Starting phenix.real_space_refine on Thu Mar 5 18:10:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9siu_54932/03_2026/9siu_54932.cif Found real_map, /net/cci-nas-00/data/ceres_data/9siu_54932/03_2026/9siu_54932.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9siu_54932/03_2026/9siu_54932.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9siu_54932/03_2026/9siu_54932.map" model { file = "/net/cci-nas-00/data/ceres_data/9siu_54932/03_2026/9siu_54932.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9siu_54932/03_2026/9siu_54932.cif" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 110 5.49 5 S 116 5.16 5 C 14877 2.51 5 N 4024 2.21 5 O 4796 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 82 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 5.08, per 1000 atoms: 0.21 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: 1.80 Conformation dependent library (CDL) restraints added in 1.1 seconds 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5078 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 36 sheets defined 33.8% alpha, 9.6% beta 37 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 3.15 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: 3.89 Time building geometry restraints manager: 2.40 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=" 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=" 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 bond pdb=" N VAL C 162 " pdb=" CA VAL C 162 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.20e-02 6.94e+03 8.64e+00 bond pdb=" N ASP A 229 " pdb=" CA ASP A 229 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.24e-02 6.50e+03 8.00e+00 bond pdb=" N ASP G 310 " pdb=" CA ASP G 310 " ideal model delta sigma weight residual 1.463 1.499 -0.035 1.29e-02 6.01e+03 7.55e+00 ... (remaining 24665 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 33031 1.79 - 3.58: 706 3.58 - 5.37: 65 5.37 - 7.16: 12 7.16 - 8.95: 2 Bond angle restraints: 33816 Sorted by residual: 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 angle pdb=" C ALA A 227 " pdb=" N LEU A 228 " pdb=" CA LEU A 228 " ideal model delta sigma weight residual 122.65 116.71 5.94 1.60e+00 3.91e-01 1.38e+01 angle pdb=" CA LYS I 145 " pdb=" C LYS I 145 " pdb=" O LYS I 145 " ideal model delta sigma weight residual 122.27 118.06 4.21 1.16e+00 7.43e-01 1.32e+01 angle pdb=" C LEU A 234 " pdb=" N PRO A 235 " pdb=" CA PRO A 235 " ideal model delta sigma weight residual 119.76 123.33 -3.57 1.00e+00 1.00e+00 1.28e+01 angle pdb=" CA GLU A 105 " pdb=" C GLU A 105 " pdb=" N HIS A 106 " ideal model delta sigma weight residual 117.63 113.22 4.41 1.25e+00 6.40e-01 1.24e+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 - 0.105: 3636 0.105 - 0.210: 112 0.210 - 0.316: 0 0.316 - 0.421: 0 0.421 - 0.526: 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 2.35 -2.87 -0.53 2.00e-01 2.50e+01 6.92e+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: 6.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.780 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 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 : 0.003 0.043 24670 Z= 0.175 Angle : 0.601 8.952 33816 Z= 0.347 Chirality : 0.043 0.526 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 covalent geometry : bond 0.00349 (24670) covalent geometry : angle 0.60136 (33816) hydrogen bonds : bond 0.15192 ( 735) hydrogen bonds : angle 6.34230 ( 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 : 0.730 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: 0.6315 time to fit residues: 474.2474 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 : 0.686 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 82 ASN A 159 HIS A 319 ASN B 105 ASN B 208 GLN D 227 GLN D 256 ASN ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 GLN C 80 GLN C 195 GLN G 77 GLN G 178 ASN G 195 GLN H 256 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.132870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.110945 restraints weight = 34282.431| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.56 r_work: 0.3393 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24670 Z= 0.120 Angle : 0.543 8.559 33816 Z= 0.294 Chirality : 0.040 0.221 3749 Planarity : 0.004 0.050 3932 Dihedral : 18.154 176.721 4458 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.75 % Favored : 96.13 % Rotamer: Outliers : 3.97 % Allowed : 25.93 % Favored : 70.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.16), residues: 2638 helix: 1.23 (0.19), residues: 767 sheet: 0.67 (0.26), residues: 433 loop : -1.11 (0.15), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 325 TYR 0.016 0.001 TYR A 292 PHE 0.019 0.001 PHE F 273 TRP 0.004 0.001 TRP G 149 HIS 0.004 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00261 (24670) covalent geometry : angle 0.54301 (33816) hydrogen bonds : bond 0.04301 ( 735) hydrogen bonds : angle 5.27296 ( 1982) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 600 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.7138 (tp-100) cc_final: 0.6768 (tp-100) REVERT: A 205 LYS cc_start: 0.8702 (mttt) cc_final: 0.8389 (mtpp) REVERT: A 283 GLU cc_start: 0.7024 (tm-30) cc_final: 0.6768 (tm-30) REVERT: A 322 MET cc_start: 0.4219 (OUTLIER) cc_final: 0.3859 (ttp) REVERT: B 68 LYS cc_start: 0.8249 (mtpp) cc_final: 0.7815 (mtpp) REVERT: I 66 GLU cc_start: 0.6031 (OUTLIER) cc_final: 0.5750 (tm-30) REVERT: I 115 MET cc_start: 0.5714 (OUTLIER) cc_final: 0.5427 (mpm) REVERT: D 68 GLU cc_start: 0.7614 (tm-30) cc_final: 0.7388 (tm-30) REVERT: D 70 