638 helix: 1.11 (0.19), residues: 760 sheet: 0.76 (0.27), residues: 415 loop : -1.28 (0.15), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 303 TYR 0.023 0.002 TYR G 265 PHE 0.020 0.002 PHE G 273 TRP 0.018 0.002 TRP A 74 HIS 0.009 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00774 / 0.33 (24670) covalent geometry : angle 0.64865 / 0.35 (33816) hydrogen bonds : bond 0.05602 / 3.81 ( 735) hydrogen bonds : angle 5.53948 / 3.96 ( 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 674 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 568 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ARG cc_start: 0.5870 (OUTLIER) cc_final: 0.5067 (ttt90) REVERT: A 205 LYS cc_start: 0.8737 (mttt) cc_final: 0.8480 (mtpp) REVERT: A 264 LYS cc_start: 0.7505 (mttt) cc_final: 0.7141 (tttt) REVERT: A 283 GLU cc_start: 0.7148 (tm-30) cc_final: 0.6868 (tm-30) REVERT: B 180 ILE cc_start: 0.7910 (mm) cc_final: 0.7671 (mp) REVERT: I 115 MET cc_start: 0.5500 (OUTLIER) cc_final: 0.5216 (mpm) REVERT: D 123 ASP cc_start: 0.7768 (m-30) cc_final: 0.7497 (m-30) REVERT: E 191 GLU cc_start: 0.7386 (mm-30) cc_final: 0.7107 (mm-30) REVERT: E 244 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8244 (mt-10) REVERT: E 302 ASP cc_start: 0.7659 (m-30) cc_final: 0.7328 (m-30) REVERT: E 303 ARG cc_start: 0.8393 (mtp85) cc_final: 0.8094 (mtp85) REVERT: F 12 LEU cc_start: 0.7787 (mp) cc_final: 0.7400 (mt) REVERT: F 66 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7730 (mttm) REVERT: F 278 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7674 (mm-30) REVERT: C 43 PHE cc_start: 0.8339 (OUTLIER) cc_final: 0.7668 (p90) REVERT: C 81 SER cc_start: 0.8816 (m) cc_final: 0.8560 (p) REVERT: C 204 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7525 (mtp85) REVERT: C 231 PHE cc_start: 0.6608 (OUTLIER) cc_final: 0.6057 (m-80) REVERT: C 322 ILE cc_start: 0.8529 (mm) cc_final: 0.8316 (mp) REVERT: G 69 LYS cc_start: 0.8181 (mptm) cc_final: 0.7906 (mptm) REVERT: G 184 GLU cc_start: 0.7075 (pm20) cc_final: 0.6838 (pm20) REVERT: G 229 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.7686 (ttp) REVERT: H 148 LEU cc_start: 0.7798 (mm) cc_final: 0.7568 (mt) REVERT: H 229 MET cc_start: 0.7433 (tmm) cc_final: 0.7003 (tmm) REVERT: H 244 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7545 (mt-10) REVERT: H 262 ASP cc_start: 0.8663 (t0) cc_final: 0.8354 (t70) REVERT: H 267 ASP cc_start: 0.7462 (p0) cc_final: 0.7148 (p0) outliers start: 106 outliers final: 60 residues processed: 621 average time/residue: 0.6537 time to fit residues: 465.4297 Evaluate side-chains 618 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 550 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 142 ARG Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 321 ILE 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 147 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 200 SER 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 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 F residue 66 LYS Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 140 ASN 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 F residue 322 ILE Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 204 ARG Chi-restraints excluded: chain C residue 231 PHE 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 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 G residue 219 CYS Chi-restraints excluded: chain G residue 229 MET Chi-restraints excluded: chain G residue 269 THR 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 244 GLU Chi-restraints excluded: chain H residue 272 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 6 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 224 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 chunk 91 optimal weight: 0.9980 chunk 140 optimal weight: 0.8980 chunk 59 optimal weight: 0.0060 chunk 28 optimal weight: 4.9990 chunk 134 optimal weight: 0.1980 chunk 197 optimal weight: 1.