Starting phenix.real_space_refine on Thu Feb 5 17:20:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l26_62770/02_2026/9l26_62770.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l26_62770/02_2026/9l26_62770.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9l26_62770/02_2026/9l26_62770.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l26_62770/02_2026/9l26_62770.map" model { file = "/net/cci-nas-00/data/ceres_data/9l26_62770/02_2026/9l26_62770.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l26_62770/02_2026/9l26_62770.cif" } resolution = 3.17 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= 0.000 sd= 0.008 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 21 5.49 5 Mg 7 5.21 5 S 94 5.16 5 C 11902 2.51 5 N 3199 2.21 5 O 3626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s 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: 18849 Number of models: 1 Model: "" Number of chains: 17 Chain: "I" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 90 Classifications: {'peptide': 18} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'TRANS': 17} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2305 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 13, 'TRANS': 278} Chain breaks: 1 Chain: "B" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2305 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 13, 'TRANS': 278} Chain breaks: 1 Chain: "C" Number of atoms: 2317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2317 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 13, 'TRANS': 279} Chain breaks: 1 Chain: "D" Number of atoms: 2316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2316 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 13, 'TRANS': 279} Chain breaks: 1 Chain: "E" Number of atoms: 2327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2327 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 13, 'TRANS': 281} Chain breaks: 1 Chain: "F" Number of atoms: 2327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2327 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 13, 'TRANS': 281} Chain breaks: 1 Chain: "G" Number of atoms: 2330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2330 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 13, 'TRANS': 281} Chain breaks: 1 Chain: "H" Number of atoms: 2308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2308 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 13, 'TRANS': 278} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 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, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.35, per 1000 atoms: 0.23 Number of scatterers: 18849 At special positions: 0 Unit cell: (134.07, 136.94, 133.66, 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 94 16.00 P 21 15.00 Mg 7 11.99 O 3626 8.00 N 3199 7.00 C 11902 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: 1.73 Conformation dependent library (CDL) restraints added in 832.4 milliseconds 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4496 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 8 sheets defined 64.9% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 43 through 61 Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 70 through 78 Processing helix chain 'A' and resid 96 through 107 Processing helix chain 'A' and resid 107 through 113 Processing helix chain 'A' and resid 113 through 118 Processing helix chain 'A' and resid 120 through 124 removed outlier: 3.751A pdb=" N GLN A 124 " --> pdb=" O PRO A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 149 Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 168 through 184 Processing helix chain 'A' and resid 193 through 198 removed outlier: 3.526A pdb=" N PHE A 197 " --> pdb=" O GLN A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 221 Processing helix chain 'A' and resid 242 through 248 Processing helix chain 'A' and resid 259 through 270 Processing helix chain 'A' and resid 282 through 290 removed outlier: 4.113A pdb=" N ILE A 286 " --> pdb=" O ASP A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 319 removed outlier: 4.150A pdb=" N ALA A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLU A 312 " --> pdb=" O ASP A 308 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLN A 319 " --> pdb=" O LYS A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 348 removed outlier: 4.335A pdb=" N PHE A 344 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS A 347 " --> pdb=" O ASP A 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 61 Processing helix chain 'B' and resid 62 through 67 removed outlier: 3.724A pdb=" N GLU B 66 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 67 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 77 Processing helix chain 'B' and resid 82 through 86 Processing helix chain 'B' and resid 96 through 113 removed outlier: 5.254A pdb=" N TYR B 109 " --> pdb=" O GLU B 105 " (cutoff:3.500A) Proline residue: B 110 - end of helix Processing helix chain 'B' and resid 113 through 118 Processing helix chain 'B' and resid 138 through 150 Processing helix chain 'B' and resid 158 through 163 removed outlier: 3.621A pdb=" N ILE B 162 " --> pdb=" O ARG B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 184 Processing helix chain 'B' and resid 193 through 198 removed outlier: 3.883A pdb=" N PHE B 197 " --> pdb=" O GLN B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 221 Processing helix chain 'B' and resid 237 through 241 Processing helix chain 'B' and resid 242 through 247 Processing helix chain 'B' and resid 259 through 271 Processing helix chain 'B' and resid 282 through 290 removed outlier: 3.670A pdb=" N ILE B 286 " --> pdb=" O ASP B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 310 Processing helix chain 'B' and resid 310 through 319 removed outlier: 3.823A pdb=" N GLN B 319 " --> pdb=" O LYS B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 348 removed outlier: 3.681A pdb=" N PHE B 344 " --> pdb=" O LYS B 340 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS B 347 " --> pdb=" O ASP B 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 61 Processing helix chain 'C' and resid 62 through 67 removed outlier: 3.853A pdb=" N GLU C 66 " --> pdb=" O ALA C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 78 Processing helix chain 'C' and resid 82 through 86 Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'C' and resid 96 through 113 removed outlier: 5.149A pdb=" N TYR C 109 " --> pdb=" O GLU C 105 " (cutoff:3.500A) Proline residue: C 110 - end of helix Processing helix chain 'C' and resid 113 through 118 removed outlier: 4.113A pdb=" N TYR C 117 " --> pdb=" O MET C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 124 removed outlier: 3.667A pdb=" N GLN C 124 " --> pdb=" O PRO C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 150 removed outlier: 3.538A pdb=" N SER C 150 " --> pdb=" O LEU C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 163 Processing helix chain 'C' and resid 168 through 184 removed outlier: 3.791A pdb=" N LYS C 172 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 198 removed outlier: 4.231A pdb=" N PHE C 197 " --> pdb=" O GLN C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 221 Processing helix chain 'C' and resid 237 through 241 Processing helix chain 'C' and resid 242 through 247 Processing helix chain 'C' and resid 