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7756 (mt-10) REVERT: D 123 ASP cc_start: 0.7704 (m-30) cc_final: 0.7424 (m-30) REVERT: D 272 GLU cc_start: 0.7984 (pt0) cc_final: 0.7751 (mt-10) REVERT: E 244 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8148 (mt-10) REVERT: F 12 LEU cc_start: 0.7681 (mp) cc_final: 0.7280 (mt) REVERT: F 66 LYS cc_start: 0.7905 (mttt) cc_final: 0.7635 (mttm) REVERT: C 81 SER cc_start: 0.8611 (OUTLIER) cc_final: 0.8282 (t) REVERT: C 302 ASP cc_start: 0.8088 (m-30) cc_final: 0.7856 (m-30) REVERT: G 29 GLU cc_start: 0.8132 (mp0) cc_final: 0.7833 (mp0) REVERT: G 124 GLU cc_start: 0.7348 (tp30) cc_final: 0.7139 (tp30) REVERT: G 184 GLU cc_start: 0.7030 (pm20) cc_final: 0.6799 (pm20) REVERT: H 262 ASP cc_start: 0.8643 (t0) cc_final: 0.8347 (t70) REVERT: H 273 PHE cc_start: 0.7929 (p90) cc_final: 0.7640 (p90) outliers start: 94 outliers final: 36 residues processed: 656 average time/residue: 0.6189 time to fit residues: 465.0460 Evaluate side-chains 612 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 572 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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 316 SER 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 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 162 THR Chi-restraints excluded: chain D residue 17 GLU 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 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 81 SER Chi-restraints excluded: chain C residue 215 VAL 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: 6.9990 chunk 71 optimal weight: 9.9990 chunk 139 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 135 optimal weight: 0.3980 chunk 150 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 153 optimal weight: 0.5980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN 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 151 ASN ** H 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 279 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.129281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.106985 restraints weight = 33852.570| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.55 r_work: 0.3341 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 24670 Z= 0.242 Angle : 0.589 7.806 33816 Z= 0.314 Chirality : 0.044 0.230 3749 Planarity : 0.005 0.054 3932 Dihedral : 18.050 176.870 4407 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.98 % Favored : 95.98 % Rotamer: Outliers : 4.27 % Allowed : 26.18 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.16), residues: 2638 helix: 1.16 (0.19), residues: 765 sheet: 0.74 (0.27), residues: 414 loop : -1.19 (0.15), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 40 TYR 0.019 0.002 TYR A 292 PHE 0.016 0.002 PHE G 43 TRP 0.012 0.002 TRP A 74 HIS 0.008 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00577 (24670) covalent geometry : angle 0.58900 (33816) hydrogen bonds : bond 0.04794 ( 735) hydrogen bonds : angle 5.37180 ( 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 682 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 581 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.7192 (tp-100) cc_final: 0.6772 (tp-100) REVERT: A 88 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7154 (mtt180) REVERT: A 142 ARG cc_start: 0.5774 (OUTLIER) cc_final: 0.4925 (ttt90) REVERT: A 205 LYS cc_start: 0.8705 (mttt) cc_final: 0.8448 (mtpp) REVERT: A 283 GLU cc_start: 0.7111 (tm-30) cc_final: 0.6857 (tm-30) REVERT: A 322 MET cc_start: 0.4176 (OUTLIER) cc_final: 0.3756 (ttp) REVERT: B 175 MET cc_start: 0.6820 (OUTLIER) cc_final: 0.6570 (tpp) REVERT: I 115 MET cc_start: 0.5682 (OUTLIER) cc_final: 0.5373 (mpm) REVERT: D 70 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7766 (mt-10) REVERT: D 123 ASP cc_start: 0.7775 (m-30) cc_final: 0.7513 (m-30) REVERT: E 191 GLU cc_start: 0.7327 (mm-30) cc_final: 0.7119 (mm-30) REVERT: E 244 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8210 (mt-10) REVERT: F 12 LEU cc_start: 0.7753 (mp) cc_final: 0.7339 (mt) REVERT: F 29 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7777 (mm-30) REVERT: F 66 LYS cc_start: 0.7962 (mttt) cc_final: 0.7717 (mttm) REVERT: C 81 SER cc_start: 0.8742 (m) cc_final: 0.8462 (p) REVERT: C 244 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7796 (mt-10) REVERT: C 259 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7526 (ptt90) REVERT: G 29 GLU cc_start: 0.8088 (mp0) cc_final: 0.7882 (mp0) REVERT: G 184 GLU cc_start: 0.7016 (pm20) cc_final: 0.6785 (pm20) REVERT: G 226 SER cc_start: 0.8425 (p) cc_final: 0.8218 (t) REVERT: G 229 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.8046 (tpp) REVERT: H 244 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7511 (mt-10) REVERT: H 267 ASP cc_start: 0.7491 (p0) cc_final: 0.7235 (p0) outliers start: 101 outliers final: 49 residues processed: 629 average time/residue: 0.6296 time to fit residues: 451.4100 Evaluate side-chains 612 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 553 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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 322 MET 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 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 144 ILE Chi-restraints excluded: chain I residue 145 LYS Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 256 ASN Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 120 GLN Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain F residue 29 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 269 