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 HIS A 319 ASN B 20 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 F 333 GLN G 77 GLN G 178 ASN H 34 GLN ** 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 = 0.3742 r_free = 0.3742 target = 0.130192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.108023 restraints weight = 33734.760| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.54 r_work: 0.3358 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 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 0.048 24670 Z= 0.144 Angle : 0.544 11.343 33816 Z= 0.301 Chirality : 0.042 0.233 3749 Planarity : 0.004 0.051 3932 Dihedral : 18.041 176.440 4402 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.83 % Favored : 96.10 % Rotamer: Outliers : 3.63 % Allowed : 28.80 % 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: -0.19 (0.16), residues: 2638 helix: 1.29 (0.19), residues: 761 sheet: 0.76 (0.27), residues: 424 loop : -1.22 (0.15), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 303 TYR 0.022 0.001 TYR A 23 PHE 0.015 0.001 PHE I 25 TRP 0.006 0.001 TRP G 264 HIS 0.005 0.001 HIS B 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (24670) covalent geometry : angle 0.54389 / 0.30 (33816) hydrogen bonds : bond 0.04423 / 2.98 ( 735) hydrogen bonds : angle 5.22143 / 3.75 ( 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 648 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 562 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ARG cc_start: 0.5688 (OUTLIER) cc_final: 0.4689 (ttt90) REVERT: A 205 LYS cc_start: 0.8741 (mttt) cc_final: 0.8467 (mtpp) REVERT: A 264 LYS cc_start: 0.7404 (mttt) cc_final: 0.7076 (tttt) REVERT: A 283 GLU cc_start: 0.7115 (tm-30) cc_final: 0.6867 (tm-30) REVERT: B 68 LYS cc_start: 0.8350 (mtpp) cc_final: 0.8087 (mtpp) REVERT: B 175 MET cc_start: 0.6911 (OUTLIER) cc_final: 0.6635 (tpp) REVERT: I 115 MET cc_start: 0.5378 (OUTLIER) cc_final: 0.5115 (mpm) REVERT: I 145 LYS cc_start: 0.6918 (mttp) cc_final: 0.6215 (ptmm) REVERT: D 123 ASP cc_start: 0.7724 (m-30) cc_final: 0.7475 (m-30) REVERT: E 191 GLU cc_start: 0.7401 (mm-30) cc_final: 0.7165 (mm-30) REVERT: E 244 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8182 (mt-10) REVERT: E 302 ASP cc_start: 0.7630 (m-30) cc_final: 0.7333 (m-30) REVERT: E 303 ARG cc_start: 0.8352 (mtp85) cc_final: 0.8111 (mtp85) REVERT: F 12 LEU cc_start: 0.7775 (mp) cc_final: 0.7395 (mt) REVERT: C 81 SER cc_start: 0.8760 (m) cc_final: 0.8493 (p) REVERT: G 69 LYS cc_start: 0.8122 (mptm) cc_final: 0.7886 (mptm) REVERT: G 184 GLU cc_start: 0.7048 (pm20) cc_final: 0.6797 (pm20) REVERT: G 302 ASP cc_start: 0.7570 (m-30) cc_final: 0.7148 (m-30) REVERT: H 249 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7728 (mtp) REVERT: H 262 ASP cc_start: 0.8667 (t0) cc_final: 0.8362 (t70) REVERT: H 267 ASP cc_start: 0.7454 (p0) cc_final: 0.7137 (p0) outliers start: 86 outliers final: 49 residues processed: 608 average time/residue: 0.6761 time to fit residues: 469.5827 Evaluate side-chains 605 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 552 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 107 LEU 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 275 HIS Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 175 MET 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 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 26 ASN 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 104 GLU 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 68 GLU 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 249 MET 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: 0.5980 chunk 149 optimal weight: 0.0370 chunk 214 optimal weight: 0.3980 chunk 166 optimal weight: 0.6980 chunk 258 optimal weight: 0.9990 chunk 136 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 122 optimal weight: 0.1980 overall best weight: 0.3858 ------------------------------------------------------------------------------- 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 333 GLN G 178 ASN H 256 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.131148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.109318 restraints weight = 33676.582| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.54 r_work: 0.3380 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1799 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= 0.128 Angle : 0.536 12.051 33816 Z= 0.295 Chirality : 