Starting phenix.real_space_refine on Sun Aug 24 20:25:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f8t_28936/08_2025/8f8t_28936.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f8t_28936/08_2025/8f8t_28936.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8f8t_28936/08_2025/8f8t_28936.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f8t_28936/08_2025/8f8t_28936.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8f8t_28936/08_2025/8f8t_28936.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f8t_28936/08_2025/8f8t_28936.map" } resolution = 3.26 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= 0.026 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 14 5.49 5 Mg 7 5.21 5 S 153 5.16 5 C 14122 2.51 5 N 3785 2.21 5 O 4312 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22393 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 1843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1843 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 14, 'TRANS': 215} Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.20, per 1000 atoms: 0.28 Number of scatterers: 22393 At special positions: 0 Unit cell: (91.8, 104.76, 246.24, 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 153 16.00 P 14 15.00 Mg 7 11.99 O 4312 8.00 N 3785 7.00 C 14122 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: 1.97 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5256 Finding SS restraints... Secondary structure from input PDB file: 159 helices and 43 sheets defined 49.9% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 78 through 93 removed outlier: 3.614A pdb=" N GLU A 93 " --> pdb=" O THR A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 112 through 126 Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 181 through 197 Processing helix chain 'A' and resid 204 through 217 removed outlier: 4.532A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N CYS A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 260 Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 261 through 262 No H-bonds generated for 'chain 'A' and resid 261 through 262' Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 289 through 295 Processing helix chain 'A' and resid 301 through 306 removed outlier: 4.407A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 348 removed outlier: 3.633A pdb=" N SER A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.974A pdb=" N GLN A 353 " --> pdb=" O SER A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 370 through 375 removed outlier: 4.508A pdb=" N CYS A 374 " --> pdb=" O VAL A 370 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE A 375 " --> pdb=" O HIS A 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 370 through 375' Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.586A pdb=" N MET B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.713A pdb=" N GLU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.913A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.702A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.667A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 289 through 295 Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 348 Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 368 through 374 removed outlier: 4.189A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.577A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.673A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 101' Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.966A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.795A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.660A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 289 through 295 Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 3.982A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 removed outlier: 3.552A pdb=" N MET D 82 " --> pdb=" O ASN D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.691A pdb=" N GLU D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 97 through 101' Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.935A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 194 through 197 Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.792A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.664A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 295 Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 337 through 348 Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 368 through 374 removed outlier: 4.035A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 removed outlier: 3.532A pdb=" N MET E 82 " --> pdb=" O ASN E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.685A pdb=" N GLU E 100 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 97 through 101' Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.938A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 172 through 175 Processing helix chain 'E' and resid 181 through 193 Processing helix chain 'E' and resid 194 through 197 Processing helix chain 'E' and resid 202 through 217 removed outlier: 3.776A pdb=" N GLU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 257 removed outlier: 3.650A pdb=" N CYS E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 262 Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 