THR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 259 ARG Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 19 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 219 optimal weight: 0.5980 chunk 255 optimal weight: 0.0970 chunk 264 optimal weight: 0.8980 chunk 239 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 211 optimal weight: 0.4980 chunk 136 optimal weight: 0.8980 chunk 88 optimal weight: 0.5980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 C 77 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 = 0.3752 r_free = 0.3752 target = 0.130951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.108879 restraints weight = 33838.289| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.54 r_work: 0.3370 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24670 Z= 0.139 Angle : 0.533 10.616 33816 Z= 0.288 Chirality : 0.041 0.203 3749 Planarity : 0.004 0.051 3932 Dihedral : 18.000 176.257 4407 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.64 % Favored : 96.25 % Rotamer: Outliers : 3.93 % Allowed : 26.60 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.16), residues: 2638 helix: 1.28 (0.19), residues: 767 sheet: 0.79 (0.27), residues: 414 loop : -1.14 (0.15), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 325 TYR 0.014 0.001 TYR G 265 PHE 0.028 0.001 PHE D 273 TRP 0.005 0.001 TRP F 33 HIS 0.006 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00316 (24670) covalent geometry : angle 0.53337 (33816) hydrogen bonds : bond 0.04104 ( 735) hydrogen bonds : angle 5.14990 ( 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 666 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 573 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7023 (mtt180) REVERT: A 142 ARG cc_start: 0.5604 (OUTLIER) cc_final: 0.5295 (tpt90) REVERT: A 205 LYS cc_start: 0.8699 (mttt) cc_final: 0.8393 (mtpp) REVERT: A 264 LYS cc_start: 0.7604 (mtmt) cc_final: 0.7285 (tttt) REVERT: A 283 GLU cc_start: 0.7088 (tm-30) cc_final: 0.6865 (tm-30) REVERT: I 115 MET cc_start: 0.5493 (OUTLIER) cc_final: 0.5217 (mpm) REVERT: I 132 LYS cc_start: 0.7651 (mmmt) cc_final: 0.7443 (mmmt) REVERT: D 70 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7728 (mt-10) REVERT: D 123 ASP cc_start: 0.7709 (m-30) cc_final: 0.7446 (m-30) REVERT: E 191 GLU cc_start: 0.7345 (mm-30) cc_final: 0.7105 (mm-30) REVERT: E 244 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8191 (mt-10) REVERT: F 12 LEU cc_start: 0.7762 (mp) cc_final: 0.7371 (mt) REVERT: F 66 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7704 (mttm) REVERT: C 81 SER cc_start: 0.8700 (m) cc_final: 0.8413 (p) REVERT: G 29 GLU cc_start: 0.8116 (mp0) cc_final: 0.7882 (mp0) REVERT: G 69 LYS cc_start: 0.8064 (mptm) cc_final: 0.7850 (mptm) REVERT: G 184 GLU cc_start: 0.7003 (pm20) cc_final: 0.6776 (pm20) REVERT: G 302 ASP cc_start: 0.7550 (m-30) cc_final: 0.7074 (m-30) REVERT: G 304 MET cc_start: 0.8117 (ttt) cc_final: 0.7750 (ttt) REVERT: H 262 ASP cc_start: 0.8662 (t0) cc_final: 0.8332 (t70) outliers start: 93 outliers final: 54 residues processed: 618 average time/residue: 0.6345 time to fit residues: 445.4540 Evaluate side-chains 625 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 567 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 88 ARG Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 316 SER 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 219 GLU Chi-restraints excluded: chain B residue 224 LEU 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 25 PHE Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 102 ILE Chi-restraints excluded: chain I residue 104 GLU Chi-restraints excluded: chain I residue 115 MET Chi-restraints excluded: chain I residue 117 LYS Chi-restraints excluded: chain I residue 128 GLU Chi-restraints excluded: chain I residue 129 MET Chi-restraints excluded: chain I residue 137 GLN Chi-restraints excluded: chain I residue 144 ILE Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 39 LYS 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 66 LYS Chi-restraints excluded: chain F residue 69 LYS 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 C residue 171 SER 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 68 GLU Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 82 CYS Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 272 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 45 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 239 optimal weight: 0.9980 chunk 108 optimal weight: 0.0000 chunk 146 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 93 optimal weight: 0.9980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS A 275 HIS A 319 ASN B 166 ASN B 208 GLN D 195 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 C 60 HIS 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.128676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.106610 restraints weight = 33878.243| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.54 r_work: 0.3336 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 24670 Z= 0.223 Angle : 0.579 11.078 33816 Z= 0.308 Chirality : 0.043 0.231 3749 Planarity : 0.005 0.053 3932 Dihedral : 17.980 176.060 4407 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.87 % Favored : 96.06 % Rotamer: Outliers : 4.22 % Allowed : 26.98 % Favored : 68.