259 through 271 Processing helix chain 'C' and resid 282 through 290 removed outlier: 3.778A pdb=" N ILE C 286 " --> pdb=" O ASP C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 319 removed outlier: 5.270A pdb=" N GLU C 312 " --> pdb=" O ASP C 308 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N TYR C 313 " --> pdb=" O ALA C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 348 removed outlier: 4.050A pdb=" N LYS C 347 " --> pdb=" O ASP C 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 61 Processing helix chain 'D' and resid 62 through 66 removed outlier: 3.871A pdb=" N GLU D 66 " --> pdb=" O ALA D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 77 Processing helix chain 'D' and resid 82 through 86 Processing helix chain 'D' and resid 89 through 93 Processing helix chain 'D' and resid 96 through 107 Processing helix chain 'D' and resid 107 through 113 Processing helix chain 'D' and resid 113 through 118 removed outlier: 3.801A pdb=" N TYR D 117 " --> pdb=" O MET D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 124 removed outlier: 6.810A pdb=" N LEU D 122 " --> pdb=" O ASN D 119 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN D 124 " --> pdb=" O PRO D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 149 Processing helix chain 'D' and resid 158 through 163 removed outlier: 3.583A pdb=" N ILE D 162 " --> pdb=" O ARG D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 184 removed outlier: 3.644A pdb=" N LYS D 172 " --> pdb=" O GLY D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 198 removed outlier: 4.257A pdb=" N PHE D 197 " --> pdb=" O GLN D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 221 Processing helix chain 'D' and resid 242 through 247 Processing helix chain 'D' and resid 259 through 271 Processing helix chain 'D' and resid 282 through 290 removed outlier: 3.613A pdb=" N ILE D 286 " --> pdb=" O ASP D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 310 Processing helix chain 'D' and resid 310 through 319 Processing helix chain 'D' and resid 340 through 348 Processing helix chain 'E' and resid 43 through 61 Processing helix chain 'E' and resid 62 through 65 Processing helix chain 'E' and resid 70 through 78 Processing helix chain 'E' and resid 96 through 107 Processing helix chain 'E' and resid 107 through 113 Processing helix chain 'E' and resid 113 through 118 removed outlier: 3.520A pdb=" N TYR E 117 " --> pdb=" O MET E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 124 removed outlier: 3.881A pdb=" N GLN E 124 " --> pdb=" O PRO E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 149 Processing helix chain 'E' and resid 158 through 163 removed outlier: 3.757A pdb=" N ILE E 162 " --> pdb=" O ARG E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 184 Processing helix chain 'E' and resid 193 through 198 removed outlier: 4.061A pdb=" N PHE E 197 " --> pdb=" O GLN E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 221 Processing helix chain 'E' and resid 237 through 241 Processing helix chain 'E' and resid 242 through 247 Processing helix chain 'E' and resid 259 through 271 Processing helix chain 'E' and resid 282 through 290 removed outlier: 4.114A pdb=" N ILE E 286 " --> pdb=" O ASP E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 319 removed outlier: 5.085A pdb=" N GLU E 312 " --> pdb=" O ASP E 308 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N TYR E 313 " --> pdb=" O ALA E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 348 removed outlier: 3.834A pdb=" N LYS E 347 " --> pdb=" O ASP E 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 61 Processing helix chain 'F' and resid 62 through 67 removed outlier: 3.682A pdb=" N GLU F 66 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL F 67 " --> pdb=" O LEU F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 78 removed outlier: 3.570A pdb=" N SER F 78 " --> pdb=" O ARG F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 86 Processing helix chain 'F' and resid 89 through 93 removed outlier: 3.558A pdb=" N ILE F 93 " --> pdb=" O PHE F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 113 removed outlier: 4.983A pdb=" N TYR F 109 " --> pdb=" O GLU F 105 " (cutoff:3.500A) Proline residue: F 110 - end of helix Processing helix chain 'F' and resid 113 through 118 removed outlier: 3.731A pdb=" N TYR F 117 " --> pdb=" O MET F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 124 removed outlier: 6.824A pdb=" N LEU F 122 " --> pdb=" O ASN F 119 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN F 124 " --> pdb=" O PRO F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 150 Processing helix chain 'F' and resid 158 through 162 Processing helix chain 'F' and resid 168 through 184 Processing helix chain 'F' and resid 193 through 198 removed outlier: 4.193A pdb=" N PHE F 197 " --> pdb=" O GLN F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 221 Processing helix chain 'F' and resid 242 through 249 Processing helix chain 'F' and resid 259 through 271 Processing helix chain 'F' and resid 282 through 290 Processing helix chain 'F' and resid 294 through 319 removed outlier: 5.203A pdb=" N GLU F 312 " --> pdb=" O ASP F 308 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N TYR F 313 " --> pdb=" O ALA F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 346 removed outlier: 3.863A pdb=" N PHE F 344 " --> pdb=" O LYS F 340 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 61 Processing helix chain 'G' and resid 62 through 67 removed outlier: 3.695A pdb=" N GLU G 66 " --> pdb=" O ALA G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 78 Processing helix chain 'G' and resid 89 through 93 Processing helix chain 'G' and resid 96 through 107 Processing helix chain 'G' and resid 107 through 113 Processing helix chain 'G' and resid 120 through 124 removed outlier: 3.916A pdb=" N GLN G 124 " --> pdb=" O PRO G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 149 Processing helix chain 'G' and resid 158 through 163 Processing helix chain 'G' and resid 168 through 184 Processing helix chain 'G' and resid 193 through 198 removed outlier: 4.061A pdb=" N PHE G 197 " --> pdb=" O GLN G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 221 Processing helix chain 'G' and resid 237 through 241 Processing helix chain 'G' and resid 242 through 247 Processing helix chain 'G' and resid 259 through 271 Processing helix chain 'G' and resid 282 through 290 removed outlier: 4.157A pdb=" N ILE G 286 " --> pdb=" O ASP G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 319 removed outlier: 5.098A pdb=" N GLU G 312 " --> pdb=" O ASP G 308 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N TYR G 313 " --> pdb=" O ALA G 309 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN G 319 " --> pdb=" O LYS G 315 " (cutoff:3.500A) Processing helix chain 'G' and resid 340 through 348 removed outlier: 3.696A pdb=" N LYS G 347 " --> pdb=" O ASP G 343 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 61 Processing helix chain 'H' and resid 62 through 67 removed outlier: 3.622A pdb=" N ALA H 65 " --> pdb=" O PRO H 62 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU H 66 " --> pdb=" O ALA H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 78 Processing helix chain 'H' and resid 82 through 86 Processing helix chain 'H' and resid 89 through 93 Processing helix chain 'H' and resid 96 