286 through 288 No H-bonds generated for 'chain 'E' and resid 286 through 288' Processing helix chain 'E' and resid 289 through 295 Processing helix chain 'E' and resid 301 through 305 Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 348 Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 368 through 374 removed outlier: 3.998A pdb=" N ARG E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 61 Processing helix chain 'F' and resid 78 through 92 removed outlier: 3.565A pdb=" N MET F 82 " --> pdb=" O ASN F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 101 removed outlier: 3.706A pdb=" N GLU F 100 " --> pdb=" O ALA F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 126 removed outlier: 3.950A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 145 Processing helix chain 'F' and resid 172 through 175 Processing helix chain 'F' and resid 181 through 193 Processing helix chain 'F' and resid 194 through 197 Processing helix chain 'F' and resid 202 through 217 removed outlier: 3.805A pdb=" N GLU F 207 " --> pdb=" O THR F 203 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 233 Processing helix chain 'F' and resid 252 through 257 removed outlier: 3.635A pdb=" N CYS F 257 " --> pdb=" O GLU F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 262 Processing helix chain 'F' and resid 263 through 268 Processing helix chain 'F' and resid 273 through 284 Processing helix chain 'F' and resid 286 through 288 No H-bonds generated for 'chain 'F' and resid 286 through 288' Processing helix chain 'F' and resid 289 through 295 Processing helix chain 'F' and resid 301 through 305 Processing helix chain 'F' and resid 308 through 321 Processing helix chain 'F' and resid 334 through 336 No H-bonds generated for 'chain 'F' and resid 334 through 336' Processing helix chain 'F' and resid 337 through 348 Processing helix chain 'F' and resid 359 through 366 Processing helix chain 'F' and resid 368 through 374 removed outlier: 4.012A pdb=" N ARG F 372 " --> pdb=" O SER F 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 61 Processing helix chain 'G' and resid 78 through 92 removed outlier: 3.559A pdb=" N MET G 82 " --> pdb=" O ASN G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 101 removed outlier: 3.692A pdb=" N GLU G 100 " --> pdb=" O ALA G 97 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N HIS G 101 " --> pdb=" O PRO G 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 97 through 101' Processing helix chain 'G' and resid 112 through 126 removed outlier: 3.964A pdb=" N ARG G 116 " --> pdb=" O PRO G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 145 Processing helix chain 'G' and resid 172 through 175 Processing helix chain 'G' and resid 181 through 193 Processing helix chain 'G' and resid 194 through 197 Processing helix chain 'G' and resid 202 through 217 removed outlier: 3.814A pdb=" N GLU G 207 " --> pdb=" O THR G 203 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE G 208 " --> pdb=" O ALA G 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 233 Processing helix chain 'G' and resid 252 through 257 removed outlier: 3.695A pdb=" N CYS G 257 " --> pdb=" O GLU G 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 262 Processing helix chain 'G' and resid 263 through 268 Processing helix chain 'G' and resid 273 through 284 Processing helix chain 'G' and resid 286 through 288 No H-bonds generated for 'chain 'G' and resid 286 through 288' Processing helix chain 'G' and resid 289 through 295 Processing helix chain 'G' and resid 301 through 305 Processing helix chain 'G' and resid 308 through 321 Processing helix chain 'G' and resid 337 through 348 Processing helix chain 'G' and resid 359 through 366 Processing helix chain 'G' and resid 368 through 374 removed outlier: 3.974A pdb=" N ARG G 372 " --> pdb=" O SER G 368 " (cutoff:3.500A) Processing helix chain 'T' and resid 63 through 77 Processing helix chain 'T' and resid 182 through 192 Processing helix chain 'T' and resid 209 through 220 Processing helix chain 'T' and resid 237 through 249 removed outlier: 3.547A pdb=" N LYS T 249 " --> pdb=" O ALA T 245 " (cutoff:3.500A) Processing helix chain 'T' and resid 265 through 275 Processing helix chain 'T' and resid 276 through 279 Processing helix chain 'T' and resid 295 through 307 Processing helix chain 'T' and resid 321 through 346 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.525A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR A 133 " --> pdb=" O THR A 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 178 removed outlier: 6.379A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 176 through 178 removed outlier: 4.024A pdb=" N GLN C 41 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.903A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ASN B 12 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET B 132 " --> pdb=" O ILE B 357 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE B 357 " --> pdb=" O MET B 132 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 176 through 178 removed outlier: 6.743A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 176 through 178 removed outlier: 3.641A pdb=" N GLN D 