0.042 0.221 3749 Planarity : 0.004 0.052 3932 Dihedral : 17.989 176.567 4402 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.71 % Favored : 96.21 % Rotamer: Outliers : 3.59 % Allowed : 28.59 % Favored : 67.82 % 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: -0.11 (0.16), residues: 2638 helix: 1.34 (0.19), residues: 767 sheet: 1.00 (0.27), residues: 408 loop : -1.22 (0.15), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 303 TYR 0.020 0.001 TYR A 292 PHE 0.016 0.001 PHE A 212 TRP 0.006 0.001 TRP G 264 HIS 0.005 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (24670) covalent geometry : angle 0.53580 / 0.30 (33816) hydrogen bonds : bond 0.04255 / 2.90 ( 735) hydrogen bonds : angle 5.07873 / 3.64 ( 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 657 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 572 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ARG cc_start: 0.5513 (OUTLIER) cc_final: 0.5284 (tpt90) REVERT: A 205 LYS cc_start: 0.8715 (mttt) cc_final: 0.8460 (mtpp) REVERT: A 264 LYS cc_start: 0.7370 (mttt) cc_final: 0.7038 (tttt) REVERT: A 283 GLU cc_start: 0.7080 (tm-30) cc_final: 0.6860 (tm-30) REVERT: A 294 TYR cc_start: 0.4962 (OUTLIER) cc_final: 0.4752 (t80) REVERT: B 48 ILE cc_start: 0.8747 (mt) cc_final: 0.8533 (mt) REVERT: B 68 LYS cc_start: 0.8312 (mtpp) cc_final: 0.8040 (mtpp) REVERT: I 115 MET cc_start: 0.5262 (OUTLIER) cc_final: 0.5020 (mpm) REVERT: I 145 LYS cc_start: 0.6866 (OUTLIER) cc_final: 0.6128 (tmmm) REVERT: D 123 ASP cc_start: 0.7687 (m-30) cc_final: 0.7460 (m-30) REVERT: E 191 GLU cc_start: 0.7401 (mm-30) cc_final: 0.7148 (mm-30) REVERT: E 244 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8138 (mt-10) REVERT: E 302 ASP cc_start: 0.7633 (m-30) cc_final: 0.7270 (m-30) REVERT: F 12 LEU cc_start: 0.7750 (mp) cc_final: 0.7387 (mt) REVERT: F 66 LYS cc_start: 0.7907 (mttm) cc_final: 0.7706 (mttm) REVERT: F 70 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7351 (mt-10) REVERT: C 81 SER cc_start: 0.8679 (m) cc_final: 0.8470 (p) REVERT: G 69 LYS cc_start: 0.8087 (mptm) cc_final: 0.7880 (mptm) REVERT: G 184 GLU cc_start: 0.7038 (pm20) cc_final: 0.6797 (pm20) REVERT: H 262 ASP cc_start: 0.8643 (t0) cc_final: 0.8341 (t70) REVERT: H 270 THR cc_start: 0.7836 (OUTLIER) cc_final: 0.7634 (p) outliers start: 85 outliers final: 52 residues processed: 619 average time/residue: 0.6537 time to fit residues: 462.4936 Evaluate side-chains 619 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 562 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 107 LEU 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 266 LYS Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain B residue 112 VAL 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 8 ILE Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 61 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 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 68 GLU Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 104 GLU 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 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 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 239 LYS Chi-restraints excluded: chain H residue 270 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 106 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 93 optimal weight: 0.1980 chunk 274 optimal weight: 10.0000 chunk 184 optimal weight: 0.7980 chunk 98 optimal weight: 0.0970 chunk 167 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 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 F 227 GLN F 333 GLN G 77 GLN G 178 ASN H 279 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.130910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.109191 restraints weight = 34020.953| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.55 r_work: 0.3376 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1854 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= 0.138 Angle : 0.540 13.332 33816 Z= 0.296 Chirality : 0.042 0.218 3749 Planarity : 0.004 0.051 3932 Dihedral : 17.958 176.640 4400 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.56 % Favored : 96.36 % Rotamer: Outliers : 2.87 % Allowed : 29.27 % Favored : 67.