through 113 removed outlier: 5.168A pdb=" N TYR H 109 " --> pdb=" O GLU H 105 " (cutoff:3.500A) Proline residue: H 110 - end of helix Processing helix chain 'H' and resid 113 through 118 removed outlier: 3.745A pdb=" N TYR H 117 " --> pdb=" O MET H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 120 through 124 Processing helix chain 'H' and resid 138 through 150 removed outlier: 3.683A pdb=" N SER H 150 " --> pdb=" O LEU H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 184 Processing helix chain 'H' and resid 193 through 198 removed outlier: 3.970A pdb=" N PHE H 197 " --> pdb=" O GLN H 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 221 Processing helix chain 'H' and resid 237 through 241 removed outlier: 3.538A pdb=" N ASP H 240 " --> pdb=" O ARG H 237 " (cutoff:3.500A) Processing helix chain 'H' and resid 242 through 247 Processing helix chain 'H' and resid 259 through 271 Processing helix chain 'H' and resid 282 through 290 removed outlier: 3.983A pdb=" N ILE H 286 " --> pdb=" O ASP H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 294 through 319 removed outlier: 5.046A pdb=" N GLU H 312 " --> pdb=" O ASP H 308 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N TYR H 313 " --> pdb=" O ALA H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 340 through 348 removed outlier: 3.545A pdb=" N LYS H 347 " --> pdb=" O ASP H 343 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 81 removed outlier: 3.794A pdb=" N PHE A 154 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ASN A 153 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N PHE A 190 " --> pdb=" O ASN A 153 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ILE A 155 " --> pdb=" O PHE A 190 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ASP A 192 " --> pdb=" O ILE A 155 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ILE A 157 " --> pdb=" O ASP A 192 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET A 230 " --> pdb=" O CYS A 187 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA A 234 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLY A 128 " --> pdb=" O LYS A 251 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N PHE A 253 " --> pdb=" O GLY A 128 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU A 130 " --> pdb=" O PHE A 253 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 80 through 81 removed outlier: 4.122A pdb=" N PHE B 154 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ASN B 153 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N PHE B 190 " --> pdb=" O ASN B 153 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE B 155 " --> pdb=" O PHE B 190 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ASP B 192 " --> pdb=" O ILE B 155 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ILE B 157 " --> pdb=" O ASP B 192 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLY B 128 " --> pdb=" O LYS B 251 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N PHE B 253 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU B 130 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 80 through 81 removed outlier: 3.900A pdb=" N PHE C 154 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASN C 153 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N PHE C 190 " --> pdb=" O ASN C 153 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE C 155 " --> pdb=" O PHE C 190 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ASP C 192 " --> pdb=" O ILE C 155 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ILE C 157 " --> pdb=" O ASP C 192 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N CYS C 187 " --> pdb=" O MET C 230 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ILE C 232 " --> pdb=" O CYS C 187 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ILE C 189 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ALA C 234 " --> pdb=" O ILE C 189 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE C 191 " --> pdb=" O ALA C 234 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY C 128 " --> pdb=" O LYS C 251 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N PHE C 253 " --> pdb=" O GLY C 128 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU C 130 " --> pdb=" O PHE C 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 80 through 81 removed outlier: 4.237A pdb=" N PHE D 154 " --> pdb=" O VAL D 81 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ASN D 153 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N PHE D 190 " --> pdb=" O ASN D 153 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE D 155 " --> pdb=" O PHE D 190 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ASP D 192 " --> pdb=" O ILE D 155 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA D 234 " --> pdb=" O ILE D 191 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N VAL D 129 " --> pdb=" O GLY D 233 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS D 251 " --> pdb=" O GLY D 128 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 80 through 81 removed outlier: 4.031A pdb=" N PHE E 154 " --> pdb=" O VAL E 81 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA E 234 " --> pdb=" O ILE E 191 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL E 129 " --> pdb=" O GLY E 233 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N THR E 235 " --> pdb=" O VAL E 129 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU E 131 " --> pdb=" O THR E 235 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLY E 128 " --> pdb=" O LYS E 251 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N PHE E 253 " --> pdb=" O GLY E 128 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU E 130 " --> pdb=" O PHE E 253 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 80 through 81 removed outlier: 3.863A pdb=" N PHE F 154 " --> pdb=" O VAL F 81 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ASN F 153 " --> pdb=" O ILE F 188 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N PHE F 190 " --> pdb=" O ASN F 153 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE F 155 " --> pdb=" O PHE F 190 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ASP F 192 " --> pdb=" O ILE F 155 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ILE F 157 " --> pdb=" O ASP F 192 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N CYS F 187 " --> pdb=" O MET F 230 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ILE F 232 " --> pdb=" O CYS F 187 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ILE F 189 " --> pdb=" O ILE F 232 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ALA F 234 " --> pdb=" O ILE F 189 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE F 191 " --> pdb=" O ALA F 234 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLY F 128 " --> pdb=" O LYS F 251 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N PHE F 253 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU F 130 " --> pdb=" O PHE F 253 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 80 through 81 removed outlier: 3.959A pdb=" N PHE G 154 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA G 234 " --> pdb=" O ILE G 191 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLY G 128 " --> pdb=" O LYS G 251 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N PHE G 253 " --> pdb=" O GLY G 128 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU G 130 " --> pdb=" O PHE G 253 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 153 through 157 removed outlier: 4.146A pdb=" N ASP H 192 " --> pdb=" O ILE H 157 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA H 234 " --> pdb=" O ILE H 191 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL H 129 " --> pdb=" O GLY H 233 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLY H 128 " --> pdb=" O LYS H 251 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N PHE H 253 " --> pdb=" O GLY H 128 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU H 130 " --> pdb=" O PHE H 253 " (cutoff:3.500A) 947 hydrogen bonds defined for protein. 