Starting phenix.real_space_refine on Fri Feb 6 03:32:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ui4_64183/02_2026/9ui4_64183.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ui4_64183/02_2026/9ui4_64183.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ui4_64183/02_2026/9ui4_64183.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ui4_64183/02_2026/9ui4_64183.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ui4_64183/02_2026/9ui4_64183.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ui4_64183/02_2026/9ui4_64183.map" } resolution = 2.91 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= 0.071 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: 6 Type Number sf(0) Gaussians P 54 5.49 5 Mg 9 5.21 5 S 117 5.16 5 C 13649 2.51 5 N 3861 2.21 5 O 4365 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22055 Number of models: 1 Model: "" Number of chains: 19 Chain: "L" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 540 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "C" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2365 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 9, 'TRANS': 297} Chain breaks: 1 Chain: "B" Number of atoms: 2327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2327 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 8, 'TRANS': 293} Chain breaks: 2 Chain: "A" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2369 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 9, 'TRANS': 298} Chain breaks: 1 Chain: "F" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2357 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 9, 'TRANS': 296} Chain breaks: 1 Chain: "I" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2365 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 9, 'TRANS': 297} Chain breaks: 1 Chain: "E" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2357 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 9, 'TRANS': 296} Chain breaks: 1 Chain: "H" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2365 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 9, 'TRANS': 297} Chain breaks: 1 Chain: "D" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2357 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 9, 'TRANS': 296} Chain breaks: 1 Chain: "G" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2365 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 9, 'TRANS': 297} Chain breaks: 1 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ANP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ANP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6123 SG CYS A 137 71.233 27.225 27.402 1.00111.42 S Time building chain proxies: 5.00, per 1000 atoms: 0.23 Number of scatterers: 22055 At special positions: 0 Unit cell: (112.88, 112.88, 202.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 117 16.00 P 54 15.00 Mg 9 11.99 O 4365 8.00 N 3861 7.00 C 13649 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: 1.84 Conformation dependent library (CDL) restraints added in 1.0 seconds 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5026 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 27 sheets defined 44.3% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'C' and resid 26 through 31 Processing helix chain 'C' and resid 34 through 45 removed outlier: 3.516A pdb=" N GLY C 45 " --> pdb=" O LEU C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 55 Processing helix chain 'C' and resid 56 through 62 Processing helix chain 'C' and resid 70 through 80 removed outlier: 4.246A pdb=" N GLU C 77 " --> pdb=" O LYS C 73 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA C 78 " --> pdb=" O ILE C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 99 removed outlier: 3.581A pdb=" N SER C 97 " --> pdb=" O HIS C 93 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU C 98 " --> pdb=" O GLN C 94 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE C 99 " --> pdb=" O ARG C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 114 Processing helix chain 'C' and resid 132 through 145 Processing helix chain 'C' and resid 167 through 179 removed outlier: 3.595A pdb=" N LEU C 171 " --> pdb=" O ARG C 167 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ARG C 177 " --> pdb=" O ALA C 173 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR C 178 " --> pdb=" O VAL C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 187 removed outlier: 3.745A pdb=" N ASP C 187 " --> pdb=" O SER C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 213 removed outlier: 3.509A pdb=" N GLN C 200 " --> pdb=" O ASN C 196 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR C 201 " --> pdb=" O THR C 197 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP C 209 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU C 213 " --> pdb=" O ASP C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 232 removed outlier: 3.638A pdb=" N ARG C 229 " --> pdb=" O THR C 225 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR C 230 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR C 232 " --> pdb=" O TYR C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 260 removed outlier: 3.513A pdb=" N PHE C 259 " --> pdb=" O LEU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 296 removed outlier: 3.577A pdb=" N ALA C 295 " --> pdb=" O ILE C 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 31 Processing helix chain 'B' and resid 36 through 44 Processing helix chain 'B' and resid 48 through 52 Processing helix chain 'B' and resid 58 through 63 removed outlier: 4.053A pdb=" N ASN B 62 " --> pdb=" O LYS B 58 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE B 63 " --> pdb=" O GLU B 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 58 through 63' Processing helix chain 'B' and resid 67 through 78 removed outlier: 3.570A pdb=" N ASP B 72 " --> pdb=" O GLU B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 96 removed outlier: 4.134A pdb=" N PHE B 92 " --> pdb=" O THR B 88 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG B 95 " --> pdb=" O GLU B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 115 removed outlier: 3.728A pdb=" N GLN B 114 " --> pdb=" O LYS B 111 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY B 115 " --> pdb=" O LEU B 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 111 through 115' Processing helix chain 'B' and resid 132 through 138 removed outlier: 3.501A pdb=" N HIS B 138 " --> pdb=" O THR B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 146 Processing helix chain 'B' and resid 167 through 178 removed outlier: 3.923A pdb=" N LEU B 171 " --> pdb=" O ARG B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 187 Processing helix chain 'B' and resid 196 through 212 removed outlier: 4.784A pdb=" N GLN B 202 " --> pdb=" O ASP B 198 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU B 203 " --> pdb=" O HIS B 199 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N GLU B 208 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ASP B 209 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N MET B 210 " --> pdb=" O GLN B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 231 Processing helix chain 'B' and resid 236 through 260 removed outlier: 4.373A pdb=" N ALA B 240 " --> pdb=" O GLY B 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 28 removed outlier: 4.070A pdb=" N ARG A 27 " --> pdb=" O PRO A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 56 through 64 removed outlier: 3.929A pdb=" N LEU A 60 " --> pdb=" O PRO A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 75 removed outlier: 3.856A pdb=" N ILE A 74 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 70 through 75' Processing helix chain 'A' and resid 88 through 99 removed outlier: 3.984A pdb=" N SER A 97 " --> pdb=" O HIS A 93 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE A 99 " --> pdb=" O ARG A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 110 Processing helix chain 'A' and resid 134 through 139 Processing helix chain 'A' and resid 167 through 175 Processing helix chain 'A' and resid 196 through 208 Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 223 through 227 removed outlier: 3.779A pdb=" N LEU A 227 " --> pdb=" O ALA A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 259 Processing helix chain 'A' and resid 288 through 296 removed outlier: 3.663A pdb=" N ILE A 292 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 44 Processing helix chain 'F' and resid 68 through 79 Processing helix chain 'F' and resid 93 through 98 Processing helix chain 'F' and resid 133 through 146 removed outlier: 3.902A pdb=" N THR F 139 " --> pdb=" O GLN F 135 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL F 142 " --> pdb=" O HIS F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 151 removed outlier: 3.695A pdb=" N ARG F 150 " --> pdb=" O PRO F 147 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY F 151 " --> pdb=" O ILE F 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 147 through 151' Processing helix chain 'F' and resid 170 through 178 removed outlier: 3.993A pdb=" N VAL F 174 " --> pdb=" O ARG F 170 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG F 177 " --> pdb=" O ALA F 173 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N TYR F 178 " --> pdb=" O VAL F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 189 Processing helix chain 'F' and resid 197 through 206 Processing helix chain 'F' and resid 209 through 214 Processing helix chain 'F' and resid 224 through 232 removed outlier: 4.483A pdb=" N THR F 230 " --> pdb=" O ALA F 226 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N TYR F 232 " --> pdb=" O TYR F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 259 removed outlier: 3.506A pdb=" N MET F 251 " --> pdb=" O ARG F 247 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP F 257 " --> pdb=" O LEU F 253 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE F 259 " --> pdb=" O LEU F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 296 removed outlier: 3.859A pdb=" N ILE F 292 " --> pdb=" O GLY F 288 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA F 293 " --> pdb=" O GLY F 289 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N HIS F 294 " --> pdb=" O ASN F 290 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 32 Processing helix chain 'I' and resid 34 through 45 removed outlier: 3.996A pdb=" N LEU I 41 " --> pdb=" O ASP I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 54 Processing helix chain 'I' and resid 56 through 62 removed outlier: 3.652A pdb=" N LEU I 60 " --> pdb=" O PRO