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.16), residues: 2638 helix: 1.40 (0.19), residues: 762 sheet: 1.03 (0.27), residues: 408 loop : -1.19 (0.15), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 40 TYR 0.021 0.001 TYR A 23 PHE 0.016 0.001 PHE I 25 TRP 0.005 0.001 TRP F 264 HIS 0.009 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (24670) covalent geometry : angle 0.53970 / 0.30 (33816) hydrogen bonds : bond 0.04234 / 2.89 ( 735) hydrogen bonds : angle 5.06405 / 3.63 ( 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 637 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 569 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 LYS cc_start: 0.8719 (mttt) cc_final: 0.8461 (mtpp) REVERT: A 264 LYS cc_start: 0.7394 (mttt) cc_final: 0.7059 (tttt) REVERT: A 283 GLU cc_start: 0.7098 (tm-30) cc_final: 0.6874 (tm-30) REVERT: A 294 TYR cc_start: 0.4985 (OUTLIER) cc_final: 0.4782 (t80) REVERT: B 48 ILE cc_start: 0.8741 (mt) cc_final: 0.8529 (mt) REVERT: B 68 LYS cc_start: 0.8342 (mtpp) cc_final: 0.8061 (mtpp) REVERT: I 66 GLU cc_start: 0.6016 (OUTLIER) cc_final: 0.5726 (tm-30) REVERT: I 115 MET cc_start: 0.5153 (OUTLIER) cc_final: 0.4924 (mpm) REVERT: I 145 LYS cc_start: 0.6889 (OUTLIER) cc_final: 0.6144 (tmmm) REVERT: D 123 ASP cc_start: 0.7671 (m-30) cc_final: 0.7444 (m-30) REVERT: E 191 GLU cc_start: 0.7416 (mm-30) cc_final: 0.7163 (mm-30) REVERT: E 244 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8140 (mt-10) REVERT: E 302 ASP cc_start: 0.7612 (m-30) cc_final: 0.7286 (m-30) REVERT: F 12 LEU cc_start: 0.7771 (mp) cc_final: 0.7402 (mt) REVERT: F 66 LYS cc_start: 0.7888 (mttm) cc_final: 0.7658 (mttm) REVERT: F 70 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7377 (mt-10) REVERT: C 81 SER cc_start: 0.8668 (m) cc_final: 0.8406 (p) REVERT: C 244 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7625 (mt-10) REVERT: C 302 ASP cc_start: 0.8164 (m-30) cc_final: 0.7963 (m-30) REVERT: C 303 ARG cc_start: 0.8318 (mtm180) cc_final: 0.8113 (mtm110) REVERT: G 184 GLU cc_start: 0.7053 (pm20) cc_final: 0.6812 (pm20) REVERT: H 262 ASP cc_start: 0.8609 (t0) cc_final: 0.8280 (t70) outliers start: 68 outliers final: 54 residues processed: 606 average time/residue: 0.6606 time to fit residues: 457.2267 Evaluate side-chains 618 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 559 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 107 LEU 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 294 TYR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain B residue 112 VAL 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 8 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 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 104 GLU Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain F residue 104 GLU 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 244 GLU 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 30 optimal weight: 0.8980 chunk 231 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 165 optimal weight: 0.6980 chunk 187 optimal weight: 0.6980 chunk 116 optimal weight: 0.8980 chunk 176 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 133 optimal weight: 0.6980 chunk 93 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 195 GLN F 333 GLN G 77 GLN G 178 ASN H 227 GLN H 279 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.130610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.108969 restraints weight = 34038.538| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.53 r_work: 0.3372 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24670 Z= 0.154 Angle : 0.555 14.148 33816 Z= 0.302 Chirality : 0.042 0.222 3749 Planarity : 0.004 0.052 3932 Dihedral : 17.949 176.722 4400 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.75 % Favored : 96.17 % Rotamer: Outliers : 3.08 % Allowed : 29.43 % Favored : 67.