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.16), residues: 2638 helix: 1.23 (0.19), residues: 765 sheet: 0.74 (0.27), residues: 420 loop : -1.22 (0.15), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 40 TYR 0.018 0.002 TYR G 265 PHE 0.026 0.002 PHE D 273 TRP 0.011 0.001 TRP A 74 HIS 0.008 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00525 (24670) covalent geometry : angle 0.57853 (33816) hydrogen bonds : bond 0.04590 ( 735) hydrogen bonds : angle 5.26970 ( 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 680 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 580 time to evaluate : 0.793 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: 0.7863 (OUTLIER) cc_final: 0.7130 (mtt180) REVERT: A 205 LYS cc_start: 0.8729 (mttt) cc_final: 0.8473 (mtpp) REVERT: A 264 LYS cc_start: 0.7562 (mtmt) cc_final: 0.7291 (tttt) REVERT: A 283 GLU cc_start: 0.7106 (tm-30) cc_final: 0.6864 (tm-30) REVERT: B 180 ILE cc_start: 0.7800 (mm) cc_final: 0.7538 (mp) REVERT: I 115 MET cc_start: 0.5451 (OUTLIER) cc_final: 0.5173 (mpm) REVERT: I 145 LYS cc_start: 0.6845 (OUTLIER) cc_final: 0.6070 (tmmm) REVERT: D 70 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7760 (mt-10) REVERT: D 123 ASP cc_start: 0.7733 (m-30) cc_final: 0.7468 (m-30) REVERT: E 191 GLU cc_start: 0.7382 (mm-30) cc_final: 0.7127 (mm-30) REVERT: E 244 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8231 (mt-10) REVERT: E 302 ASP cc_start: 0.7621 (m-30) cc_final: 0.7321 (m-30) REVERT: F 12 LEU cc_start: 0.7773 (mp) cc_final: 0.7399 (mt) REVERT: F 66 LYS cc_start: 0.7908 (mttt) cc_final: 0.7660 (mttm) REVERT: C 81 SER cc_start: 0.8744 (m) cc_final: 0.8477 (p) REVERT: C 244 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7715 (mt-10) REVERT: C 259 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7469 (ptt90) REVERT: C 322 ILE cc_start: 0.8522 (mm) cc_final: 0.8320 (mp) REVERT: G 69 LYS cc_start: 0.8150 (mptm) cc_final: 0.7902 (mptm) REVERT: G 184 GLU cc_start: 0.7063 (pm20) cc_final: 0.6815 (pm20) REVERT: G 302 ASP cc_start: 0.7558 (m-30) cc_final: 0.7069 (m-30) REVERT: H 229 MET cc_start: 0.7412 (tmm) cc_final: 0.7017 (tmm) REVERT: H 244 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7471 (mt-10) REVERT: H 267 ASP cc_start: 0.7470 (p0) cc_final: 0.7170 (p0) outliers start: 100 outliers final: 58 residues processed: 632 average time/residue: 0.6309 time to fit residues: 454.6548 Evaluate side-chains 632 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 568 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 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 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 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 104 GLU Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain I residue 115 MET Chi-restraints excluded: chain I residue 117 LYS Chi-restraints excluded: chain I residue 128 GLU Chi-restraints excluded: chain I residue 129 MET Chi-restraints excluded: chain I residue 137 GLN Chi-restraints excluded: chain I residue 144 ILE 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 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 185 ASP Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain F residue 69 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 244 GLU Chi-restraints excluded: chain C residue 259 ARG Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 239 LYS Chi-restraints excluded: chain H residue 244 GLU Chi-restraints excluded: chain H residue 272 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 49 optimal weight: 1.9990 chunk 205 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 240 optimal weight: 0.9990 chunk 171 optimal weight: 0.8980 chunk 193 optimal weight: 2.9990 chunk 273 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 121 optimal weight: 0.4980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 ASN B 166 ASN ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 GLN ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 GLN G 77 GLN G 178 ASN ** H 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.129617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.107474 restraints weight = 33666.243| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.54 r_work: 0.3349 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 24670 Z= 0.177 Angle : 0.555 11.255 33816 Z= 0.297 Chirality : 0.042 0.218 3749 Planarity : 0.004 0.052 3932 Dihedral : 17.968 175.886 4407 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.75 % Favored : 96.17 % Rotamer: Outliers : 3.93 % Allowed : 28.12 % Favored : 67.95 % 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: 1.32 (0.19), residues: 765 sheet: 0.71 (0.27), residues: 420 loop : -1.25 (0.15), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 142 TYR 0.019 0.001 TYR A 23 PHE 0.024 0.001 PHE D 273 TRP 0.007 0.001 TRP G 264 HIS 0.004 0.001 HIS F 60 Details of bonding type rmsd covalent geometry : bond 0.00413 (24670) covalent geometry : angle 0.55538 (33816) hydrogen bonds : bond 0.04289 ( 735) hydrogen bonds : angle 5.18442 ( 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 661 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 568 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 LYS cc_start: 0.8726 (mttt) cc_final: 0.8481 (mtpp) REVERT: A 264 LYS cc_start: 0.7537 (mtmt) cc_final: 0.7310 (tttt) REVERT: A 283 GLU cc_start: 0.7133 (tm-30) cc_final: 0.6896 (tm-30) REVERT: B 68 LYS cc_start: 0.8362 (mtpp) cc_final: 0.8085 (mtpp) REVERT: B 180 ILE cc_start: 0.7773 (mm) cc_final: 0.7492 (mp) REVERT: I 115 MET cc_start: 0.5305 (OUTLIER) cc_final: 0.5050 (mpm) REVERT: I 145 LYS cc_start: 0.6848 (OUTLIER) cc_final: 0.6140 (ptmm) REVERT: D 70 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7720 (mt-10) REVERT: D 123 ASP cc_start: 