I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 82 removed outlier: 3.796A pdb=" N LYS I 73 " --> pdb=" O ALA I 69 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA I 79 " --> pdb=" O LEU I 75 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS I 80 " --> pdb=" O THR I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 94 Processing helix chain 'I' and resid 95 through 98 removed outlier: 4.420A pdb=" N GLU I 98 " --> pdb=" O ARG I 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 95 through 98' Processing helix chain 'I' and resid 106 through 113 Processing helix chain 'I' and resid 135 through 144 removed outlier: 4.327A pdb=" N LEU I 140 " --> pdb=" O ILE I 136 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA I 141 " --> pdb=" O CYS I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 178 removed outlier: 4.025A pdb=" N LEU I 171 " --> pdb=" O ARG I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 199 through 212 removed outlier: 3.619A pdb=" N TYR I 205 " --> pdb=" O THR I 201 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLU I 208 " --> pdb=" O LEU I 204 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ASP I 209 " --> pdb=" O TYR I 205 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N MET I 210 " --> pdb=" O GLN I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 259 Processing helix chain 'I' and resid 289 through 295 Processing helix chain 'E' and resid 34 through 38 Processing helix chain 'E' and resid 41 through 45 removed outlier: 4.026A pdb=" N GLY E 45 " --> pdb=" O GLU E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 54 Processing helix chain 'E' and resid 56 through 62 Processing helix chain 'E' and resid 67 through 80 Processing helix chain 'E' and resid 90 through 96 removed outlier: 3.950A pdb=" N GLN E 94 " --> pdb=" O THR E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 113 Processing helix chain 'E' and resid 132 through 141 removed outlier: 3.510A pdb=" N ILE E 136 " --> pdb=" O GLY E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 179 removed outlier: 4.475A pdb=" N VAL E 174 " --> pdb=" O ARG E 170 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG E 177 " --> pdb=" O ALA E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 187 removed outlier: 3.816A pdb=" N VAL E 185 " --> pdb=" O SER E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 207 Processing helix chain 'E' and resid 207 through 212 Processing helix chain 'E' and resid 227 through 232 removed outlier: 3.599A pdb=" N TYR E 232 " --> pdb=" O TYR E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 259 removed outlier: 3.822A pdb=" N PHE E 259 " --> pdb=" O LEU E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 294 removed outlier: 3.505A pdb=" N ILE E 292 " --> pdb=" O GLY E 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 43 Processing helix chain 'H' and resid 48 through 54 removed outlier: 3.715A pdb=" N ALA H 53 " --> pdb=" O VAL H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 62 removed outlier: 3.504A pdb=" N ILE H 61 " --> pdb=" O LYS H 58 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN H 62 " --> pdb=" O GLU H 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 58 through 62' Processing helix chain 'H' and resid 67 through 82 removed outlier: 3.596A pdb=" N LYS H 73 " --> pdb=" O ALA H 69 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS H 80 " --> pdb=" O THR H 76 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL H 82 " --> pdb=" O ALA H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'H' and resid 94 through 99 Processing helix chain 'H' and resid 106 through 113 Processing helix chain 'H' and resid 132 through 144 removed outlier: 3.961A pdb=" N CYS H 137 " --> pdb=" O LYS H 133 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA H 141 " --> pdb=" O CYS H 137 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL H 142 " --> pdb=" O HIS H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 169 through 178 Processing helix chain 'H' and resid 181 through 189 Processing helix chain 'H' and resid 196 through 211 removed outlier: 3.506A pdb=" N GLN H 200 " --> pdb=" O ASN H 196 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N THR H 201 " --> pdb=" O THR H 197 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLN H 202 " --> pdb=" O ASP H 198 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP H 209 " --> pdb=" O TYR H 205 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET H 210 " --> pdb=" O GLN H 206 " (cutoff:3.500A) Processing helix chain 'H' and resid 223 through 232 removed outlier: 3.963A pdb=" N LEU H 227 " --> pdb=" O SER H 223 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR H 228 " --> pdb=" O ALA H 224 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR H 230 " --> pdb=" O ALA H 226 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR H 232 " --> pdb=" O TYR H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 234 through 256 removed outlier: 3.589A pdb=" N LEU H 238 " --> pdb=" O GLY H 234 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N SER H 239 " --> pdb=" O ARG H 235 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ALA H 240 " --> pdb=" O GLY H 236 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET H 251 " --> pdb=" O ARG H 247 " (cutoff:3.500A) Processing helix chain 'H' and resid 288 through 296 removed outlier: 3.586A pdb=" N ILE H 292 " --> pdb=" O GLY H 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 45 Processing helix chain 'D' and resid 48 through 55 Processing helix chain 'D' and resid 58 through 63 removed outlier: 3.904A pdb=" N ASN D 62 " --> pdb=" O LYS D 58 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE D 63 " --> pdb=" O GLU D 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 58 through 63' Processing helix chain 'D' and resid 67 through 82 removed outlier: 3.844A pdb=" N LEU D 81 " --> pdb=" O GLU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 98 Processing helix chain 'D' and resid 108 through 113 Processing helix chain 'D' and resid 132 through 144 removed outlier: 3.564A pdb=" N VAL D 142 " --> pdb=" O HIS D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 179 removed outlier: 3.911A pdb=" N LEU D 171 " --> pdb=" O ARG D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 188 removed outlier: 3.660A pdb=" N LEU D 186 " --> pdb=" O GLY D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 211 Processing helix chain 'D' and resid 227 through 232 Processing helix chain 'D' and resid 237 through 260 Processing helix chain 'D' and resid 289 through 296 Processing helix chain 'G' and resid 24 through 30 removed outlier: 3.688A pdb=" N GLN G 30 " --> pdb=" O ARG G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 41 removed outlier: 3.864A pdb=" N LYS G 40 " --> pdb=" O ASN G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 54 Processing helix chain 'G' and resid 56 through 62 Processing helix chain 'G' and resid 67 through 82 Processing helix chain 'G' and resid 88 through 97 removed outlier: 3.681A pdb=" N PHE G 92 " --> pdb=" O THR G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 113 Processing helix chain 'G' and resid 132 through 144 Processing helix chain 'G' and resid 167 through 176 Processing helix chain 'G' and resid 196 through 208 removed outlier: 3.678A pdb=" N LEU G 204 " --> pdb=" O GLN G 200 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 214 removed outlier: 3.556A pdb=" N GLU G 213 " --> pdb=" O ASP G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 232 removed outlier: 3.588A pdb=" N THR G 230 " --> pdb=" O ALA G 226 " (cutoff:3.500A) Processing helix chain 'G' and resid 237 through 260 Processing helix chain 'G' and resid 288 through 296 removed outlier: 3.737A pdb=" N ILE G 292 " --> pdb=" O GLY G 288 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA G 293 " --> pdb=" O GLY G 289 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 87 through 88 removed outlier: 5.756A pdb=" N ALA D 157 " --> pdb=" O ALA D 190 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ALA D 192 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N TYR D 159 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N LYS D 156 " --> pdb=" O TYR D 216 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU D 218 " --> pdb=" O LYS D 156 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N VAL D 264 " --> pdb=" O ALA D 217 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU D 219 " --> pdb=" O VAL D 264 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N THR D 266 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N VAL D 221 " --> pdb=" O THR D 266 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N THR D 123 " --> pdb=" O ILE D 265 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ASN D 267 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N MET D 125 " --> pdb=" O ASN D 267 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE D 327 " --> pdb=" O ARG D 310 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA D 328 " --> pdb=" O GLY D 335 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY D 333 " --> pdb=" O ASN D 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 156 through 160 removed outlier: 6.739A pdb=" N LYS C 156 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N ILE C 220 " --> pdb=" O LYS C 156 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N MET C 158 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ARG C 299 " --> pdb=" O TYR C 315 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 269 through 271 Processing sheet with id=AA4, first strand: chain 'B' and resid 160 through 161 removed outlier: 6.359A pdb=" N ILE B 160 " --> pdb=" O ASP B 222 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR B 266 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LEU B 300 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLU B 124 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 309 through 310 Processing sheet with id=AA6, first strand: chain 'A' and resid 266 through 267 removed outlier: 6.317A pdb=" N MET A 125 " --> pdb=" O ASN A 267 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 156 through 157 removed outlier: 6.411A pdb=" N LYS A 156 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 269 through 271 Processing sheet with id=AA9, first strand: chain 'A' and resid 328 through 330 Processing sheet with id=AB1, first strand: chain 'F' and resid 101 through 102 Processing sheet with id=AB2, first strand: chain 'F' and resid 124 through 127 removed outlier: 7.987A pdb=" N GLU F 124 " --> pdb=" O