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.16), residues: 2638 helix: 1.35 (0.19), residues: 768 sheet: 0.99 (0.27), residues: 411 loop : -1.20 (0.15), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 325 TYR 0.022 0.001 TYR A 23 PHE 0.018 0.001 PHE F 273 TRP 0.006 0.001 TRP G 264 HIS 0.010 0.001 HIS A 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (24670) covalent geometry : angle 0.55470 / 0.30 (33816) hydrogen bonds : bond 0.04302 / 2.94 ( 735) hydrogen bonds : angle 5.09597 / 3.65 ( 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 637 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 564 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 LYS cc_start: 0.8734 (mttt) cc_final: 0.8474 (mtpp) REVERT: A 264 LYS cc_start: 0.7400 (mttt) cc_final: 0.7065 (tttt) REVERT: A 276 LEU cc_start: 0.7914 (mt) cc_final: 0.7679 (mm) REVERT: A 283 GLU cc_start: 0.7115 (tm-30) cc_final: 0.6899 (tm-30) REVERT: B 68 LYS cc_start: 0.8344 (mtpp) cc_final: 0.8058 (mtpp) REVERT: I 66 GLU cc_start: 0.5947 (OUTLIER) cc_final: 0.5674 (tm-30) REVERT: I 115 MET cc_start: 0.5077 (OUTLIER) cc_final: 0.4858 (mpm) REVERT: I 145 LYS cc_start: 0.6896 (OUTLIER) cc_final: 0.6207 (ptmm) REVERT: D 123 ASP cc_start: 0.7682 (m-30) cc_final: 0.7452 (m-30) REVERT: E 191 GLU cc_start: 0.7395 (mm-30) cc_final: 0.7144 (mm-30) REVERT: E 244 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8172 (mt-10) REVERT: E 302 ASP cc_start: 0.7564 (m-30) cc_final: 0.7232 (m-30) REVERT: F 12 LEU cc_start: 0.7768 (mp) cc_final: 0.7403 (mt) REVERT: F 66 LYS cc_start: 0.7868 (mttm) cc_final: 0.7630 (mttm) REVERT: F 70 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7374 (mt-10) REVERT: C 81 SER cc_start: 0.8669 (m) cc_final: 0.8410 (p) REVERT: C 244 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7615 (mt-10) REVERT: C 302 ASP cc_start: 0.8178 (m-30) cc_final: 0.7972 (m-30) REVERT: C 303 ARG cc_start: 0.8336 (mtm180) cc_final: 0.8131 (mtm110) REVERT: G 184 GLU cc_start: 0.7083 (pm20) cc_final: 0.6821 (pm20) REVERT: H 262 ASP cc_start: 0.8606 (t0) cc_final: 0.8326 (t70) outliers start: 73 outliers final: 54 residues processed: 604 average time/residue: 0.6790 time to fit residues: 468.6650 Evaluate side-chains 608 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 550 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 107 LEU 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 316 SER Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain I residue 7 ILE 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 66 GLU 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 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 104 GLU 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 244 GLU 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 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 239 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 130 optimal weight: 0.6980 chunk 228 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 158 optimal weight: 0.8980 chunk 211 optimal weight: 2.9990 chunk 262 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 120 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 152 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** I 137 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 F 333 GLN G 77 GLN G 178 ASN H 279 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.130200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.108513 restraints weight = 33841.193| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.54 r_work: 0.3366 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 24670 Z= 0.167 Angle : 0.568 15.401 33816 Z= 0.308 Chirality : 0.042 0.224 3749 Planarity : 0.004 0.052 3932 Dihedral : 17.945 176.836 4400 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.02 % Favored : 95.91 % Rotamer: Outliers : 2.79 % Allowed : 29.81 % Favored : 67.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.16), residues: 2638 helix: 1.33 (0.19), residues: 767 sheet: 0.91 (0.27), residues: 421 loop : -1.23 (0.15), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG F 325 TYR 0.023 0.001 TYR A 23 PHE 0.019 0.001 PHE F 273 TRP 0.008 0.001 TRP H 149 HIS 0.004 0.001 HIS F 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (24670) covalent geometry : angle 0.56796 / 0.31 (33816) hydrogen bonds : bond 0.04399 / 3.01 ( 735) hydrogen bonds : angle 5.14359 / 3.68 ( 1982) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11210.20 seconds wall clock time: 191 minutes 29.82 seconds (11489.82 seconds total)