0.7720 (m-30) cc_final: 0.7470 (m-30) REVERT: E 191 GLU cc_start: 0.7421 (mm-30) cc_final: 0.7197 (mm-30) REVERT: E 244 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8214 (mt-10) REVERT: E 302 ASP cc_start: 0.7607 (m-30) cc_final: 0.7288 (m-30) REVERT: F 12 LEU cc_start: 0.7783 (mp) cc_final: 0.7391 (mt) REVERT: F 66 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7729 (mttm) REVERT: C 43 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.7475 (p90) REVERT: C 81 SER cc_start: 0.8735 (OUTLIER) cc_final: 0.8455 (p) REVERT: G 69 LYS cc_start: 0.8132 (mptm) cc_final: 0.7900 (mptm) REVERT: G 184 GLU cc_start: 0.7098 (pm20) cc_final: 0.6823 (pm20) REVERT: G 302 ASP cc_start: 0.7551 (m-30) cc_final: 0.7086 (m-30) REVERT: H 229 MET cc_start: 0.7382 (tmm) cc_final: 0.6980 (tmm) REVERT: H 244 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7488 (mt-10) REVERT: H 267 ASP cc_start: 0.7452 (p0) cc_final: 0.7131 (p0) outliers start: 93 outliers final: 60 residues processed: 616 average time/residue: 0.6321 time to fit residues: 444.1410 Evaluate side-chains 639 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 573 time to evaluate : 0.812 ------------------------------------------------------------------------------- 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 120 GLU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain 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 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 144 ILE Chi-restraints excluded: chain I residue 145 LYS Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 163 ASP Chi-restraints excluded: chain D residue 39 LYS 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 215 VAL Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain F residue 66 LYS Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain F residue 85 SER 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 43 PHE Chi-restraints excluded: chain C residue 81 SER 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 68 GLU 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 G residue 322 ILE Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 174 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 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: 4.9990 chunk 71 optimal weight: 0.9980 chunk 224 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 chunk 88 optimal weight: 0.5980 chunk 91 optimal weight: 0.4980 chunk 140 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 134 optimal weight: 0.3980 chunk 197 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS A 275 HIS A 319 ASN B 166 ASN ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 GLN ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 GLN G 77 GLN G 178 ASN ** H 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 279 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.129825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.108095 restraints weight = 34036.538| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.54 r_work: 0.3358 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1789 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= 0.160 Angle : 0.550 11.828 33816 Z= 0.295 Chirality : 0.041 0.210 3749 Planarity : 0.004 0.052 3932 Dihedral : 17.917 175.907 4405 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.83 % Favored : 96.10 % Rotamer: Outliers : 4.05 % Allowed : 28.34 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.16), residues: 2638 helix: 1.37 (0.19), residues: 765 sheet: 0.88 (0.27), residues: 414 loop : -1.24 (0.15), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 40 TYR 0.024 0.001 TYR A 23 PHE 0.028 0.001 PHE D 273 TRP 0.007 0.001 TRP G 264 HIS 0.004 0.001 HIS F 60 Details of bonding type rmsd covalent geometry : bond 0.00371 (24670) covalent geometry : angle 0.54963 (33816) hydrogen bonds : bond 0.04164 ( 735) hydrogen bonds : angle 5.12250 ( 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 679 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 583 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 GLU cc_start: 0.5398 (OUTLIER) cc_final: 0.5191 (pp20) REVERT: A 205 LYS cc_start: 0.8705 (mttt) cc_final: 0.8456 (mtpp) REVERT: A 264 LYS cc_start: 0.7524 (mtmt) cc_final: 0.7276 (tttt) REVERT: A 275 HIS cc_start: 0.6163 (OUTLIER) cc_final: 0.5846 (p90) REVERT: A 276 LEU cc_start: 0.8039 (mt) cc_final: 0.7807 (mm) REVERT: A 283 GLU cc_start: 0.7130 (tm-30) cc_final: 0.6894 (tm-30) REVERT: B 68 LYS cc_start: 0.8346 (mtpp) cc_final: 0.8067 (mtpp) REVERT: B 175 MET cc_start: 0.7040 (OUTLIER) cc_final: 0.6740 (tpp) REVERT: I 115 MET cc_start: 0.5135 (OUTLIER) cc_final: 0.4899 (mpm) REVERT: I 145 LYS cc_start: 0.6875 (OUTLIER) cc_final: 0.6102 (tmmm) REVERT: D 17 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7427 (pm20) REVERT: D 70 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7673 (mt-10) REVERT: D 123 ASP cc_start: 0.7697 (m-30) cc_final: 0.7442 (m-30) REVERT: E 191 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7178 (mm-30) REVERT: E 244 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8178 (mt-10) REVERT: E 302 ASP cc_start: 0.7628 (m-30) cc_final: 0.7277 (m-30) REVERT: F 12 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7398 (mt) REVERT: F 66 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7621 (mttm) REVERT: C 81 SER cc_start: 0.8680 (m) cc_final: 0.8430 (p) REVERT: C 231 PHE cc_start: 0.6590 (OUTLIER) cc_final: 0.6066 (m-80) REVERT: C 302 ASP cc_start: 0.8213 (m-30) cc_final: 0.7971 (m-30) REVERT: G 69 LYS