2688 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: 3.42 Time building geometry restraints manager: 2.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3182 1.32 - 1.45: 4562 1.45 - 1.57: 11208 1.57 - 1.70: 37 1.70 - 1.82: 162 Bond restraints: 19151 Sorted by residual: bond pdb=" C4 ATP E 401 " pdb=" C5 ATP E 401 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.95e+01 bond pdb=" C4 ATP B 401 " pdb=" C5 ATP B 401 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.76e+01 bond pdb=" C4 ATP H 401 " pdb=" C5 ATP H 401 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.67e+01 bond pdb=" C4 ATP F 401 " pdb=" C5 ATP F 401 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.54e+01 bond pdb=" C4 ATP C 401 " pdb=" C5 ATP C 401 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.47e+01 ... (remaining 19146 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.20: 25647 4.20 - 8.40: 175 8.40 - 12.59: 17 12.59 - 16.79: 8 16.79 - 20.99: 7 Bond angle restraints: 25854 Sorted by residual: angle pdb=" PB ATP E 401 " pdb=" O3B ATP E 401 " pdb=" PG ATP E 401 " ideal model delta sigma weight residual 139.87 118.88 20.99 1.00e+00 1.00e+00 4.41e+02 angle pdb=" PB ATP H 401 " pdb=" O3B ATP H 401 " pdb=" PG ATP H 401 " ideal model delta sigma weight residual 139.87 120.59 19.28 1.00e+00 1.00e+00 3.72e+02 angle pdb=" PB ATP G 401 " pdb=" O3B ATP G 401 " pdb=" PG ATP G 401 " ideal model delta sigma weight residual 139.87 120.64 19.23 1.00e+00 1.00e+00 3.70e+02 angle pdb=" PB ATP D 401 " pdb=" O3B ATP D 401 " pdb=" PG ATP D 401 " ideal model delta sigma weight residual 139.87 120.95 18.92 1.00e+00 1.00e+00 3.58e+02 angle pdb=" PB ATP C 401 " pdb=" O3B ATP C 401 " pdb=" PG ATP C 401 " ideal model delta sigma weight residual 139.87 121.10 18.77 1.00e+00 1.00e+00 3.52e+02 ... (remaining 25849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 10139 17.95 - 35.91: 1440 35.91 - 53.86: 358 53.86 - 71.82: 58 71.82 - 89.77: 29 Dihedral angle restraints: 12024 sinusoidal: 5124 harmonic: 6900 Sorted by residual: dihedral pdb=" CA LEU D 184 " pdb=" C LEU D 184 " pdb=" N GLN D 185 " pdb=" CA GLN D 185 " ideal model delta harmonic sigma weight residual -180.00 -156.51 -23.49 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA LEU F 184 " pdb=" C LEU F 184 " pdb=" N GLN F 185 " pdb=" CA GLN F 185 " ideal model delta harmonic sigma weight residual -180.00 -156.84 -23.16 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA LEU G 184 " pdb=" C LEU G 184 " pdb=" N GLN G 185 " pdb=" CA GLN G 185 " ideal model delta harmonic sigma weight residual -180.00 -156.84 -23.16 0 5.00e+00 4.00e-02 2.14e+01 ... (remaining 12021 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 2603 0.072 - 0.145: 329 0.145 - 0.217: 14 0.217 - 0.289: 7 0.289 - 0.361: 2 Chirality restraints: 2955 Sorted by residual: chirality pdb=" CA ASP B 308 " pdb=" N ASP B 308 " pdb=" C ASP B 308 " pdb=" CB ASP B 308 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" CG LEU H 198 " pdb=" CB LEU H 198 " pdb=" CD1 LEU H 198 " pdb=" CD2 LEU H 198 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CG LEU G 276 " pdb=" CB LEU G 276 " pdb=" CD1 LEU G 276 " pdb=" CD2 LEU G 276 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 2952 not shown) Planarity restraints: 3251 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 120 " 0.067 5.00e-02 4.00e+02 1.02e-01 1.68e+01 pdb=" N PRO D 121 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO D 121 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO D 121 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 61 " -0.044 5.00e-02 4.00e+02 6.75e-02 7.29e+00 pdb=" N PRO B 62 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 62 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 62 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 245 " -0.027 2.00e-02 2.50e+03 1.72e-02 5.20e+00 pdb=" CG PHE H 245 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE H 245 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE H 245 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE H 245 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE H 245 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE H 245 " -0.010 2.00e-02 2.50e+03 ... (remaining 3248 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 54 2.41 - 3.03: 10741 3.03 - 3.66: 30109 3.66 - 4.28: 44982 4.28 - 4.90: 74986 Nonbonded interactions: 160872 Sorted by model distance: nonbonded pdb=" O3G ATP C 401 " pdb="MG MG C 402 " model vdw 1.791 2.170 nonbonded pdb="MG MG A 401 " pdb=" O3G ATP B 401 " model vdw 1.841 2.170 nonbonded pdb="MG MG A 401 " pdb=" O2B ATP B 401 " model vdw 1.938 2.170 nonbonded pdb=" CG2 THR H 140 " pdb="MG MG H 402 " model vdw 2.016 2.590 nonbonded pdb=" OG1 THR D 140 " pdb="MG MG D 402 " model vdw 2.021 2.170 ... (remaining 160867 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 43 through 349) selection = (chain 'B' and resid 43 through 349) selection = (chain 'C' and (resid 43 through 319 or resid 337 through 349)) selection = (chain 'D' and (resid 43 through 319 or resid 337 through 349)) selection = (chain 'E' and (resid 43 through 319 or resid 337 through 349)) selection = (chain 'F' and (resid 43 through 319 or resid 337 through 349)) selection = (chain 'G' and (resid 43 through 319 or resid 337 through 349)) selection = (chain 'H' and (resid 43 through 319 or resid 337 through 349)) } 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: 13.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.240 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 18.050 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 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 : 0.006 0.124 19151 Z= 0.363 Angle : 0.930 20.991 25854 Z= 0.631 Chirality : 0.048 0.361 2955 Planarity : 0.005 0.102 3251 Dihedral : 17.647 89.770 7528 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.29 % Allowed : 22.42 % Favored : 77.29 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.17), residues: 2315 helix: 0.60 (0.14), residues: 1264 sheet: -0.21 (0.44), residues: 143 loop : 0.47 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 74 TYR 0.010 0.001 TYR E 72 PHE 0.033 0.002 PHE A 344 TRP 0.008 0.001 TRP B 220 HIS 0.002 0.001 HIS G 206 Details of bonding type rmsd covalent geometry : bond 0.00597 (19151) covalent geometry : angle 0.93045 (25854) hydrogen bonds : bond 0.16031 ( 947) hydrogen bonds : angle 5.55342 ( 2688) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 304 time to evaluate : 0.771 Fit side-chains REVERT: C 308 ASP cc_start: 0.7040 (t70) cc_final: 0.6633 (t0) REVERT: H 280 GLU cc_start: 0.7180 (tt0) cc_final: 0.6978 (tt0) outliers start: 6 outliers final: 3 residues processed: 305 average time/residue: 0.1280 time to fit residues: 60.1065 Evaluate