LEU F 300 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N LEU F 302 " --> pdb=" O GLU F 124 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N PHE F 126 " --> pdb=" O LEU F 302 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR F 301 " --> pdb=" O LYS F 313 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS F 313 " --> pdb=" O TYR F 301 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'F' and resid 269 through 271 Processing sheet with id=AB4, first strand: chain 'I' and resid 125 through 126 removed outlier: 6.411A pdb=" N PHE I 126 " --> pdb=" O LEU I 302 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N LYS I 304 " --> pdb=" O PHE I 126 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 157 through 159 removed outlier: 3.947A pdb=" N ALA I 190 " --> pdb=" O ALA I 157 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 220 through 221 Processing sheet with id=AB7, first strand: chain 'E' and resid 101 through 102 Processing sheet with id=AB8, first strand: chain 'E' and resid 263 through 264 Processing sheet with id=AB9, first strand: chain 'E' and resid 269 through 271 Processing sheet with id=AC1, first strand: chain 'E' and resid 328 through 329 removed outlier: 3.560A pdb=" N ALA E 328 " --> pdb=" O GLY E 335 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 265 through 267 removed outlier: 3.681A pdb=" N GLY H 127 " --> pdb=" O ASN H 267 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE H 327 " --> pdb=" O ARG H 310 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 156 through 157 removed outlier: 7.609A pdb=" N LYS H 156 " --> pdb=" O ALA H 217 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'H' and resid 160 through 161 removed outlier: 5.860A pdb=" N ILE H 160 " --> pdb=" O ASP H 222 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'H' and resid 269 through 270 Processing sheet with id=AC6, first strand: chain 'D' and resid 269 through 271 Processing sheet with id=AC7, first strand: chain 'G' and resid 101 through 102 Processing sheet with id=AC8, first strand: chain 'G' and resid 189 through 193 removed outlier: 6.314A pdb=" N LYS G 156 " --> pdb=" O LEU G 218 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N ILE G 220 " --> pdb=" O LYS G 156 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N MET G 158 " --> pdb=" O ILE G 220 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA G 262 " --> pdb=" O ALA G 217 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N THR G 123 " --> pdb=" O ILE G 265 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ASN G 267 " --> pdb=" O THR G 123 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N MET G 125 " --> pdb=" O ASN G 267 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR G 298 " --> pdb=" O ILE G 122 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 269 through 270 764 hydrogen bonds defined for protein. 2187 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.02 Time building geometry restraints manager: 2.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7139 1.34 - 1.46: 3189 1.46 - 1.58: 11809 1.58 - 1.70: 86 1.70 - 1.82: 202 Bond restraints: 22425 Sorted by residual: bond pdb=" CA LYS E 80 " pdb=" C LYS E 80 " ideal model delta sigma weight residual 1.523 1.584 -0.060 1.80e-02 3.09e+03 1.13e+01 bond pdb=" CB GLU B 91 " pdb=" CG GLU B 91 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.23e+00 bond pdb=" CB ARG A 215 " pdb=" CG ARG A 215 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.94e+00 bond pdb=" CB GLN A 114 " pdb=" CG GLN A 114 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.35e+00 bond pdb=" CB GLN H 202 " pdb=" CG GLN H 202 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.25e+00 ... (remaining 22420 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 30118 2.65 - 5.30: 253 5.30 - 7.96: 31 7.96 - 10.61: 5 10.61 - 13.26: 2 Bond angle restraints: 30409 Sorted by residual: angle pdb=" CA ARG A 215 " pdb=" CB ARG A 215 " pdb=" CG ARG A 215 " ideal model delta sigma weight residual 114.10 122.67 -8.57 2.00e+00 2.50e-01 1.84e+01 angle pdb=" C ASP A 222 " pdb=" CA ASP A 222 " pdb=" CB ASP A 222 " ideal model delta sigma weight residual 115.79 111.00 4.79 1.19e+00 7.06e-01 1.62e+01 angle pdb=" N ILE I 25 " pdb=" CA ILE I 25 " pdb=" C ILE I 25 " ideal model delta sigma weight residual 112.80 108.40 4.40 1.15e+00 7.56e-01 1.47e+01 angle pdb=" CA LEU B 245 " pdb=" CB LEU B 245 " pdb=" CG LEU B 245 " ideal model delta sigma weight residual 116.30 129.56 -13.26 3.50e+00 8.16e-02 1.44e+01 angle pdb=" CA GLN A 114 " pdb=" CB GLN A 114 " pdb=" CG GLN A 114 " ideal model delta sigma weight residual 114.10 121.65 -7.55 2.00e+00 2.50e-01 1.43e+01 ... (remaining 30404 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.69: 12308 28.69 - 57.38: 1242 57.38 - 86.07: 122 86.07 - 114.76: 12 114.76 - 143.45: 2 Dihedral angle restraints: 13686 sinusoidal: 5824 harmonic: 7862 Sorted by residual: dihedral pdb=" CA ILE F 160 " pdb=" C ILE F 160 " pdb=" N ASP F 161 " pdb=" CA ASP F 161 " ideal model delta harmonic sigma weight residual 180.00 155.87 24.13 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA TYR I 191 " pdb=" C TYR I 191 " pdb=" N ALA I 192 " pdb=" CA ALA I 192 " ideal model delta harmonic sigma weight residual -180.00 -160.01 -19.99 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" O1B ANP G 402 " pdb=" N3B ANP G 402 " pdb=" PB ANP G 402 " pdb=" PG ANP G 402 " ideal model delta sinusoidal sigma weight residual 35.15 153.82 -118.67 1 3.00e+01 1.11e-03 1.58e+01 ... (remaining 13683 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2752 0.049 - 0.097: 578 0.097 - 0.146: 127 0.146 - 0.194: 7 0.194 - 0.243: 2 Chirality restraints: 3466 Sorted by residual: chirality pdb=" CG LEU H 75 " pdb=" CB LEU H 75 " pdb=" CD1 LEU H 75 " pdb=" CD2 LEU H 75 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB ILE I 220 " pdb=" CA ILE I 220 " pdb=" CG1 ILE I 220 " pdb=" CG2 ILE I 220 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CG LEU B 249 " pdb=" CB LEU B 249 " pdb=" CD1 LEU B 249 " pdb=" CD2 LEU B 249 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.35e-01 ... (remaining 3463 not shown) Planarity restraints: 3803 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN I 23 " -0.044 5.00e-02 4.00e+02 6.80e-02 7.39e+00 pdb=" N PRO I 24 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO I 24 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO I 24 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 146 " -0.040 5.00e-02 4.00e+02 6.09e-02 5.92e+00 pdb=" N PRO E 147 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO E 147 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 147 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 167 " -0.037 5.00e-02 4.00e+02 5.64e-02 5.08e+00 pdb=" N PRO C 168 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO C 168 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 168 " -0.031 5.00e-02 4.00e+02 ... (remaining 3800 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 39 2.53 - 3.12: 16947 3.12 - 3.72: 36076 3.72 - 4.31: 50549 4.31 - 4.90: 81952 Nonbonded interactions: 185563 Sorted by model distance: nonbonded pdb=" OG1 THR B 134 " pdb="MG MG B 601 " model vdw 1.942 2.170 nonbonded pdb=" O3A ANP D 402 " pdb="MG MG D 403 " model vdw 1.951 2.170 nonbonded pdb=" N GLY G 132 " pdb="MG MG G 403 " model vdw 1.963 2.250 nonbonded pdb=" O ARG B 130 " pdb="MG MG B 601 " model vdw 1.998 2.170 nonbonded pdb="MG MG E 601 " pdb=" O3G ANP D 401 " model vdw 2.009 2.170 ... (remaining 185558 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 147 or resid 152 through 273 or resid 284 throu \ gh 336)) selection = (chain 'B' and (resid 22 through 273 or resid 284 through 336)) selection = (chain 'C' and (resid 22 through 147 or resid 152 through 273 or resid 284 throu \ gh 336)) selection = (chain 'D' and (resid 22 through 147 or resid 152 through 273 or resid 284 throu \ gh 336)) selection = (chain 'E' and (resid 22 through 147 or resid 152 through 273 or resid 284 throu \ gh 336)) selection = (chain 'F' and (resid 22 through 147 or resid 152 through 273 or resid 284 throu \ gh 336)) selection = (chain 'G' and (resid 22 through 147 or resid 152 through 273 or resid 284 throu \ gh 336)) selection = (chain 'H' and (resid 22 through 147 or resid 152 through 273 or resid 284 throu \ gh 336)) selection = (chain 'I' and (resid 22 through 147 or resid 152 through 273 or resid 284 throu \ gh 336)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 18.790 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6632 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 0.060 22425 Z= 0.137 Angle : 0.643 13.260 30409 Z= 0.332 Chirality : 0.042 0.243 3466 Planarity : 0.004 0.068 3803 Dihedral : 20.401 143.455 8660 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.62 % Favored : 92.13 % Rotamer: Outliers : 5.82 % Allowed : 41.81 % Favored : 52.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.16), residues: 2718 helix: -0.44 (0.16), residues: 1020 sheet: -2.21 (0.27), residues: 365 loop : -2.25 (0.16), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 170 TYR 0.017 0.001 TYR G 46 PHE 0.025 0.002 PHE E 166 HIS 0.016 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00302 (22425) covalent geometry : angle 0.64326 (30409) hydrogen bonds : bond 0.16259 ( 764) hydrogen bonds : angle 7.38611 ( 2187) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 264 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 146 LEU cc_start: 0.5657 (OUTLIER) cc_final: 0.5265 (mp) REVERT: C 187 ASP cc_start: 0.7547 (t0) cc_final: 0.7075 (t0) REVERT: C 219 LEU cc_start: 0.6835 (OUTLIER) cc_final: 0.6542 (tp) REVERT: C 243 MET cc_start: 0.7216 (mpt) cc_final: 0.6400 (tpt) REVERT: C 330 ASN cc_start: 0.6190 (m-40) cc_final: 0.5810 (t0) REVERT: B 77 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6649 (mp0) REVERT: B 84 MET cc_start: 0.4215 (mtt) cc_final: 0.3761 (mmt) REVERT: B 172 LEU cc_start: 0.6931 (tm) cc_final: 0.6606 (tp) REVERT: B 191 TYR cc_start: 0.6282 (OUTLIER) cc_final: 0.5690 (m-80) REVERT: B 252 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7571 (tt) REVERT: B 327 PHE cc_start: 0.6618 (OUTLIER) cc_final: 0.6082 (m-10) REVERT: A 34 ASN cc_start: 0.7410 (OUTLIER) cc_final: 0.6904 (p0) REVERT: A 101 GLN cc_start: 0.6021 (OUTLIER) cc_final: 0.5787 (pm20) REVERT: A 158 MET cc_start: 0.7131 (ttt) cc_final: 0.6852 (mtp) REVERT: A 187 ASP cc_start: 0.6586 (m-30) cc_final: 0.6174 (t0) REVERT: A 231 ASP cc_start: 0.8008 (t0) cc_final: 0.7728 (t0) REVERT: A 253 LEU cc_start: 0.4517 (OUTLIER) cc_final: 0.3783 (pp) REVERT: A 268 GLN cc_start: 0.6113 (OUTLIER) cc_final: 0.5451 (mm-40) REVERT: F 34 ASN cc_start: 0.8473 (t0) cc_final: 0.8061 (t0) REVERT: F 150 ARG cc_start: 0.4439 (mtm110) cc_final: 0.2030 (ttp-170) REVERT: F 158 MET cc_start: 0.7391 (mtt) cc_final: 0.6931 (ttt) REVERT: F 191 TYR cc_start: 0.3908 (OUTLIER) cc_final: 0.3067 (p90) REVERT: F 193 ARG cc_start: 0.5875 (ttt-90) cc_final: 0.4581 (tpm170) REVERT: F 326 MET cc_start: 0.5766 (mpp) cc_final: 0.5247 (mpp) REVERT: I 64 LYS cc_start: 0.7419 (mmmm) cc_final: 0.6951 (ptmt) REVERT: I 96 ARG cc_start: 0.4059 (ptm160) cc_final: 0.1361 (ptt90) REVERT: I 136 ILE cc_start: 0.6698 (OUTLIER) cc_final: 0.6199 (pp) REVERT: I 243 MET cc_start: 0.5989 (OUTLIER) cc_final: 0.5696 (mpm) REVERT: I 244 HIS cc_start: 0.7340 (OUTLIER) cc_final: 0.7097 (t-170) REVERT: E 42 GLU cc_start: 0.6591 (mt-10) cc_final: 0.6318 (tp30) REVERT: E 84 MET cc_start: 0.3212 (OUTLIER) cc_final: 0.2525 (ppp) REVERT: E 126 PHE cc_start: 0.6352 (p90) cc_final: 0.6119 (p90) REVERT: E 209 ASP cc_start: 0.6079 (OUTLIER) cc_final: 0.5127 (m-30) REVERT: E 243 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.8043 (mtt) REVERT: E 247 ARG cc_start: 0.7557 (mtm180) cc_final: 0.7228 (mmm160) REVERT: E 251 MET cc_start: 0.6229 (tpp) cc_final: 0.5755 (tmm) REVERT: E 265 ILE cc_start: 0.3303 (OUTLIER) cc_final: 0.2895 (mt) REVERT: E 320 LEU cc_start: 0.6527 (OUTLIER) cc_final: 0.6205 (tt) REVERT: H 103 THR cc_start: 0.4319 (OUTLIER) cc_final: 0.3999 (t) REVERT: H 111 LYS cc_start: 0.7663 (OUTLIER) cc_final: 0.6600 (mtmt) REVERT: D 39 LYS cc_start: 0.7619 (mmtt) cc_final: 0.7213 (tmtt) REVERT: D 135 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.7596 (mp-120) REVERT: D 243 MET cc_start: 0.8275 (tpt) cc_final: 0.7888 (mmm) REVERT: G 43 GLU cc_start: 0.7246 (pt0) cc_final: 0.6469 (tm-30) REVERT: G 118 GLU cc_start: 0.4715 (tt0) cc_final: 0.4389 (mt-10) REVERT: G 306 ARG cc_start: 0.7308 (OUTLIER) cc_final: 0.6001 (mmm-85) REVERT: G 310 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.5566 (mpp-170) outliers start: 130 outliers final: 79 residues processed: 361 average time/residue: 0.4430 time to fit residues: 188.1569 Evaluate side-chains 355 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 252 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 248 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 216 TYR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 46 TYR Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 176 GLU Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 311 ILE Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 170 ARG Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 223 SER Chi-restraints excluded: chain I residue 243 MET Chi-restraints excluded: chain I residue 244 HIS Chi-restraints excluded: chain I residue 302 LEU Chi-restraints excluded: chain I residue 309 THR Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 111 LYS Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 222 ASP Chi-restraints excluded: chain H residue 315 TYR Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 315 TYR Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 306 ARG Chi-restraints excluded: chain G residue 310 ARG Chi-restraints excluded: chain G residue 315 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.4980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 23 GLN C 244 HIS A 93 HIS ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 145 GLN H 93 HIS D 202 GLN ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 330 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.199140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.177638 restraints weight = 39119.660| |-----------------------------------------------------------------------------| r_work (start): 0.4289 rms_B_bonded: 2.28 r_work: 0.4206 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.0758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22425 Z= 0.158 Angle : 0.617 10.888 30409 Z= 0.321 Chirality : 0.043 0.186 3466 Planarity : 0.004 0.063 3803 Dihedral : 14.122 143.398 3758 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.35 % Favored : 91.43 % Rotamer: Outliers : 9.94 % Allowed : 36.88 % Favored : 53.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.16), residues: 2718 helix: -0.29 (0.16), residues: 1055 sheet: -2.26 (0.27), residues: 364 loop : -2.23 (0.17), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 229 TYR 0.018 0.002 TYR B 191 PHE 0.028 0.002 PHE F 126 HIS 0.010 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00355 (22425) covalent geometry : angle 0.61687 (30409) hydrogen bonds : bond 0.03817 ( 764) hydrogen bonds : angle 5.68126 ( 2187) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 222 poor density : 273 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 146 LEU cc_start: 0.5608 (OUTLIER) cc_final: 0.5143 (mp) REVERT: C 187 ASP cc_start: 0.7641 (t0) cc_final: 0.7144 (t0) REVERT: B 66 ILE cc_start: 0.3633 (OUTLIER) cc_final: 0.3415 (mp) REVERT: B 77 GLU cc_start: 0.7179 (mp0) cc_final: 0.6888 (mp0) REVERT: B 84 MET cc_start: 0.4335 (mtt) cc_final: 0.3810 (mmt) REVERT: B 158 MET cc_start: 0.6823 (OUTLIER) cc_final: 0.6544 (mpt) REVERT: B 161 ASP cc_start: 0.6085 (t0) cc_final: 0.5594 (t70) REVERT: B 169 GLU cc_start: 0.5848 (OUTLIER) cc_final: 0.5407 (pp20) REVERT: B 191 TYR cc_start: 0.6408 (OUTLIER) cc_final: 0.5620 (m-80) REVERT: B 252 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7561 (tt) REVERT: B 327 PHE cc_start: 0.6248 (OUTLIER) cc_final: 0.5742 (m-10) REVERT: A 34 ASN cc_start: 0.7415 (OUTLIER) cc_final: 0.6901 (p0) REVERT: A 84 MET cc_start: 0.3785 (tpt) cc_final: 0.3580 (tpt) REVERT: A 158 MET cc_start: 0.7231 (ttt) cc_final: 0.6969 (mtp) REVERT: A 187 ASP cc_start: 0.6727 (m-30) cc_final: 0.6254 (t0) REVERT: A 231 ASP cc_start: 0.8051 (t0) cc_final: 0.7786 (t0) REVERT: A 247 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.7197 (mtt-85) REVERT: A 253 LEU cc_start: 0.4637 (OUTLIER) cc_final: 0.3883 (pp) REVERT: F 34 ASN cc_start: 0.8188 (t0) cc_final: 0.7721 (t0) REVERT: F 133 LYS cc_start: 0.5988 (OUTLIER) cc_final: 0.4088 (mttp) REVERT: F 158 MET cc_start: 0.7383 (mtt) cc_final: 0.6971 (ttt) REVERT: F 178 TYR cc_start: 0.6501 (m-80) cc_final: 0.3571 (m-80) REVERT: F 191 TYR cc_start: 0.3884 (OUTLIER) cc_final: 0.3035 (p90) REVERT: F 193 ARG cc_start: 0.5939 (ttt-90) cc_final: 0.4605 (tpm170) REVERT: F 245 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6744 (tp) REVERT: F 326 MET cc_start: 0.5805 (mpp) cc_final: 0.5209 (mpp) REVERT: I 128 GLU cc_start: 0.6556 (OUTLIER) cc_final: 0.6244 (pp20) REVERT: I 136 ILE cc_start: 0.6925 (OUTLIER) cc_final: 0.6539 (pp) REVERT: I 216 TYR cc_start: 0.6295 (OUTLIER) cc_final: 0.5053 (t80) REVERT: I 254 ARG cc_start: 0.6282 (OUTLIER) cc_final: 0.4346 (ptm160) REVERT: E 84 MET cc_start: 0.3244 (pmm) cc_final: 0.2721 (ppp) REVERT: E 247 ARG cc_start: 0.7554 (mtm180) cc_final: 0.7256 (mmm160) REVERT: E 251 MET cc_start: 0.6223 (tpp) cc_final: 0.5784 (tmm) REVERT: E 265 ILE cc_start: 0.2873 (OUTLIER) cc_final: 0.2464 (mt) REVERT: E 320 LEU cc_start: 0.6512 (OUTLIER) cc_final: 0.6061 (tt) REVERT: H 125 MET cc_start: 0.6863 (OUTLIER) cc_final: 0.5425 (pmm) REVERT: D 39 LYS cc_start: 0.7516 (mmtt) cc_final: 0.7129 (tmtt) REVERT: D 84 MET cc_start: 0.5000 (OUTLIER) cc_final: 0.3986 (mmm) REVERT: D 243 MET cc_start: 0.8298 (tpt) cc_final: 0.7885 (mmm) REVERT: D 251 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.8124 (tpp) REVERT: D 287 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7600 (tp) REVERT: G 43 GLU cc_start: 0.7296 (pt0) cc_final: 0.6530 (tm-30) REVERT: G 118 GLU cc_start: 0.4786 (tt0) cc_final: 0.4414 (mt-10) REVERT: G 310 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.5497 (mpp-170) outliers start: 222 outliers final: 83 residues processed: 446 average time/residue: 0.4426 time to fit residues: 233.3970 Evaluate side-chains 353 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 246 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 216 TYR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain F residue 46 TYR Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 144 CYS Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 311 ILE Chi-restraints excluded: chain I residue 84 MET Chi-restraints excluded: chain I residue 93 HIS Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 128 GLU Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 170 ARG Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 223 SER Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 254 ARG Chi-restraints excluded: chain I residue 300 LEU Chi-restraints excluded: chain I residue 301 TYR Chi-restraints excluded: chain I residue 309 THR Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 125 MET Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 196 ASN Chi-restraints excluded: chain H residue 200 GLN Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 222 ASP Chi-restraints excluded: chain H residue 266 THR Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 315 TYR Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 251 MET Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain G residue 23 GLN Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain G residue 310 ARG Chi-restraints excluded: chain G residue 315 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 246 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 166 optimal weight: 0.4980 chunk 227 optimal weight: 0.9980 chunk 83 optimal weight: 6.9990 chunk 202 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 98 optimal weight: 0.0670 chunk 238 optimal weight: 0.5980 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 23 GLN C 244 HIS A 101 GLN ** A 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 145 GLN ** E 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 HIS D 135 GLN D 202 GLN ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 330 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.201781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.179908 restraints weight = 39279.803| |-----------------------------------------------------------------------------| r_work (start): 0.4313 rms_B_bonded: 2.23 r_work: 0.4246 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.4246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6604 moved from start: 0.0834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22425 Z= 0.118 Angle : 0.581 10.511 30409 Z= 0.300 Chirality : 0.041 0.214 3466 Planarity : 0.004 0.064 3803 Dihedral : 13.277 143.318 3664 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.70 % Favored : 93.08 % Rotamer: Outliers : 9.36 % Allowed : 38.05 % Favored : 52.