cc_start: 0.8130 (mptm) cc_final: 0.7891 (mptm) REVERT: G 184 GLU cc_start: 0.7071 (pm20) cc_final: 0.6811 (pm20) REVERT: H 229 MET cc_start: 0.7303 (tmm) cc_final: 0.6880 (tmm) REVERT: H 262 ASP cc_start: 0.8632 (t0) cc_final: 0.8342 (t70) outliers start: 96 outliers final: 60 residues processed: 634 average time/residue: 0.6336 time to fit residues: 457.7633 Evaluate side-chains 645 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 576 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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 109 GLU Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 177 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 7 ILE Chi-restraints excluded: chain I residue 8 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 106 ASN Chi-restraints excluded: chain I residue 115 MET Chi-restraints excluded: chain I residue 117 LYS Chi-restraints excluded: chain I residue 128 GLU Chi-restraints excluded: chain I residue 129 MET Chi-restraints excluded: chain I residue 137 GLN Chi-restraints excluded: chain I residue 144 ILE Chi-restraints excluded: chain I residue 145 LYS Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 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 215 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 66 LYS Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 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 231 PHE 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 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 G residue 322 ILE Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 174 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 266 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 149 optimal weight: 0.0050 chunk 214 optimal weight: 0.7980 chunk 166 optimal weight: 0.9990 chunk 258 optimal weight: 0.7980 chunk 136 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 13 optimal weight: 0.0970 chunk 122 optimal weight: 0.8980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS A 319 ASN B 166 ASN ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 GLN ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 178 ASN F 195 GLN G 77 GLN G 178 ASN H 256 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.130491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.108881 restraints weight = 33724.031| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.53 r_work: 0.3369 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24670 Z= 0.139 Angle : 0.545 12.521 33816 Z= 0.291 Chirality : 0.041 0.201 3749 Planarity : 0.004 0.051 3932 Dihedral : 17.893 175.936 4405 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.71 % Favored : 96.21 % Rotamer: Outliers : 3.76 % Allowed : 28.76 % 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: -0.12 (0.16), residues: 2638 helix: 1.39 (0.19), residues: 768 sheet: 0.82 (0.27), residues: 424 loop : -1.23 (0.15), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 274 TYR 0.020 0.001 TYR A 292 PHE 0.022 0.001 PHE F 273 TRP 0.005 0.001 TRP G 264 HIS 0.005 0.001 HIS D 317 Details of bonding type rmsd covalent geometry : bond 0.00318 (24670) covalent geometry : angle 0.54472 (33816) hydrogen bonds : bond 0.04026 ( 735) hydrogen bonds : angle 5.05354 ( 1982) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 574 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 LYS cc_start: 0.8689 (mttt) cc_final: 0.8427 (mtpp) REVERT: A 264 LYS cc_start: 0.7513 (mtmt) cc_final: 0.7278 (tttt) REVERT: A 283 GLU cc_start: 0.7102 (tm-30) cc_final: 0.6877 (tm-30) REVERT: B 68 LYS cc_start: 0.8349 (mtpp) cc_final: 0.8065 (mtpp) REVERT: B 175 MET cc_start: 0.7032 (OUTLIER) cc_final: 0.6785 (tpp) REVERT: I 66 GLU cc_start: 0.5990 (OUTLIER) cc_final: 0.5704 (tm-30) REVERT: I 115 MET cc_start: 0.5098 (OUTLIER) cc_final: 0.4879 (mpm) REVERT: I 145 LYS cc_start: 0.6866 (OUTLIER) cc_final: 0.6124 (tttm) REVERT: D 17 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7446 (pm20) REVERT: D 70 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7646 (mt-10) REVERT: D 123 ASP cc_start: 0.7684 (m-30) cc_final: 0.7438 (m-30) REVERT: E 191 GLU cc_start: 0.7438 (mm-30) cc_final: 0.7186 (mm-30) REVERT: E 244 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8168 (mt-10) REVERT: F 12 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7402 (mt) REVERT: F 153 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8301 (mtmm) REVERT: C 81 SER cc_start: 0.8624 (OUTLIER) cc_final: 0.8400 (p) REVERT: C 231 PHE cc_start: 0.6589 (OUTLIER) cc_final: 0.6061 (m-80) REVERT: C 307 LYS cc_start: 0.8623 (mtmm) cc_final: 0.8291 (mtmm) REVERT: G 69 LYS cc_start: 0.8108 (mptm) cc_final: 0.7864 (mptm) REVERT: G 184 GLU cc_start: 0.7048 (pm20) cc_final: 0.6784 (pm20) REVERT: H 229 MET cc_start: 0.7304 (tmm) cc_final: 0.6887 (tmm) REVERT: H 262 ASP cc_start: 0.8620 (t0) cc_final: 0.8364 (t70) outliers start: 89 outliers final: 57 residues processed: 619 average time/residue: 0.6321 time to fit residues: 446.2331 Evaluate side-chains 631 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 565 time to evaluate : 0.789 ------------------------------------------------------------------------------- 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 120 GLU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 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 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 144 ILE Chi-restraints excluded: chain I residue 145 LYS Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 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 