side-chains 293 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 290 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain H residue 80 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 104 HIS E 119 ASN F 236 ASN F 289 ASN G 236 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.173700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.130198 restraints weight = 25351.227| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.51 r_work: 0.3366 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.0744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19151 Z= 0.133 Angle : 0.538 9.881 25854 Z= 0.267 Chirality : 0.040 0.155 2955 Planarity : 0.004 0.061 3251 Dihedral : 10.271 86.539 2776 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.03 % Allowed : 21.74 % Favored : 76.23 % 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: 1.27 (0.17), residues: 2315 helix: 1.22 (0.15), residues: 1290 sheet: -0.49 (0.39), residues: 168 loop : 0.79 (0.21), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 201 TYR 0.008 0.001 TYR A 167 PHE 0.018 0.001 PHE A 344 TRP 0.004 0.001 TRP F 166 HIS 0.002 0.000 HIS G 206 Details of bonding type rmsd covalent geometry : bond 0.00307 (19151) covalent geometry : angle 0.53755 (25854) hydrogen bonds : bond 0.03726 ( 947) hydrogen bonds : angle 4.49996 ( 2688) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 317 time to evaluate : 0.638 Fit side-chains REVERT: B 150 SER cc_start: 0.8747 (p) cc_final: 0.8271 (p) REVERT: C 149 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8193 (mt-10) REVERT: C 308 ASP cc_start: 0.7097 (t70) cc_final: 0.6686 (t0) REVERT: D 313 TYR cc_start: 0.8091 (t80) cc_final: 0.7832 (t80) REVERT: F 311 LYS cc_start: 0.8197 (ttmt) cc_final: 0.7986 (ttmm) REVERT: H 280 GLU cc_start: 0.7256 (tt0) cc_final: 0.7033 (tt0) outliers start: 42 outliers final: 24 residues processed: 341 average time/residue: 0.1332 time to fit residues: 69.9513 Evaluate side-chains 316 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 291 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain F residue 177 MET Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 236 ASN Chi-restraints excluded: chain G residue 341 THR Chi-restraints excluded: chain H residue 187 CYS Chi-restraints excluded: chain H residue 255 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 64 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 232 optimal weight: 7.9990 chunk 193 optimal weight: 6.9990 chunk 201 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 211 optimal weight: 10.0000 chunk 197 optimal weight: 6.9990 chunk 25 optimal weight: 30.0000 chunk 69 optimal weight: 0.6980 chunk 67 optimal weight: 0.2980 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 236 ASN F 236 ASN G 236 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.170249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.127101 restraints weight = 25736.216| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.46 r_work: 0.3359 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 19151 Z= 0.187 Angle : 0.546 8.414 25854 Z= 0.270 Chirality : 0.041 0.158 2955 Planarity : 0.004 0.047 3251 Dihedral : 10.338 88.282 2772 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.43 % Allowed : 21.01 % Favored : 75.56 % 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: 1.42 (0.18), residues: 2315 helix: 1.36 (0.15), residues: 1291 sheet: -0.62 (0.38), residues: 174 loop : 0.89 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 247 TYR 0.011 0.001 TYR F 132 PHE 0.012 0.001 PHE E 154 TRP 0.008 0.001 TRP A 220 HIS 0.002 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00450 (19151) covalent geometry : angle 0.54568 (25854) hydrogen bonds : bond 0.03573 ( 947) hydrogen bonds : angle 4.43116 ( 2688) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 300 time to evaluate : 0.707 Fit side-chains REVERT: A 270 LEU cc_start: 0.4689 (mm) cc_final: 0.4325 (tt) REVERT: B 55 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7222 (tt0) REVERT: B 150 SER cc_start: 0.8821 (p) cc_final: 0.8351 (p) REVERT: C 308 ASP cc_start: 0.7168 (t70) cc_final: 0.6781 (t0) REVERT: C 313 TYR cc_start: 0.7150 (t80) cc_final: 0.6836 (t80) REVERT: D 207 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8109 (tt0) REVERT: D 313 TYR cc_start: 0.8179 (t80) cc_final: 0.7950 (t80) REVERT: F 159 MET cc_start: 0.8221 (tpp) cc_final: 0.8015 (mmm) REVERT: F 311 LYS cc_start: 0.8235 (ttmt) cc_final: 0.8026 (ttmm) REVERT: G 207 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8131 (pt0) REVERT: H 117 TYR cc_start: 0.5200 (m-80) cc_final: 0.4851 (m-80) REVERT: H 132 TYR cc_start: 0.8298 (p90) cc_final: 0.8037 (p90) REVERT: H 280 GLU cc_start: 0.7296 (tt0) cc_final: 0.7047 (tt0) outliers start: 71 outliers final: 38 residues processed: 350 average time/residue: 0.1301 time to fit residues: 70.1649 Evaluate side-chains 325 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 284 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 221 ASP Chi-restraints excluded: chain E residue 236 ASN Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain F residue 177 MET Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 203 SER Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain G residue 341 THR Chi-restraints excluded: chain H residue 80 ILE Chi-restraints excluded: chain H residue 187 CYS Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 255 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 224 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 126 optimal weight: 0.0870 chunk 100 optimal weight: 1.9990 chunk 191 optimal weight: 5.9990 chunk 43 optimal weight: 0.5980 chunk 28 optimal weight: 8.9990 chunk 160 optimal weight: 0.7980 overall best weight: 1.2962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 GLN E 236 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.171885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.129776 restraints weight = 25642.800| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.79 r_work: 0.3346 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19151 Z= 0.132 Angle : 0.511 8.982 25854 Z= 0.252 Chirality : 0.040 0.154 2955 Planarity : 0.003 0.043 3251 Dihedral : 10.205 89.037 2772 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.90 % Allowed : 22.46 % Favored : 74.64 % 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: 1.62 (0.18), residues: 2315 helix: 1.53 (0.15), residues: 1292 sheet: -0.64 (0.37), residues: 186 loop : 1.02 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 247 TYR 0.009 0.001 TYR C 167 PHE 0.020 0.001 PHE H 245 TRP 0.005 0.001 TRP F 166 HIS 0.002 0.000 HIS G 206 Details of bonding type rmsd covalent geometry : bond 0.00314 (19151) covalent geometry : angle 0.51068 (25854) hydrogen bonds : bond 0.03188 ( 947) hydrogen bonds : angle 4.32909 ( 2688) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 311 time to evaluate : 0.712 Fit side-chains revert: symmetry clash REVERT: A 206 HIS cc_start: 0.5904 (OUTLIER) cc_final: 0.5357 (m-70) REVERT: A 270 LEU cc_start: 0.4720 (mm) cc_final: 0.4347 (tt) REVERT: B 55 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.7097 (tt0) REVERT: B 150 SER cc_start: 0.8792 (p) cc_final: 0.8288 (p) REVERT: B 300 GLU cc_start: 0.8463 (tp30) cc_final: 0.8191 (tp30) REVERT: C 53 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.6395 (mp10) REVERT: C 308 ASP cc_start: 0.7113 (t70) cc_final: 0.6729 (t0) REVERT: C 313 TYR cc_start: 0.7145 (t80) cc_final: 0.6788 (t80) REVERT: D 207 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7872 (tt0) REVERT: D 313 TYR cc_start: 0.8180 (t80) cc_final: 0.7960 (t80) REVERT: F 311 LYS cc_start: 0.8235 (ttmt) cc_final: 0.8030 (ttmm) REVERT: G 207 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7930 (pt0) REVERT: H 117 TYR cc_start: 0.5140 (m-80) cc_final: 0.4831 (m-80) outliers start: 60 outliers final: 41 residues processed: 348 average time/residue: 0.1239 time to fit residues: 66.6934 Evaluate side-chains 332 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 286 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 CYS Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 221 ASP Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain F residue 141 MET Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 177 MET Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain G residue 341 THR Chi-restraints excluded: chain H residue 80 ILE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 187 CYS Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 255 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 98 optimal weight: 0.8980 chunk 188 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 chunk 116 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 142 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 GLN E 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.170568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.128210 restraints weight = 25570.584| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.67 r_work: 0.3357 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19151 Z= 0.166 Angle : 0.532 9.316 25854 Z= 0.261 Chirality : 0.041 0.148 2955 Planarity : 0.003 0.044 3251 Dihedral : 10.182 89.266 2772 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.43 % Allowed : 22.32 % Favored : 74.25 % 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: 1.65 (0.18), residues: 2315 helix: 1.55 (0.15), residues: 1291 sheet: -0.68 (0.37), residues: 185 loop : 1.05 (0.22), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 247 TYR 0.008 0.001 TYR C 167 PHE 0.021 0.001 PHE H 245 TRP 0.009 0.001 TRP B 54 HIS 0.002 0.000 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00398 (19151) covalent geometry : angle 0.53179 (25854) hydrogen bonds : bond 0.03222 ( 947) hydrogen bonds : angle 4.32964 ( 2688) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 298 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 ARG cc_start: 0.5533 (mtm110) cc_final: 0.5155 (mtm110) REVERT: A 206 HIS cc_start: 0.5964 (OUTLIER) cc_final: 0.5393 (m-70) REVERT: A 270 LEU cc_start: 0.4786 (mm) cc_final: 0.4413 (tt) REVERT: B 55 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.7095 (tt0) REVERT: B 150 SER cc_start: 0.8806 (p) cc_final: 0.8303 (p) REVERT: C 53 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.6401 (mp10) REVERT: C 308 ASP cc_start: 0.7160 (t70) cc_final: 0.6774 (t0) REVERT: C 313 TYR cc_start: 0.7212 (t80) cc_final: 0.6839 (t80) REVERT: D 207 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7877 (tt0) REVERT: D 313 TYR cc_start: 0.8228 (t80) cc_final: 0.8022 (t80) REVERT: D 350 MET cc_start: 0.4839 (tpp) cc_final: 0.4538 (tpp) REVERT: G 207 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7955 (pt0) REVERT: H 117 TYR cc_start: 0.5225 (m-80) cc_final: 0.4800 (m-80) REVERT: H 132 TYR cc_start: 0.8218 (p90) cc_final: 0.7859 (p90) outliers start: 71 outliers final: 49 residues processed: 347 average time/residue: 0.1304 time to fit residues: 70.3374 Evaluate side-chains 340 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 286 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 187 CYS Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 236 ASN Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 221 ASP Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain F residue 141 MET Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 177 MET Chi-restraints excluded: chain G residue 203 SER Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain G residue 341 THR Chi-restraints excluded: chain H residue 80 ILE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 187 CYS Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 255 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 197 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 chunk 150 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 225 optimal weight: 0.6980 chunk 210 optimal weight: 7.9990 chunk 219 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.173323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.130389 restraints weight = 25421.979| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.45 r_work: 0.3400 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19151 Z= 0.111 Angle : 0.496 9.367 25854 Z= 0.244 Chirality : 0.040 0.142 2955 Planarity : 0.003 0.043 3251 Dihedral : 9.989 88.922 2772 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.43 % Allowed : 22.08 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.18), residues: 2315 helix: 1.69 (0.15), residues: 1295 sheet: -0.74 (0.37), residues: 182 loop : 1.15 (0.23), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 247 TYR 0.009 0.001 TYR C 167 PHE 0.015 0.001 PHE H 245 TRP 0.006 0.001 TRP B 54 HIS 0.002 0.000 HIS G 206 Details of bonding type rmsd covalent geometry : bond 0.00260 (19151) covalent geometry : angle 0.49619 (25854) hydrogen bonds : bond 0.02916 ( 947) hydrogen bonds : angle 4.24425 ( 2688) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 309 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.7291 (mmm) cc_final: 0.6894 (mmm) REVERT: A 201 ARG cc_start: 0.5604 (mtm110) cc_final: 0.4945 (mtm110) REVERT: A 206 HIS cc_start: 0.6027 (OUTLIER) cc_final: 0.5388 (m-70) REVERT: B 55 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7274 (tt0) REVERT: B 150 SER cc_start: 0.8806 (p) cc_final: 0.8316 (p) REVERT: B 300 GLU cc_start: 0.8527 (tp30) cc_final: 0.8240 (tp30) REVERT: C 53 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.6591 (mp10) REVERT: C 308 ASP cc_start: 0.7199 (t70) cc_final: 0.6801 (t0) REVERT: C 313 TYR cc_start: 0.7247 (t80) cc_final: 0.6891 (t80) REVERT: D 207 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8087 (tt0) REVERT: D 313 TYR cc_start: 0.8229 (t80) cc_final: 0.8017 (t80) REVERT: D 350 MET cc_start: 0.4960 (tpp) cc_final: 0.4719 (tpp) REVERT: E 237 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.6973 (mtp85) REVERT: E 284 GLN cc_start: 0.8808 (tp40) cc_final: 0.8417 (tp40) REVERT: G 207 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.8063 (pt0) REVERT: H 117 TYR cc_start: 0.5163 (m-80) cc_final: 0.4692 (m-80) outliers start: 71 outliers final: 43 residues processed: 355 average time/residue: 0.1404 time to fit residues: 77.0072 Evaluate side-chains 343 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 294 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 187 CYS Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 237 ARG Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain F residue 141 MET Chi-restraints excluded: chain F residue 177 MET Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 177 MET Chi-restraints excluded: chain G residue 203 SER Chi-restraints excluded: chain G residue 