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.16), residues: 2718 helix: -0.17 (0.16), residues: 1071 sheet: -2.21 (0.27), residues: 367 loop : -2.26 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 130 TYR 0.016 0.001 TYR B 191 PHE 0.022 0.001 PHE A 248 HIS 0.012 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00263 (22425) covalent geometry : angle 0.58100 (30409) hydrogen bonds : bond 0.03177 ( 764) hydrogen bonds : angle 5.31398 ( 2187) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 278 time to evaluate : 0.799 Fit side-chains revert: symmetry clash REVERT: C 107 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7282 (mtpp) REVERT: C 146 LEU cc_start: 0.5545 (OUTLIER) cc_final: 0.5146 (mp) REVERT: C 159 TYR cc_start: 0.4681 (m-80) cc_final: 0.3951 (m-80) REVERT: C 187 ASP cc_start: 0.7593 (t0) cc_final: 0.7104 (t0) REVERT: C 330 ASN cc_start: 0.6137 (m-40) cc_final: 0.5770 (t0) REVERT: B 77 GLU cc_start: 0.7129 (mp0) cc_final: 0.6798 (mp0) REVERT: B 84 MET cc_start: 0.4202 (mtt) cc_final: 0.3766 (mmt) REVERT: B 158 MET cc_start: 0.6855 (OUTLIER) cc_final: 0.6547 (mpt) REVERT: B 169 GLU cc_start: 0.5812 (OUTLIER) cc_final: 0.5387 (pp20) REVERT: B 172 LEU cc_start: 0.6810 (tm) cc_final: 0.6441 (tp) REVERT: B 191 TYR cc_start: 0.6295 (OUTLIER) cc_final: 0.5593 (m-80) REVERT: B 252 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7576 (tt) REVERT: B 327 PHE cc_start: 0.6316 (OUTLIER) cc_final: 0.5818 (m-10) REVERT: A 34 ASN cc_start: 0.7364 (OUTLIER) cc_final: 0.6843 (p0) REVERT: A 112 LEU cc_start: 0.6486 (OUTLIER) cc_final: 0.6285 (mm) REVERT: A 158 MET cc_start: 0.7246 (ttt) cc_final: 0.6989 (mtp) REVERT: A 187 ASP cc_start: 0.6757 (m-30) cc_final: 0.6329 (t0) REVERT: A 231 ASP cc_start: 0.8009 (t0) cc_final: 0.7737 (t0) REVERT: A 247 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.7116 (mtt-85) REVERT: A 253 LEU cc_start: 0.4629 (OUTLIER) cc_final: 0.3874 (pp) REVERT: F 34 ASN cc_start: 0.8214 (t0) cc_final: 0.7752 (t0) REVERT: F 133 LYS cc_start: 0.5887 (OUTLIER) cc_final: 0.3917 (mttp) REVERT: F 158 MET cc_start: 0.7369 (mtt) cc_final: 0.6932 (ttt) REVERT: F 169 GLU cc_start: 0.6874 (OUTLIER) cc_final: 0.6329 (mp0) REVERT: F 178 TYR cc_start: 0.6407 (m-80) cc_final: 0.3653 (m-80) REVERT: F 191 TYR cc_start: 0.3807 (OUTLIER) cc_final: 0.2904 (p90) REVERT: F 193 ARG cc_start: 0.5818 (ttt-90) cc_final: 0.4640 (tpm170) REVERT: F 248 PHE cc_start: 0.5499 (OUTLIER) cc_final: 0.4839 (m-80) REVERT: F 251 MET cc_start: 0.6012 (ttt) cc_final: 0.5805 (ttt) REVERT: F 326 MET cc_start: 0.5656 (OUTLIER) cc_final: 0.5168 (mpp) REVERT: I 216 TYR cc_start: 0.6326 (OUTLIER) cc_final: 0.5025 (t80) REVERT: I 254 ARG cc_start: 0.6209 (OUTLIER) cc_final: 0.4307 (ptm160) REVERT: E 84 MET cc_start: 0.3190 (pmm) cc_final: 0.2635 (ppp) REVERT: E 209 ASP cc_start: 0.6324 (OUTLIER) cc_final: 0.5613 (m-30) REVERT: E 218 LEU cc_start: 0.6256 (OUTLIER) cc_final: 0.5685 (mm) REVERT: E 247 ARG cc_start: 0.7573 (mtm180) cc_final: 0.7275 (mmm160) REVERT: E 251 MET cc_start: 0.6138 (tpp) cc_final: 0.5729 (tmm) REVERT: E 265 ILE cc_start: 0.2925 (OUTLIER) cc_final: 0.2599 (mt) REVERT: E 320 LEU cc_start: 0.6516 (OUTLIER) cc_final: 0.6202 (tt) REVERT: H 92 PHE cc_start: 0.4525 (OUTLIER) cc_final: 0.4157 (m-10) REVERT: D 39 LYS cc_start: 0.7581 (mmtt) cc_final: 0.7186 (tmtt) REVERT: D 84 MET cc_start: 0.4988 (OUTLIER) cc_final: 0.3900 (mmm) REVERT: D 243 MET cc_start: 0.8265 (tpt) cc_final: 0.7892 (mmm) REVERT: D 251 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.8193 (tpp) REVERT: G 43 GLU cc_start: 0.7245 (pt0) cc_final: 0.6488 (tm-30) outliers start: 209 outliers final: 69 residues processed: 437 average time/residue: 0.4842 time to fit residues: 249.6551 Evaluate side-chains 344 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 250 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 216 TYR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 46 TYR Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 144 CYS Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 248 PHE Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 326 MET Chi-restraints excluded: chain F residue 330 ASN Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 170 ARG Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 254 ARG Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 92 PHE Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 196 ASN Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 222 ASP Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 291 ILE Chi-restraints excluded: chain H residue 315 TYR Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 251 MET Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain G residue 23 GLN Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain G residue 205 TYR Chi-restraints excluded: chain G residue 315 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 249 optimal weight: 0.6980 chunk 216 optimal weight: 7.9990 chunk 238 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 204 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 185 optimal weight: 0.7980 chunk 182 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 23 GLN C 242 GLN C 244 HIS F 23 GLN I 145 GLN ** I 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 202 GLN ** E 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN D 202 GLN G 23 GLN ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 272 GLN G 330 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.202136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.181003 restraints weight = 39291.365| |-----------------------------------------------------------------------------| r_work (start): 0.4323 rms_B_bonded: 2.22 r_work: 0.4244 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.4244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22425 Z= 0.118 Angle : 0.583 9.244 30409 Z= 0.299 Chirality : 0.041 0.188 3466 Planarity : 0.004 0.065 3803 Dihedral : 13.144 143.181 3642 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.40 % Favored : 92.38 % Rotamer: Outliers : 9.22 % Allowed : 38.14 % Favored : 52.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.16), residues: 2718 helix: -0.06 (0.16), residues: 1063 sheet: -2.23 (0.27), residues: 371 loop : -2.19 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 130 TYR 0.016 0.001 TYR B 191 PHE 0.024 0.002 PHE F 126 HIS 0.012 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00265 (22425) covalent geometry : angle 0.58279 (30409) hydrogen bonds : bond 0.02994 ( 764) hydrogen bonds : angle 5.16927 ( 2187) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 283 time to evaluate : 0.840 Fit side-chains revert: symmetry clash REVERT: C 96 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.6599 (mtp180) REVERT: C 107 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7270 (mtpp) REVERT: C 146 LEU cc_start: 0.5665 (OUTLIER) cc_final: 0.5274 (mp) REVERT: C 159 TYR cc_start: 0.4727 (m-80) cc_final: 0.4180 (m-80) REVERT: C 187 ASP cc_start: 0.7570 (t0) cc_final: 0.7095 (t0) REVERT: C 330 ASN cc_start: 0.6130 (m-40) cc_final: 0.5726 (t0) REVERT: B 66 ILE cc_start: 0.3660 (OUTLIER) cc_final: 0.2813 (tt) REVERT: B 77 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6802 (mp0) REVERT: B 84 MET cc_start: 0.4260 (mtt) cc_final: 0.3793 (mmt) REVERT: B 169 GLU cc_start: 0.5832 (OUTLIER) cc_final: 0.5328 (pp20) REVERT: B 172 LEU cc_start: 0.6793 (tm) cc_final: 0.6416 (tp) REVERT: B 191 TYR cc_start: 0.6281 (OUTLIER) cc_final: 0.5583 (m-80) REVERT: B 248 PHE cc_start: 0.6019 (OUTLIER) cc_final: 0.5110 (t80) REVERT: B 252 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7574 (tt) REVERT: B 327 PHE cc_start: 0.6296 (OUTLIER) cc_final: 0.5741 (m-10) REVERT: A 34 ASN cc_start: 0.7370 (OUTLIER) cc_final: 0.6837 (p0) REVERT: A 112 LEU cc_start: 0.6421 (OUTLIER) cc_final: 0.6216 (mm) REVERT: A 158 MET cc_start: 0.7229 (ttt) cc_final: 0.6995 (mtp) REVERT: A 187 ASP cc_start: 0.6762 (m-30) cc_final: 0.6327 (t0) REVERT: A 231 ASP cc_start: 0.8000 (t0) cc_final: 0.7717 (t0) REVERT: A 253 LEU cc_start: 0.4634 (OUTLIER) cc_final: 0.3874 (pp) REVERT: A 273 VAL cc_start: 0.7140 (OUTLIER) cc_final: 0.6885 (t) REVERT: F 34 ASN cc_start: 0.8228 (t0) cc_final: 0.7749 (t0) REVERT: F 106 SER cc_start: 0.6026 (OUTLIER) cc_final: 0.5599 (t) REVERT: F 128 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6991 (pt0) REVERT: F 133 LYS cc_start: 0.5617 (OUTLIER) cc_final: 0.4880 (mtpp) REVERT: F 158 MET cc_start: 0.7386 (mtt) cc_final: 0.6928 (ttt) REVERT: F 169 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6301 (mp0) REVERT: F 178 TYR cc_start: 0.6346 (m-80) cc_final: 0.3618 (m-80) REVERT: F 191 TYR cc_start: 0.3784 (OUTLIER) cc_final: 0.2890 (p90) REVERT: F 193 ARG cc_start: 0.5851 (ttt-90) cc_final: 0.4651 (tpm170) REVERT: F 326 MET cc_start: 0.5657 (OUTLIER) cc_final: 0.5140 (mpp) REVERT: I 84 MET cc_start: 0.6594 (ttp) cc_final: 0.6120 (tpt) REVERT: I 197 THR cc_start: 0.4146 (p) cc_final: 0.3628 (t) REVERT: I 198 ASP cc_start: 0.6061 (m-30) cc_final: 0.5592 (m-30) REVERT: I 216 TYR cc_start: 0.6319 (OUTLIER) cc_final: 0.5062 (t80) REVERT: I 254 ARG cc_start: 0.6213 (OUTLIER) cc_final: 0.4158 (ptm160) REVERT: E 84 MET cc_start: 0.3198 (pmm) cc_final: 0.2563 (ppp) REVERT: E 126 PHE cc_start: 0.6372 (p90) cc_final: 0.6169 (p90) REVERT: E 209 ASP cc_start: 0.6362 (OUTLIER) cc_final: 0.5649 (m-30) REVERT: E 218 LEU cc_start: 0.6239 (OUTLIER) cc_final: 0.5650 (mm) REVERT: E 243 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.7995 (mtt) REVERT: E 247 ARG cc_start: 0.7631 (mtm180) cc_final: 0.7300 (mmm160) REVERT: E 251 MET cc_start: 0.6233 (tpp) cc_final: 0.5715 (tmm) REVERT: E 265 ILE cc_start: 0.2908 (OUTLIER) cc_final: 0.2631 (mt) REVERT: E 320 LEU cc_start: 0.6537 (OUTLIER) cc_final: 0.6242 (tt) REVERT: H 66 ILE cc_start: 0.5761 (OUTLIER) cc_final: 0.5501 (mm) REVERT: H 92 PHE cc_start: 0.4586 (OUTLIER) cc_final: 0.4230 (m-10) REVERT: H 104 THR cc_start: 0.4724 (OUTLIER) cc_final: 0.4196 (t) REVERT: D 39 LYS cc_start: 0.7597 (mmtt) cc_final: 0.7178 (tmtt) REVERT: D 84 MET cc_start: 0.4988 (OUTLIER) cc_final: 0.3882 (mmm) REVERT: D 135 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7386 (mp-120) REVERT: D 243 MET cc_start: 0.8269 (tpt) cc_final: 0.7912 (mmm) REVERT: G 43 GLU cc_start: 0.7255 (pt0) cc_final: 0.6519 (tm-30) outliers start: 206 outliers final: 87 residues processed: 437 average time/residue: 