68 GLU Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 153 LYS 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 81 SER Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 269 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 G residue 322 ILE Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 174 SER Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 239 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 106 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 274 optimal weight: 9.9990 chunk 184 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS A 275 HIS A 319 ASN ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 GLN ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 ASN F 178 ASN F 195 GLN G 77 GLN G 178 ASN H 227 GLN H 279 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.129895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.108143 restraints weight = 33971.657| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.54 r_work: 0.3357 rms_B_bonded: 1.95 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: 0.7990 moved from start: 0.1953 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= 0.169 Angle : 0.562 13.367 33816 Z= 0.299 Chirality : 0.041 0.210 3749 Planarity : 0.004 0.052 3932 Dihedral : 17.875 176.058 4405 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.98 % Favored : 95.98 % Rotamer: Outliers : 3.63 % Allowed : 28.76 % Favored : 67.61 % 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: 1.38 (0.19), residues: 766 sheet: 0.85 (0.27), residues: 414 loop : -1.23 (0.15), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 325 TYR 0.018 0.001 TYR A 23 PHE 0.019 0.001 PHE D 273 TRP 0.007 0.001 TRP A 74 HIS 0.004 0.001 HIS F 60 Details of bonding type rmsd covalent geometry : bond 0.00394 (24670) covalent geometry : angle 0.56197 (33816) hydrogen bonds : bond 0.04169 ( 735) hydrogen bonds : angle 5.08195 ( 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 668 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 582 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.6562 (pp20) cc_final: 0.6210 (pp20) REVERT: A 205 LYS cc_start: 0.8694 (mttt) cc_final: 0.8436 (mtpp) REVERT: A 276 LEU cc_start: 0.8016 (mt) cc_final: 0.7782 (mm) REVERT: A 283 GLU cc_start: 0.7134 (tm-30) cc_final: 0.6909 (tm-30) REVERT: A 294 TYR cc_start: 0.5062 (OUTLIER) cc_final: 0.4800 (t80) REVERT: B 68 LYS cc_start: 0.8367 (mtpp) cc_final: 0.8086 (mtpp) REVERT: B 175 MET cc_start: 0.7022 (OUTLIER) cc_final: 0.6810 (tpp) REVERT: I 115 MET cc_start: 0.5031 (OUTLIER) cc_final: 0.4818 (mpm) REVERT: I 145 LYS cc_start: 0.6885 (OUTLIER) cc_final: 0.6204 (tmtp) REVERT: D 17 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7469 (pm20) REVERT: D 70 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7658 (mt-10) REVERT: D 123 ASP cc_start: 0.7697 (m-30) cc_final: 0.7448 (m-30) REVERT: E 191 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7181 (mm-30) REVERT: E 244 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8170 (mt-10) REVERT: F 12 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7406 (mt) REVERT: F 153 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8309 (mtmm) REVERT: C 81 SER cc_start: 0.8686 (OUTLIER) cc_final: 0.8427 (p) REVERT: C 231 PHE cc_start: 0.6604 (OUTLIER) cc_final: 0.6077 (m-80) REVERT: C 302 ASP cc_start: 0.8172 (m-30) cc_final: 0.7920 (m-30) REVERT: C 307 LYS cc_start: 0.8622 (mtmm) cc_final: 0.8316 (mtmm) REVERT: G 69 LYS cc_start: 0.8135 (mptm) cc_final: 0.7897 (mptm) REVERT: G 184 GLU cc_start: 0.7055 (pm20) cc_final: 0.6802 (pm20) REVERT: H 229 MET cc_start: 0.7315 (tmm) cc_final: 0.6895 (tmm) REVERT: H 262 ASP cc_start: 0.8633 (t0) cc_final: 0.8364 (t70) outliers start: 86 outliers final: 60 residues processed: 626 average time/residue: 0.6188 time to fit residues: 442.1442 Evaluate side-chains 645 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 576 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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 120 GLU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 221 GLU 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 322 MET Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 190 VAL 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 25 PHE 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 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 144 ILE Chi-restraints excluded: chain I residue 145 LYS Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 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 45 LEU Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 153 LYS 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 81 SER Chi-restraints excluded: chain C residue 215 VAL 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 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 157 ILE Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 174 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 30 optimal weight: 4.9990 chunk 231 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 165 optimal weight: 0.9980 chunk 187 optimal weight: 1.9990 chunk 116 optimal weight: 0.0670 chunk 176 optimal weight: 0.0980 chunk 56 optimal weight: 0.0370 chunk 133 optimal weight: 0.0970 chunk 93 optimal weight: 0.9990 overall best weight: 0.