205 ASP Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain G residue 341 THR Chi-restraints excluded: chain H residue 80 ILE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 187 CYS Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 255 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 145 optimal weight: 0.8980 chunk 189 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 195 optimal weight: 0.1980 chunk 206 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 185 optimal weight: 0.9980 chunk 152 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.172683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.129733 restraints weight = 25540.730| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.48 r_work: 0.3400 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19151 Z= 0.127 Angle : 0.509 9.530 25854 Z= 0.248 Chirality : 0.040 0.143 2955 Planarity : 0.003 0.043 3251 Dihedral : 9.926 88.988 2772 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.19 % Allowed : 22.61 % Favored : 74.20 % 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: 1.89 (0.18), residues: 2315 helix: 1.74 (0.15), residues: 1295 sheet: -0.71 (0.37), residues: 182 loop : 1.18 (0.23), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 74 TYR 0.009 0.001 TYR C 167 PHE 0.015 0.001 PHE H 245 TRP 0.009 0.001 TRP A 54 HIS 0.002 0.000 HIS G 206 Details of bonding type rmsd covalent geometry : bond 0.00303 (19151) covalent geometry : angle 0.50872 (25854) hydrogen bonds : bond 0.02911 ( 947) hydrogen bonds : angle 4.20852 ( 2688) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 291 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.7208 (mmm) cc_final: 0.6726 (mmm) REVERT: A 201 ARG cc_start: 0.5561 (mtm110) cc_final: 0.4903 (mtm110) REVERT: A 206 HIS cc_start: 0.5966 (OUTLIER) cc_final: 0.5320 (m-70) REVERT: B 55 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7242 (tt0) REVERT: B 150 SER cc_start: 0.8823 (p) cc_final: 0.8333 (p) REVERT: B 300 GLU cc_start: 0.8482 (tp30) cc_final: 0.8203 (tp30) REVERT: C 53 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.6503 (mp10) REVERT: C 308 ASP cc_start: 0.7179 (t70) cc_final: 0.6773 (t0) REVERT: C 313 TYR cc_start: 0.7242 (t80) cc_final: 0.6881 (t80) REVERT: D 207 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8060 (tt0) REVERT: D 313 TYR cc_start: 0.8210 (t80) cc_final: 0.7992 (t80) REVERT: E 237 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.6952 (mtp85) REVERT: G 207 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.8049 (pt0) REVERT: H 117 TYR cc_start: 0.5140 (m-80) cc_final: 0.4684 (m-80) outliers start: 66 outliers final: 49 residues processed: 335 average time/residue: 0.1364 time to fit residues: 70.6500 Evaluate side-chains 338 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 283 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 187 CYS Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 236 ASN Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 221 ASP Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 237 ARG Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain F residue 141 MET Chi-restraints excluded: chain F residue 177 MET Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 177 MET Chi-restraints excluded: chain G residue 203 SER Chi-restraints excluded: chain G residue 205 ASP Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain G residue 341 THR Chi-restraints excluded: chain H residue 80 ILE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 187 CYS Chi-restraints excluded: chain H residue 215 GLU Chi-restraints excluded: chain H residue 255 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 87 optimal weight: 6.9990 chunk 202 optimal weight: 10.0000 chunk 115 optimal weight: 9.9990 chunk 114 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 chunk 221 optimal weight: 8.9990 chunk 58 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 204 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 chunk 27 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 ASN H 193 GLN H 236 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.164019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.123253 restraints weight = 25630.308| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.28 r_work: 0.3299 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.078 19151 Z= 0.350 Angle : 0.700 8.857 25854 Z= 0.347 Chirality : 0.046 0.247 2955 Planarity : 0.005 0.067 3251 Dihedral : 10.397 87.581 2772 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.43 % Allowed : 22.17 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.18), residues: 2315 helix: 1.24 (0.15), residues: 1279 sheet: -1.00 (0.35), residues: 194 loop : 0.72 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 247 TYR 0.023 0.002 TYR C 264 PHE 0.019 0.003 PHE E 154 TRP 0.016 0.002 TRP B 54 HIS 0.005 0.001 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00844 (19151) covalent geometry : angle 0.70038 (25854) hydrogen bonds : bond 0.04010 ( 947) hydrogen bonds : angle 4.68181 ( 2688) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 278 time to evaluate : 0.830 Fit side-chains REVERT: B 55 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7320 (tt0) REVERT: B 150 SER cc_start: 0.8857 (p) cc_final: 0.8399 (p) REVERT: C 53 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.6468 (mp10) REVERT: C 308 ASP cc_start: 0.7199 (t70) cc_final: 0.6803 (t0) REVERT: C 313 TYR cc_start: 0.7299 (t80) cc_final: 0.6875 (t80) REVERT: D 207 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8172 (tt0) REVERT: D 308 ASP cc_start: 0.7927 (t0) cc_final: 0.7698 (t0) REVERT: E 237 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7057 (mtp85) REVERT: G 207 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8173 (pt0) REVERT: H 117 TYR cc_start: 0.5377 (m-80) cc_final: 0.4964 (m-80) REVERT: H 132 TYR cc_start: 0.8394 (p90) cc_final: 0.8142 (p90) outliers start: 71 outliers final: 43 residues processed: 329 average time/residue: 0.1384 time to fit residues: 69.5889 Evaluate side-chains 322 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 274 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 236 ASN Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 237 ARG Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain F residue 141 MET Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 177 MET Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain F residue 223 LEU Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 203 SER Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain G residue 341 THR Chi-restraints excluded: chain H residue 80 ILE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 187 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 23 optimal weight: 8.9990 chunk 131 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 150 optimal weight: 0.6980 chunk 17 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 183 optimal weight: 4.9990 chunk 210 optimal weight: 7.9990 chunk 211 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 GLN D 289 ASN F 87 ASN H 236 ASN H 239 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.170409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.127188 restraints weight = 25383.827| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.46 r_work: 0.3335 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 19151 Z= 