0.4842 time to fit residues: 249.5581 Evaluate side-chains 365 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 246 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 248 PHE Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 216 TYR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 46 TYR Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 144 CYS Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 176 GLU Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 311 ILE Chi-restraints excluded: chain F residue 326 MET Chi-restraints excluded: chain F residue 330 ASN Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 170 ARG Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 202 GLN Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 220 ILE Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 254 ARG Chi-restraints excluded: chain I residue 302 LEU Chi-restraints excluded: chain I residue 309 THR Chi-restraints excluded: chain I residue 332 ASP Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 66 ILE Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 92 PHE Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 196 ASN Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 222 ASP Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 315 TYR Chi-restraints excluded: chain H residue 319 CYS Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain G residue 23 GLN Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain G residue 205 TYR Chi-restraints excluded: chain G residue 315 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 121 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 223 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 233 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 151 optimal weight: 3.9990 chunk 175 optimal weight: 0.6980 chunk 155 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 23 GLN C 244 HIS F 62 ASN I 145 GLN E 101 GLN ** E 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN D 202 GLN ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 330 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.199815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.178388 restraints weight = 38918.534| |-----------------------------------------------------------------------------| r_work (start): 0.4298 rms_B_bonded: 2.23 r_work: 0.4218 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.4218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22425 Z= 0.150 Angle : 0.627 12.800 30409 Z= 0.321 Chirality : 0.043 0.211 3466 Planarity : 0.004 0.062 3803 Dihedral : 13.292 144.394 3638 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.20 % Favored : 91.57 % Rotamer: Outliers : 10.34 % Allowed : 37.82 % Favored : 51.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.16), residues: 2718 helix: -0.14 (0.16), residues: 1066 sheet: -2.27 (0.27), residues: 372 loop : -2.24 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 229 TYR 0.018 0.001 TYR B 191 PHE 0.028 0.002 PHE F 126 HIS 0.013 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00342 (22425) covalent geometry : angle 0.62679 (30409) hydrogen bonds : bond 0.03211 ( 764) hydrogen bonds : angle 5.24883 ( 2187) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 231 poor density : 275 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 96 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.6635 (mtp180) REVERT: C 107 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7280 (mtpp) REVERT: C 146 LEU cc_start: 0.5661 (OUTLIER) cc_final: 0.5203 (mp) REVERT: C 187 ASP cc_start: 0.7610 (t0) cc_final: 0.7133 (t0) REVERT: B 66 ILE cc_start: 0.3370 (OUTLIER) cc_final: 0.2523 (tt) REVERT: B 77 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6795 (mp0) REVERT: B 84 MET cc_start: 0.4384 (mtt) cc_final: 0.3834 (mmt) REVERT: B 158 MET cc_start: 0.6855 (OUTLIER) cc_final: 0.6566 (mpt) REVERT: B 161 ASP cc_start: 0.5999 (t0) cc_final: 0.5485 (t70) REVERT: B 169 GLU cc_start: 0.5922 (OUTLIER) cc_final: 0.5400 (pp20) REVERT: B 172 LEU cc_start: 0.6822 (tm) cc_final: 0.6460 (tp) REVERT: B 191 TYR cc_start: 0.6356 (OUTLIER) cc_final: 0.5540 (m-80) REVERT: B 204 LEU cc_start: 0.8165 (mm) cc_final: 0.7703 (mm) REVERT: B 248 PHE cc_start: 0.6058 (OUTLIER) cc_final: 0.5051 (t80) REVERT: B 252 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7550 (tt) REVERT: B 327 PHE cc_start: 0.6409 (OUTLIER) cc_final: 0.5803 (m-10) REVERT: A 34 ASN cc_start: 0.7426 (OUTLIER) cc_final: 0.6875 (p0) REVERT: A 158 MET cc_start: 0.7280 (ttt) cc_final: 0.7015 (mtp) REVERT: A 187 ASP cc_start: 0.6803 (m-30) cc_final: 0.6370 (t0) REVERT: A 231 ASP cc_start: 0.8019 (t0) cc_final: 0.7733 (t0) REVERT: A 247 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.7161 (mtt-85) REVERT: A 253 LEU cc_start: 0.4630 (OUTLIER) cc_final: 0.3861 (pp) REVERT: A 273 VAL cc_start: 0.7121 (OUTLIER) cc_final: 0.6861 (t) REVERT: F 34 ASN cc_start: 0.8247 (t0) cc_final: 0.7785 (t0) REVERT: F 128 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.7116 (pt0) REVERT: F 133 LYS cc_start: 0.5903 (OUTLIER) cc_final: 0.3995 (mttp) REVERT: F 146 LEU cc_start: 0.6127 (OUTLIER) cc_final: 0.5889 (tt) REVERT: F 158 MET cc_start: 0.7417 (mtt) cc_final: 0.7025 (ttt) REVERT: F 169 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.6400 (mp0) REVERT: F 178 TYR cc_start: 0.6477 (m-80) cc_final: 0.3635 (m-80) REVERT: F 191 TYR cc_start: 0.3852 (OUTLIER) cc_final: 0.2947 (p90) REVERT: F 193 ARG cc_start: 0.5866 (ttt-90) cc_final: 0.4552 (tpm170) REVERT: F 326 MET cc_start: 0.5678 (OUTLIER) cc_final: 0.5095 (mpp) REVERT: I 84 MET cc_start: 0.6585 (ttp) cc_final: 0.6086 (tpt) REVERT: I 178 TYR cc_start: 0.4014 (OUTLIER) cc_final: 0.1669 (m-80) REVERT: I 197 THR cc_start: 0.3956 (OUTLIER) cc_final: 0.3393 (t) REVERT: I 198 ASP cc_start: 0.6232 (m-30) cc_final: 0.6007 (m-30) REVERT: I 216 TYR cc_start: 0.6343 (OUTLIER) cc_final: 0.5100 (t80) REVERT: I 254 ARG cc_start: 0.6294 (OUTLIER) cc_final: 0.4324 (ptm160) REVERT: E 84 MET cc_start: 0.3302 (pmm) cc_final: 0.2703 (ppp) REVERT: E 156 LYS cc_start: 0.3783 (OUTLIER) cc_final: 0.3371 (ttpt) REVERT: E 158 MET cc_start: 0.6254 (OUTLIER) cc_final: 0.5936 (mtt) REVERT: E 243 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8013 (mtt) REVERT: E 247 ARG cc_start: 0.7573 (mtm180) cc_final: 0.7281 (mmm160) REVERT: E 251 MET cc_start: 0.6180 (tpp) cc_final: 0.5794 (tmm) REVERT: E 265 ILE cc_start: 0.3030 (OUTLIER) cc_final: 0.2625 (mt) REVERT: E 320 LEU cc_start: 0.6547 (OUTLIER) cc_final: 0.6145 (tt) REVERT: H 92 PHE cc_start: 0.4660 (OUTLIER) cc_final: 0.4266 (m-10) REVERT: H 104 THR cc_start: 0.4777 (OUTLIER) cc_final: 0.4220 (t) REVERT: H 249 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.8036 (mp) REVERT: D 39 LYS cc_start: 0.7616 (mmtt) cc_final: 0.7195 (tmtt) REVERT: D 84 MET cc_start: 0.5031 (OUTLIER) cc_final: 0.3921 (mmm) REVERT: D 243 MET cc_start: 0.8270 (tpt) cc_final: 0.7871 (mmm) REVERT: D 251 MET cc_start: 0.8594 (tpt) cc_final: 0.8353 (tpt) REVERT: D 255 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7961 (mp) REVERT: D 287 ILE cc_start: 0.7973 (OUTLIER) cc_final: 0.7529 (tp) REVERT: G 43 GLU cc_start: 0.7230 (pt0) cc_final: 0.6503 (tm-30) REVERT: G 58 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.7151 (ptmt) REVERT: G 299 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7366 (mtm180) REVERT: G 310 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.5421 (mpp-170) outliers start: 231 outliers final: 102 residues processed: 451 average time/residue: 0.5095 time to fit residues: 269.8468 Evaluate side-chains 389 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 248 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 248 PHE Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 216 TYR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 46 TYR Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 144 CYS Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 311 ILE Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 326 MET Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 170 ARG Chi-restraints excluded: chain I residue 178 TYR Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 254 ARG Chi-restraints excluded: chain I residue 302 LEU Chi-restraints excluded: chain I residue 309 THR Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 92 PHE Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 196 ASN Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 222 ASP Chi-restraints excluded: chain H residue 249 LEU Chi-restraints excluded: chain H residue 266 THR Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 315 TYR Chi-restraints excluded: chain H residue 319 CYS Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 205 TYR Chi-restraints excluded: chain G residue 299 ARG Chi-restraints excluded: chain G residue 310 ARG Chi-restraints excluded: chain G residue 315 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 175 optimal weight: 0.8980 chunk 227 optimal weight: 0.6980 chunk 178 optimal weight: 9.9990 chunk 68 optimal weight: 20.0000 chunk 12 optimal weight: 0.5980 chunk 46 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 50 optimal weight: 0.0970 chunk 179 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 244 HIS I 145 GLN ** I 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN D 202 GLN ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 196 ASN G 330 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.202124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.180617 restraints weight = 39541.070| |-----------------------------------------------------------------------------| r_work (start): 0.4321 rms_B_bonded: 2.31 r_work: 0.4241 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.4241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22425 Z= 0.121 Angle : 0.602 11.409 30409 Z= 0.307 Chirality : 0.042 0.219 3466 Planarity : 0.004 0.062 3803 Dihedral : 13.118 143.472 3638 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.99 % Favored : 92.79 % Rotamer: Outliers : 9.62 % Allowed : 38.54 % Favored : 51.