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS A 275 HIS A 319 ASN ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 GLN D 256 ASN E 75 ASN E 77 GLN F 178 ASN F 195 GLN G 178 ASN H 140 ASN H 279 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.132199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.110662 restraints weight = 34020.693| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.54 r_work: 0.3396 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 24670 Z= 0.112 Angle : 0.547 14.437 33816 Z= 0.292 Chirality : 0.040 0.181 3749 Planarity : 0.004 0.051 3932 Dihedral : 17.828 176.082 4405 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.56 % Favored : 96.36 % Rotamer: Outliers : 2.79 % Allowed : 29.56 % Favored : 67.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.16), residues: 2638 helix: 1.31 (0.19), residues: 784 sheet: 0.83 (0.27), residues: 423 loop : -1.21 (0.15), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 115 TYR 0.015 0.001 TYR A 23 PHE 0.030 0.001 PHE D 273 TRP 0.009 0.001 TRP A 208 HIS 0.012 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00247 (24670) covalent geometry : angle 0.54675 (33816) hydrogen bonds : bond 0.03819 ( 735) hydrogen bonds : angle 4.91753 ( 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 653 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 587 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 LYS cc_start: 0.8678 (mttt) cc_final: 0.8421 (mtpp) REVERT: A 264 LYS cc_start: 0.7513 (tttt) cc_final: 0.7221 (tttt) REVERT: A 276 LEU cc_start: 0.7928 (mt) cc_final: 0.7716 (mm) REVERT: A 283 GLU cc_start: 0.7100 (tm-30) cc_final: 0.6898 (tm-30) REVERT: B 48 ILE cc_start: 0.8757 (mt) cc_final: 0.8505 (mt) REVERT: B 68 LYS cc_start: 0.8291 (mtpp) cc_final: 0.8015 (mtpp) REVERT: I 145 LYS cc_start: 0.6836 (OUTLIER) cc_final: 0.6166 (ptmm) REVERT: D 17 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7483 (pm20) REVERT: D 70 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7635 (mt-10) REVERT: D 123 ASP cc_start: 0.7622 (m-30) cc_final: 0.7398 (m-30) REVERT: E 191 GLU cc_start: 0.7406 (mm-30) cc_final: 0.7159 (mm-30) REVERT: F 12 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7389 (mt) REVERT: C 81 SER cc_start: 0.8608 (OUTLIER) cc_final: 0.8364 (p) REVERT: C 169 TYR cc_start: 0.8599 (m-80) cc_final: 0.8147 (m-80) REVERT: C 231 PHE cc_start: 0.6590 (OUTLIER) cc_final: 0.6066 (m-80) REVERT: C 303 ARG cc_start: 0.8333 (mtm180) cc_final: 0.8069 (mtm110) REVERT: C 307 LYS cc_start: 0.8540 (mtmm) cc_final: 0.8306 (mtmm) REVERT: G 69 LYS cc_start: 0.8077 (mptm) cc_final: 0.7866 (mptm) REVERT: G 320 MET cc_start: 0.8457 (mmm) cc_final: 0.8214 (mpp) REVERT: H 229 MET cc_start: 0.7253 (tmm) cc_final: 0.6866 (tmm) REVERT: H 262 ASP cc_start: 0.8617 (t0) cc_final: 0.8411 (t70) outliers start: 66 outliers final: 50 residues processed: 622 average time/residue: 0.6184 time to fit residues: 438.8505 Evaluate side-chains 628 residues out of total 2377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 573 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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 120 GLU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 112 VAL 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 77 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 117 LYS Chi-restraints excluded: chain I residue 128 GLU Chi-restraints excluded: chain I residue 144 ILE Chi-restraints excluded: chain I residue 145 LYS Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain E residue 45 LEU 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 12 LEU Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 85 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 81 SER Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 219 CYS Chi-restraints excluded: chain G residue 226 SER Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain H residue 157 ILE 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: 0.0870 chunk 228 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 chunk 158 optimal weight: 0.9990 chunk 211 optimal weight: 2.9990 chunk 262 optimal weight: 0.0670 chunk 8 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 105 optimal weight: 0.0050 chunk 76 optimal weight: 0.8980 chunk 152 optimal weight: 0.6980 overall best weight: 0.2910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS A 319 ASN ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 GLN ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 GLN ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 GLN G 178 ASN H 279 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.132102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.110598 restraints weight = 33964.195| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.54 r_work: 0.3388 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.147 24670 Z= 0.146 Angle : 0.708 59.009 33816 Z= 0.411 Chirality : 0.040 0.182 3749 Planarity : 0.004 0.053 3932 Dihedral : 17.815 176.084 4402 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.56 % Favored : 96.36 % Rotamer: Outliers : 2.62 % Allowed : 30.28 % Favored : 67.10 % Cbeta Deviations : 0.04 % 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: 1.28 (0.19), residues: 785 sheet: 0.83 (0.27), residues: 423 loop : -1.21 (0.15), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 303 TYR 0.012 0.001 TYR G 265 PHE 0.030 0.001 PHE D 273 TRP 0.008 0.001 TRP A 208 HIS 0.076 0.002 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00323 (24670) covalent geometry : angle 0.70844 (33816) hydrogen bonds : bond 0.03817 ( 735) hydrogen bonds : angle 4.92783 ( 1982) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10597.80 seconds wall clock time: 180 minutes 36.80 seconds (10836.80 seconds total)