0.144 Angle : 0.553 9.237 25854 Z= 0.273 Chirality : 0.041 0.246 2955 Planarity : 0.003 0.044 3251 Dihedral : 10.228 85.657 2772 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.66 % Allowed : 23.09 % Favored : 74.25 % 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: 1.59 (0.18), residues: 2315 helix: 1.57 (0.15), residues: 1284 sheet: -0.91 (0.36), residues: 196 loop : 0.98 (0.23), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 247 TYR 0.018 0.001 TYR C 264 PHE 0.016 0.001 PHE H 245 TRP 0.008 0.001 TRP A 54 HIS 0.002 0.000 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00344 (19151) covalent geometry : angle 0.55267 (25854) hydrogen bonds : bond 0.03186 ( 947) hydrogen bonds : angle 4.41837 ( 2688) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 288 time to evaluate : 0.722 Fit side-chains REVERT: A 74 ARG cc_start: 0.7449 (mtp85) cc_final: 0.7185 (mtp85) REVERT: A 113 MET cc_start: 0.7272 (mmm) cc_final: 0.6881 (mmm) REVERT: A 201 ARG cc_start: 0.5481 (mtm110) cc_final: 0.5159 (mtm110) REVERT: B 150 SER cc_start: 0.8864 (p) cc_final: 0.8413 (p) REVERT: C 53 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.6571 (mp10) REVERT: C 308 ASP cc_start: 0.7150 (t70) cc_final: 0.6742 (t0) REVERT: C 313 TYR cc_start: 0.7270 (t80) cc_final: 0.6841 (t80) REVERT: D 207 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8122 (tt0) REVERT: E 237 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.6997 (mtp85) REVERT: G 207 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8083 (pt0) REVERT: G 350 MET cc_start: 0.7093 (tpp) cc_final: 0.6861 (tpp) REVERT: H 117 TYR cc_start: 0.5309 (m-80) cc_final: 0.4894 (m-80) REVERT: H 132 TYR cc_start: 0.8338 (p90) cc_final: 0.7958 (p90) outliers start: 55 outliers final: 39 residues processed: 329 average time/residue: 0.1364 time to fit residues: 69.0449 Evaluate side-chains 325 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 282 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 237 ARG Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain F residue 141 MET Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 177 MET Chi-restraints excluded: chain G residue 203 SER Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 341 THR Chi-restraints excluded: chain H residue 80 ILE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 187 CYS Chi-restraints excluded: chain H residue 279 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 0 optimal weight: 10.0000 chunk 195 optimal weight: 2.9990 chunk 219 optimal weight: 3.9990 chunk 171 optimal weight: 6.9990 chunk 209 optimal weight: 5.9990 chunk 134 optimal weight: 0.5980 chunk 226 optimal weight: 0.9990 chunk 41 optimal weight: 0.3980 chunk 199 optimal weight: 5.9990 chunk 119 optimal weight: 0.0770 chunk 50 optimal weight: 3.9990 overall best weight: 1.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 GLN C 124 GLN D 289 ASN F 87 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.171991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.128946 restraints weight = 25297.973| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.47 r_work: 0.3387 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 19151 Z= 0.125 Angle : 0.533 8.955 25854 Z= 0.263 Chirality : 0.040 0.185 2955 Planarity : 0.003 0.044 3251 Dihedral : 10.135 86.448 2772 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.17 % Allowed : 23.48 % Favored : 74.35 % 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: 1.79 (0.18), residues: 2315 helix: 1.75 (0.15), residues: 1280 sheet: -0.88 (0.36), residues: 188 loop : 1.03 (0.23), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 252 TYR 0.015 0.001 TYR C 167 PHE 0.014 0.001 PHE H 245 TRP 0.008 0.001 TRP A 54 HIS 0.002 0.000 HIS G 206 Details of bonding type rmsd covalent geometry : bond 0.00301 (19151) covalent geometry : angle 0.53320 (25854) hydrogen bonds : bond 0.02977 ( 947) hydrogen bonds : angle 4.29665 ( 2688) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 286 time to evaluate : 0.814 Fit side-chains REVERT: A 74 ARG cc_start: 0.7435 (mtp85) cc_final: 0.7177 (mtp85) REVERT: A 113 MET cc_start: 0.7237 (mmm) cc_final: 0.6802 (mmm) REVERT: A 201 ARG cc_start: 0.5479 (mtm110) cc_final: 0.4902 (mtm110) REVERT: B 124 GLN cc_start: 0.8448 (pm20) cc_final: 0.8067 (pm20) REVERT: B 150 SER cc_start: 0.8845 (p) cc_final: 0.8387 (p) REVERT: B 252 ARG cc_start: 0.8839 (mtm-85) cc_final: 0.8603 (mtm-85) REVERT: B 300 GLU cc_start: 0.8488 (tp30) cc_final: 0.8203 (tp30) REVERT: C 53 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.6588 (mp10) REVERT: C 308 ASP cc_start: 0.7179 (t70) cc_final: 0.6775 (t0) REVERT: C 313 TYR cc_start: 0.7240 (t80) cc_final: 0.6854 (t80) REVERT: D 207 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8145 (tt0) REVERT: E 237 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.6965 (mtp85) REVERT: G 350 MET cc_start: 0.7124 (tpp) cc_final: 0.6909 (tpp) REVERT: H 117 TYR cc_start: 0.5268 (m-80) cc_final: 0.4846 (m-80) REVERT: H 132 TYR cc_start: 0.8329 (p90) cc_final: 0.7977 (p90) outliers start: 45 outliers final: 36 residues processed: 315 average time/residue: 0.1533 time to fit residues: 73.4914 Evaluate side-chains 322 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 283 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain C residue 53 GLN Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 237 ARG Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain F residue 141 MET Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 177 MET Chi-restraints excluded: chain G residue 203 SER Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 341 THR Chi-restraints excluded: chain H residue 80 ILE Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 187 CYS Chi-restraints excluded: chain H residue 279 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 97 optimal weight: 0.8980 chunk 6 optimal weight: 20.0000 chunk 198 optimal weight: 0.5980 chunk 146 optimal weight: 4.9990 chunk 209 optimal weight: 4.9990 chunk 118 optimal weight: 8.9990 chunk 90 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 192 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 104 optimal weight: 4.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 87 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.169061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.126542 restraints weight = 25622.225| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.85 r_work: 0.3311 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 19151 Z= 0.197 Angle : 0.573 8.663 25854 Z= 0.283 Chirality : 0.042 0.194 2955 Planarity : 0.004 0.044 3251 Dihedral : 10.153 89.227 2772 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.13 % Allowed : 23.48 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.18), residues: 2315 helix: 1.64 (0.15), residues: 1279 sheet: -0.81 (0.36), residues: 186 loop : 0.97 (0.23), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 247 TYR 0.020 0.001 TYR C 264 PHE 0.017 0.002 PHE H 245 TRP 0.009 0.001 TRP F 166 HIS 0.002 0.001 HIS D 206 Details of bonding type rmsd covalent geometry : bond 0.00477 (19151) covalent geometry : angle 0.57344 (25854) hydrogen bonds : bond 0.03233 ( 947) hydrogen bonds : angle 4.37277 ( 2688) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7036.13 seconds wall clock time: 120 minutes 44.17 seconds (7244.17 seconds total)