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.16), residues: 2718 helix: -0.08 (0.16), residues: 1069 sheet: -2.19 (0.27), residues: 372 loop : -2.23 (0.17), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 170 TYR 0.017 0.001 TYR G 46 PHE 0.025 0.001 PHE F 126 HIS 0.011 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00273 (22425) covalent geometry : angle 0.60187 (30409) hydrogen bonds : bond 0.02896 ( 764) hydrogen bonds : angle 5.06628 ( 2187) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 215 poor density : 274 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 107 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7289 (mtpp) REVERT: C 146 LEU cc_start: 0.5713 (OUTLIER) cc_final: 0.5316 (mp) REVERT: C 159 TYR cc_start: 0.4838 (m-80) cc_final: 0.4255 (m-80) REVERT: C 187 ASP cc_start: 0.7576 (t0) cc_final: 0.7091 (t0) REVERT: C 330 ASN cc_start: 0.6139 (m-40) cc_final: 0.5742 (t0) REVERT: B 66 ILE cc_start: 0.3447 (OUTLIER) cc_final: 0.2588 (tt) REVERT: B 77 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6778 (mp0) REVERT: B 84 MET cc_start: 0.4402 (mtt) cc_final: 0.3874 (mmt) REVERT: B 158 MET cc_start: 0.6970 (OUTLIER) cc_final: 0.6739 (mpt) REVERT: B 169 GLU cc_start: 0.5902 (OUTLIER) cc_final: 0.5391 (pp20) REVERT: B 172 LEU cc_start: 0.6839 (tm) cc_final: 0.6504 (tp) REVERT: B 191 TYR cc_start: 0.6236 (OUTLIER) cc_final: 0.5375 (m-80) REVERT: B 252 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7579 (tt) REVERT: B 327 PHE cc_start: 0.6290 (OUTLIER) cc_final: 0.5653 (m-10) REVERT: A 34 ASN cc_start: 0.7431 (OUTLIER) cc_final: 0.6862 (p0) REVERT: A 158 MET cc_start: 0.7237 (ttt) cc_final: 0.6980 (mtp) REVERT: A 187 ASP cc_start: 0.6740 (m-30) cc_final: 0.6325 (t0) REVERT: A 231 ASP cc_start: 0.8004 (t0) cc_final: 0.7722 (t0) REVERT: A 247 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.7235 (mtt-85) REVERT: A 253 LEU cc_start: 0.4603 (OUTLIER) cc_final: 0.3819 (pp) REVERT: A 273 VAL cc_start: 0.7128 (OUTLIER) cc_final: 0.6875 (t) REVERT: F 34 ASN cc_start: 0.8266 (t0) cc_final: 0.7789 (t0) REVERT: F 106 SER cc_start: 0.6106 (OUTLIER) cc_final: 0.5679 (t) REVERT: F 133 LYS cc_start: 0.5846 (OUTLIER) cc_final: 0.4180 (mttp) REVERT: F 158 MET cc_start: 0.7365 (mtt) cc_final: 0.6968 (ttt) REVERT: F 169 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.6348 (mp0) REVERT: F 178 TYR cc_start: 0.6427 (m-80) cc_final: 0.3564 (m-80) REVERT: F 191 TYR cc_start: 0.3863 (OUTLIER) cc_final: 0.2903 (p90) REVERT: F 193 ARG cc_start: 0.5799 (ttt-90) cc_final: 0.4563 (tpm170) REVERT: F 326 MET cc_start: 0.5691 (OUTLIER) cc_final: 0.5189 (mpp) REVERT: I 84 MET cc_start: 0.6565 (ttp) cc_final: 0.6125 (tpt) REVERT: I 136 ILE cc_start: 0.7088 (OUTLIER) cc_final: 0.6711 (pp) REVERT: I 178 TYR cc_start: 0.3998 (OUTLIER) cc_final: 0.1644 (m-80) REVERT: I 197 THR cc_start: 0.4005 (OUTLIER) cc_final: 0.3473 (t) REVERT: I 198 ASP cc_start: 0.6214 (m-30) cc_final: 0.5818 (m-30) REVERT: I 216 TYR cc_start: 0.6321 (OUTLIER) cc_final: 0.4968 (t80) REVERT: I 254 ARG cc_start: 0.6181 (OUTLIER) cc_final: 0.4203 (ptm160) REVERT: E 126 PHE cc_start: 0.6391 (p90) cc_final: 0.6189 (p90) REVERT: E 243 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.7955 (mtt) REVERT: E 247 ARG cc_start: 0.7624 (mtm180) cc_final: 0.7279 (mmm160) REVERT: E 251 MET cc_start: 0.6168 (tpp) cc_final: 0.5764 (tmm) REVERT: E 265 ILE cc_start: 0.2867 (OUTLIER) cc_final: 0.2567 (mt) REVERT: E 320 LEU cc_start: 0.6595 (OUTLIER) cc_final: 0.6301 (tt) REVERT: H 92 PHE cc_start: 0.4631 (OUTLIER) cc_final: 0.4290 (m-10) REVERT: H 104 THR cc_start: 0.4754 (OUTLIER) cc_final: 0.4260 (t) REVERT: D 39 LYS cc_start: 0.7611 (mmtt) cc_final: 0.7190 (tmtt) REVERT: D 243 MET cc_start: 0.8296 (tpt) cc_final: 0.7945 (mmm) REVERT: D 287 ILE cc_start: 0.7917 (OUTLIER) cc_final: 0.7509 (tp) REVERT: G 43 GLU cc_start: 0.7270 (pt0) cc_final: 0.6520 (tm-30) REVERT: G 58 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7158 (ptmt) REVERT: G 299 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.7406 (mtm180) outliers start: 215 outliers final: 95 residues processed: 438 average time/residue: 0.4632 time to fit residues: 239.7595 Evaluate side-chains 381 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 255 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 248 PHE Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 216 TYR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 46 TYR Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 144 CYS Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 176 GLU Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 311 ILE Chi-restraints excluded: chain F residue 322 GLU Chi-restraints excluded: chain F residue 326 MET Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 170 ARG Chi-restraints excluded: chain I residue 178 TYR Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 220 ILE Chi-restraints excluded: chain I residue 254 ARG Chi-restraints excluded: chain I residue 302 LEU Chi-restraints excluded: chain I residue 309 THR Chi-restraints excluded: chain I residue 329 ILE Chi-restraints excluded: chain I residue 332 ASP Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 92 PHE Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 196 ASN Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 222 ASP Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 315 TYR Chi-restraints excluded: chain H residue 319 CYS Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 205 TYR Chi-restraints excluded: chain G residue 257 ASP Chi-restraints excluded: chain G residue 299 ARG Chi-restraints excluded: chain G residue 315 TYR Chi-restraints excluded: chain G residue 334 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 11 optimal weight: 5.9990 chunk 65 optimal weight: 0.0000 chunk 155 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 139 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 241 optimal weight: 6.9990 chunk 259 optimal weight: 5.9990 chunk 236 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 overall best weight: 1.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 23 GLN C 244 HIS I 145 GLN ** I 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN D 202 GLN ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 330 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.199702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.177960 restraints weight = 39293.152| |-----------------------------------------------------------------------------| r_work (start): 0.4291 rms_B_bonded: 2.30 r_work: 0.4211 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22425 Z= 0.156 Angle : 0.651 11.073 30409 Z= 0.332 Chirality : 0.043 0.216 3466 Planarity : 0.004 0.062 3803 Dihedral : 13.335 143.935 3637 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.39 % Favored : 91.39 % Rotamer: Outliers : 9.22 % Allowed : 38.63 % Favored : 52.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.16), residues: 2718 helix: -0.19 (0.16), residues: 1073 sheet: -2.19 (0.28), residues: 356 loop : -2.30 (0.17), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 229 TYR 0.019 0.002 TYR B 191 PHE 0.031 0.002 PHE A 248 HIS 0.014 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00357 (22425) covalent geometry : angle 0.65053 (30409) hydrogen bonds : bond 0.03217 ( 764) hydrogen bonds : angle 5.21520 ( 2187) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 269 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 96 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.6627 (mtp180) REVERT: C 107 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7393 (mtpp) REVERT: C 146 LEU cc_start: 0.5596 (OUTLIER) cc_final: 0.5132 (mp) REVERT: C 159 TYR cc_start: 0.4993 (m-80) cc_final: 0.4136 (m-80) REVERT: C 187 ASP cc_start: 0.7607 (t0) cc_final: 0.7143 (t0) REVERT: B 66 ILE cc_start: 0.3400 (OUTLIER) cc_final: 0.2547 (tt) REVERT: B 77 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6840 (mp0) REVERT: B 84 MET cc_start: 0.4516 (mtt) cc_final: 0.3916 (mmt) REVERT: B 158 MET cc_start: 0.7072 (OUTLIER) cc_final: 0.6814 (mpt) REVERT: B 161 ASP cc_start: 0.6055 (t0) cc_final: 0.5504 (t70) REVERT: B 169 GLU cc_start: 0.5890 (OUTLIER) cc_final: 0.5349 (pp20) REVERT: B 172 LEU cc_start: 0.6888 (tm) cc_final: 0.6539 (tp) REVERT: B 191 TYR cc_start: 0.6312 (OUTLIER) cc_final: 0.5503 (m-80) REVERT: B 223 SER cc_start: 0.6764 (OUTLIER) cc_final: 0.6203 (m) REVERT: B 327 PHE cc_start: 0.6380 (OUTLIER) cc_final: 0.5752 (m-10) REVERT: A 34 ASN cc_start: 0.7495 (OUTLIER) cc_final: 0.6922 (p0) REVERT: A 158 MET cc_start: 0.7315 (ttt) cc_final: 0.7051 (mtp) REVERT: A 187 ASP cc_start: 0.6795 (m-30) cc_final: 0.6352 (t0) REVERT: A 209 ASP cc_start: 0.6650 (OUTLIER) cc_final: 0.6429 (m-30) REVERT: A 231 ASP cc_start: 0.8043 (t0) cc_final: 0.7832 (t0) REVERT: A 247 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.7178 (mtt-85) REVERT: A 253 LEU cc_start: 0.4634 (OUTLIER) cc_final: 0.3862 (pp) REVERT: A 273 VAL cc_start: 0.7086 (OUTLIER) cc_final: 0.6840 (t) REVERT: F 34 ASN cc_start: 0.8249 (t0) cc_final: 0.7800 (t0) REVERT: F 128 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7217 (pt0) REVERT: F 133 LYS cc_start: 0.5918 (OUTLIER) cc_final: 0.4883 (mtpp) REVERT: F 158 MET cc_start: 0.7328 (mtt) cc_final: 0.6983 (ttt) REVERT: F 169 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.6251 (mp0) REVERT: F 178 TYR cc_start: 0.6516 (m-80) cc_final: 0.3575 (m-80) REVERT: F 191 TYR cc_start: 0.3709 (OUTLIER) cc_final: 0.2823 (p90) REVERT: F 193 ARG cc_start: 0.6009 (ttt-90) cc_final: 0.4556 (tpm170) REVERT: F 330 ASN cc_start: 0.5454 (OUTLIER) cc_final: 0.5240 (m-40) REVERT: I 84 MET cc_start: 0.6597 (ttp) cc_final: 0.6112 (tpt) REVERT: I 136 ILE cc_start: 0.7178 (OUTLIER) cc_final: 0.6727 (pp) REVERT: I 178 TYR cc_start: 0.4103 (OUTLIER) cc_final: 0.1622 (m-80) REVERT: I 197 THR cc_start: 0.3894 (OUTLIER) cc_final: 0.3358 (t) REVERT: I 216 TYR cc_start: 0.6315 (OUTLIER) cc_final: 0.5029 (t80) REVERT: I 254 ARG cc_start: 0.6283 (OUTLIER) cc_final: 0.4343 (ptm160) REVERT: E 209 ASP cc_start: 0.6361 (OUTLIER) cc_final: 0.5373 (m-30) REVERT: E 243 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8092 (mtt) REVERT: E 247 ARG cc_start: 0.7582 (mtm180) cc_final: 0.7290 (mmm160) REVERT: E 250 ARG cc_start: 0.7172 (OUTLIER) cc_final: 0.6903 (mmm-85) REVERT: E 251 MET cc_start: 0.6243 (tpp) cc_final: 0.5818 (tmm) REVERT: E 265 ILE cc_start: 0.2900 (OUTLIER) cc_final: 0.2469 (mt) REVERT: E 297 THR cc_start: 0.4424 (p) cc_final: 0.4207 (p) REVERT: E 320 LEU cc_start: 0.6592 (OUTLIER) cc_final: 0.6199 (tt) REVERT: H 92 PHE cc_start: 0.4631 (OUTLIER) cc_final: 0.4200 (m-10) REVERT: H 96 ARG cc_start: 0.5474 (OUTLIER) cc_final: 0.4755 (tmt170) REVERT: H 104 THR cc_start: 0.4795 (OUTLIER) cc_final: 0.4241 (t) REVERT: D 39 LYS cc_start: 0.7586 (mmtt) cc_final: 0.7167 (tmtt) REVERT: D 84 MET cc_start: 0.5160 (OUTLIER) cc_final: 0.4072 (mmm) REVERT: D 135 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7519 (mp-120) REVERT: D 243 MET cc_start: 0.8298 (tpt) cc_final: 0.7893 (mmm) REVERT: D 251 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.8239 (tpt) REVERT: D 255 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7932 (mp) REVERT: D 287 ILE cc_start: 0.7972 (OUTLIER) cc_final: 0.7528 (tp) REVERT: G 43 GLU cc_start: 0.7271 (pt0) cc_final: 0.6515 (tm-30) REVERT: G 58 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7146 (ptmt) REVERT: G 299 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7290 (mtm180) REVERT: G 310 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.5356 (mpp-170) outliers start: 206 outliers final: 106 residues processed: 427 average time/residue: 0.4497 time to fit residues: 226.5908 Evaluate side-chains 400 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 253 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 248 PHE Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 216 TYR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 46 TYR Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 144 CYS Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 311 ILE Chi-restraints excluded: chain F residue 330 ASN Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 170 ARG Chi-restraints excluded: chain I residue 178 TYR Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 254 ARG Chi-restraints excluded: chain I residue 302 LEU Chi-restraints excluded: chain I residue 309 THR Chi-restraints excluded: chain I residue 332 ASP Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 250 ARG Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 92 PHE Chi-restraints excluded: chain H residue 96 ARG Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 196 ASN Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 222 ASP Chi-restraints excluded: chain H residue 266 THR Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 291 ILE Chi-restraints excluded: chain H residue 315 TYR Chi-restraints excluded: chain H residue 319 CYS Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 251 MET Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain G residue 23 GLN Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 299 ARG Chi-restraints excluded: chain G residue 310 ARG Chi-restraints excluded: chain G residue 315 TYR Chi-restraints excluded: chain G residue 334 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 94 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 256 optimal weight: 0.7980 chunk 82 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 7 optimal weight: 0.5980 chunk 222 optimal weight: 3.9990 chunk 62 optimal weight: 0.0980 chunk 220 optimal weight: 0.3980 chunk 27 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 23 GLN ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 244 HIS A 114 GLN F 244 HIS I 145 GLN ** I 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN D 202 GLN ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 330 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.203239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.182471 restraints weight = 38949.820| |-----------------------------------------------------------------------------| r_work (start): 0.4340 rms_B_bonded: 2.23 r_work: 0.4264 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.4264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6564 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22425 Z= 0.114 Angle : 0.616 10.642 30409 Z= 0.313 Chirality : 0.042 0.244 3466 Planarity : 0.004 0.061 3803 Dihedral : 13.026 143.265 3635 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.88 % Favored : 92.90 % Rotamer: Outliers : 7.48 % Allowed : 40.20 % Favored : 52.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.16), residues: 2718 helix: -0.16 (0.16), residues: 1088 sheet: -1.97 (0.27), residues: 370 loop : -2.28 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 150 TYR 0.017 0.001 TYR G 46 PHE 0.026 0.001 PHE A 248 HIS 0.014 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00256 (22425) covalent geometry : angle 0.61627 (30409) hydrogen bonds : bond 0.02809 ( 764) hydrogen bonds : angle 5.00441 ( 2187) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 282 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 96 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.6630 (mtp180) REVERT: C 107 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7309 (mtpp) REVERT: C 146 LEU cc_start: 0.5837 (OUTLIER) cc_final: 0.5455 (mp) REVERT: C 159 TYR cc_start: 0.4556 (m-80) cc_final: 0.3990 (m-80) REVERT: C 187 ASP cc_start: 0.7528 (t0) cc_final: 0.7065 (t0) REVERT: C 330 ASN cc_start: 0.6092 (m-40) cc_final: 0.5715 (t0) REVERT: B 66 ILE cc_start: 0.3350 (OUTLIER) cc_final: 0.2510 (tt) REVERT: B 77 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6810 (mp0) REVERT: B 84 MET cc_start: 0.4514 (mtt) cc_final: 0.3937 (mmt) REVERT: B 158 MET cc_start: 0.6970 (OUTLIER) cc_final: 0.6765 (mpt) REVERT: B 169 GLU cc_start: 0.5791 (OUTLIER) cc_final: 0.5321 (pp20) REVERT: B 172 LEU cc_start: 0.6937 (tm) cc_final: 0.6620 (tp) REVERT: B 191 TYR cc_start: 0.6267 (OUTLIER) cc_final: 0.5567 (m-80) REVERT: B 223 SER cc_start: 0.6547 (OUTLIER) cc_final: 0.5996 (m) REVERT: B 327 PHE cc_start: 0.6238 (OUTLIER) cc_final: 0.5555 (m-10) REVERT: A 34 ASN cc_start: 0.7480 (OUTLIER) cc_final: 0.6870 (p0) REVERT: A 112 LEU cc_start: 0.6201 (OUTLIER) cc_final: 0.5963 (mm) REVERT: A 158 MET cc_start: 0.7282 (ttt) cc_final: 0.7023 (mtp) REVERT: A 187 ASP cc_start: 0.6630 (m-30) cc_final: 0.6269 (t0) REVERT: A 231 ASP cc_start: 0.7991 (t0) cc_final: 0.7714 (t0) REVERT: A 247 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.7162 (mtt-85) REVERT: A 253 LEU cc_start: 0.4610 (OUTLIER) cc_final: 0.3849 (pp) REVERT: F 34 ASN cc_start: 0.8264 (t0) cc_final: 0.7809 (t0) REVERT: F 106 SER cc_start: 0.6104 (OUTLIER) cc_final: 0.5661 (t) REVERT: F 133 LYS cc_start: 0.5750 (OUTLIER) cc_final: 0.4806 (mtpp) REVERT: F 150 ARG cc_start: 0.4255 (mtm110) cc_final: 0.1393 (ttt-90) REVERT: F 158 MET cc_start: 0.7276 (mtt) cc_final: 0.6939 (ttt) REVERT: F 191 TYR cc_start: 0.3768 (OUTLIER) cc_final: 0.2857 (p90) REVERT: F 193 ARG cc_start: 0.5823 (ttt-90) cc_final: 0.4562 (tpm170) REVERT: F 326 MET cc_start: 0.5637 (mpp) cc_final: 0.4982 (mpp) REVERT: I 84 MET cc_start: 0.6450 (ttp) cc_final: 0.6098 (tpt) REVERT: I 136 ILE cc_start: 0.7090 (OUTLIER) cc_final: 0.6738 (pp) REVERT: I 178 TYR cc_start: 0.3996 (OUTLIER) cc_final: 0.1649 (m-80) REVERT: I 198 ASP cc_start: 0.6117 (m-30) cc_final: 0.5888 (m-30) REVERT: I 216 TYR cc_start: 0.6298 (OUTLIER) cc_final: 0.4967 (t80) REVERT: I 254 ARG cc_start: 0.6193 (OUTLIER) cc_final: 0.4183 (ptm160) REVERT: E 42 GLU cc_start: 0.6627 (mm-30) cc_final: 0.5929 (mt-10) REVERT: E 126 PHE cc_start: 0.6420 (p90) cc_final: 0.6171 (p90) REVERT: E 159 TYR cc_start: 0.5714 (t80) cc_final: 0.4978 (t80) REVERT: E 209 ASP cc_start: 0.6212 (OUTLIER) cc_final: 0.5292 (m-30) REVERT: E 210 MET cc_start: 0.6870 (ptp) cc_final: 0.6609 (mpp) REVERT: E 243 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.7953 (mtt) REVERT: E 247 ARG cc_start: 0.7613 (mtm180) cc_final: 0.7294 (mmm160) REVERT: E 251 MET cc_start: 0.6284 (tpp) cc_final: 0.5817 (tmm) REVERT: E 265 ILE cc_start: 0.2710 (OUTLIER) cc_final: 0.2444 (mt) REVERT: E 320 LEU cc_start: 0.6505 (OUTLIER) cc_final: 0.6261 (tt) REVERT: H 96 ARG cc_start: 0.5367 (OUTLIER) cc_final: 0.4681 (tmt170) REVERT: H 111 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.6694 (mtmt) REVERT: D 39 LYS cc_start: 0.7560 (mmtt) cc_final: 0.7149 (tmtt) REVERT: D 84 MET cc_start: 0.5095 (OUTLIER) cc_final: 0.3908 (mmm) REVERT: D 243 MET cc_start: 0.8251 (tpt) cc_final: 0.7939 (mmm) REVERT: D 287 ILE cc_start: 0.7902 (OUTLIER) cc_final: 0.7502 (tp) REVERT: G 43 GLU cc_start: 0.7266 (pt0) cc_final: 0.6543 (tm-30) REVERT: G 58 LYS cc_start: 0.7713 (OUTLIER) cc_final: 0.7218 (ptmt) outliers start: 167 outliers final: 76 residues processed: 410 average time/residue: 0.5209 time to fit residues: 249.4711 Evaluate side-chains 367 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 261 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 216 TYR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 144 CYS Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 170 ARG Chi-restraints excluded: chain I residue 178 TYR Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 254 ARG Chi-restraints excluded: chain I residue 302 LEU Chi-restraints excluded: chain I residue 309 THR Chi-restraints excluded: chain I residue 311 ILE Chi-restraints excluded: chain I residue 329 ILE Chi-restraints excluded: chain I residue 332 ASP Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 92 PHE Chi-restraints excluded: chain H residue 96 ARG Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 111 LYS Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 196 ASN Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 222 ASP Chi-restraints excluded: chain H residue 315 TYR Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain G residue 205 TYR Chi-restraints excluded: chain G residue 315 TYR Chi-restraints excluded: chain G residue 334 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.1814 > 50: distance: 45 - 51: 26.429 distance: 51 - 52: 11.802 distance: 52 - 53: 29.555 distance: 52 - 55: 7.670 distance: 53 - 54: 28.900 distance: 53 - 60: 27.906 distance: 55 - 56: 11.238 distance: 56 - 57: 16.575 distance: 57 - 58: 40.425 distance: 58 - 59: 57.082 distance: 60 - 61: 41.219 distance: 61 - 62: 24.969 distance: 61 - 64: 58.155 distance: 62 - 68: 3.444 distance: 65 - 66: 40.397 distance: 65 - 67: 39.456 distance: 68 - 69: 52.981 distance: 69 - 72: 56.098 distance: 70 - 76: 30.605 distance: 73 - 75: 40.633 distance: 76 - 77: 21.196 distance: 77 - 78: 16.921 distance: 77 - 80: 33.052 distance: 78 - 79: 36.269 distance: 78 - 85: 13.843 distance: 80 - 81: 7.681 distance: 81 - 82: 29.555 distance: 82 - 83: 13.106 distance: 82 - 84: 11.597 distance: 85 - 86: 39.210 distance: 86 - 87: 39.899 distance: 87 - 88: 39.585 distance: 89 - 90: 40.252 distance: 90 - 91: 40.300 distance: 91 - 92: 33.181 distance: 94 - 95: 3.817 distance: 94 - 97: 8.066 distance: 95 - 101: 13.263 distance: 97 - 98: 50.601 distance: 97 - 99: 64.554 distance: 98 - 100: 55.208 distance: 101 - 102: 26.800 distance: 102 - 105: 13.352 distance: 103 - 104: 27.674 distance: 103 - 110: 26.627 distance: 106 - 107: 40.619 distance: 107 - 109: 23.340 distance: 110 - 111: 34.976 distance: 111 - 112: 38.504 distance: 111 - 114: 39.486 distance: 112 - 113: 39.362 distance: 114 - 116: 47.667 distance: 117 - 118: 49.151 distance: 118 - 119: 7.240 distance: 119 - 121: 34.532