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.985A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET C 132 " --> pdb=" O ILE C 357 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE C 357 " --> pdb=" O MET C 132 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 176 through 178 removed outlier: 6.603A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 176 through 178 removed outlier: 3.776A pdb=" N GLN E 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 4.010A pdb=" N THR D 106 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ASN D 12 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE D 357 " --> pdb=" O MET D 132 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 176 through 178 removed outlier: 6.607A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 176 through 178 removed outlier: 3.646A pdb=" N GLN F 41 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 32 removed outlier: 3.989A pdb=" N THR E 106 " --> pdb=" O CYS E 10 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ASN E 12 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE E 357 " --> pdb=" O MET E 132 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'E' and resid 176 through 178 removed outlier: 6.621A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 176 through 178 removed outlier: 3.586A pdb=" N GLN G 41 " --> pdb=" O ALA E 170 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AD4, first strand: chain 'F' and resid 29 through 32 removed outlier: 3.984A pdb=" N THR F 106 " --> pdb=" O CYS F 10 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ASN F 12 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET F 132 " --> pdb=" O ILE F 357 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE F 357 " --> pdb=" O MET F 132 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AD6, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AD7, first strand: chain 'F' and resid 169 through 170 Processing sheet with id=AD8, first strand: chain 'F' and resid 169 through 170 removed outlier: 6.594A pdb=" N ASN F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 238 through 241 Processing sheet with id=AE1, first strand: chain 'G' and resid 29 through 32 removed outlier: 3.980A pdb=" N THR G 106 " --> pdb=" O CYS G 10 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ASN G 12 " --> pdb=" O THR G 106 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET G 132 " --> pdb=" O ILE G 357 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE G 357 " --> pdb=" O MET G 132 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AE3, first strand: chain 'G' and resid 71 through 72 Processing sheet with id=AE4, first strand: chain 'G' and resid 169 through 170 Processing sheet with id=AE5, first strand: chain 'G' and resid 169 through 170 removed outlier: 6.575A pdb=" N ASN G 297 " --> pdb=" O ILE G 330 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 238 through 241 Processing sheet with id=AE7, first strand: chain 'T' and resid 199 through 201 removed outlier: 6.968A pdb=" N LEU T 257 " --> pdb=" O LYS T 286 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N MET T 285 " --> pdb=" O GLY T 316 " (cutoff:3.500A) 1106 hydrogen bonds defined for protein. 2871 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: 5.67 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6853 1.34 - 1.46: 5052 1.46 - 1.58: 10674 1.58 - 1.70: 21 1.70 - 1.82: 271 Bond restraints: 22871 Sorted by residual: bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.95e+00 bond pdb=" CE1 HIC D 73 " pdb=" NE2 HIC D 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.85e+00 bond pdb=" CE1 HIC E 73 " pdb=" NE2 HIC E 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.79e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.75e+00 bond pdb=" CE1 HIC G 73 " pdb=" NE2 HIC G 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.74e+00 ... (remaining 22866 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 29303 1.82 - 3.65: 1397 3.65 - 5.47: 239 5.47 - 7.29: 72 7.29 - 9.11: 16 Bond angle restraints: 31027 Sorted by residual: angle pdb=" C GLY F 46 " pdb=" N MET F 47 " pdb=" CA MET F 47 " ideal model delta sigma weight residual 122.08 128.79 -6.71 1.47e+00 4.63e-01 2.09e+01 angle pdb=" C ARG B 39 " pdb=" N HIS B 40 " pdb=" CA HIS B 40 " ideal model delta sigma weight residual 122.06 113.75 8.31 1.86e+00 2.89e-01 2.00e+01 angle pdb=" C GLY E 46 " pdb=" N MET E 47 " pdb=" CA MET E 47 " ideal model delta sigma weight residual 122.08 128.65 -6.57 1.47e+00 4.63e-01 2.00e+01 angle pdb=" C ASP A 286 " pdb=" N ILE A 287 " pdb=" CA ILE A 287 " ideal model delta sigma weight residual 120.53 126.77 -6.24 1.41e+00 5.03e-01 1.96e+01 angle pdb=" C GLY G 46 " pdb=" N MET G 47 " pdb=" CA MET G 47 " ideal model delta sigma weight residual 122.08 128.55 -6.47 1.47e+00 4.63e-01 1.94e+01 ... (remaining 31022 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.36: 13441 35.36 - 70.73: 350 70.73 - 106.09: 11 106.09 - 141.45: 6 141.45 - 176.81: 6 Dihedral angle restraints: 13814 sinusoidal: 5615 harmonic: 8199 Sorted by residual: dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 123.19 176.81 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP D 401 " pdb=" O5' ADP D 401 " pdb=" PA ADP D 401 " pdb=" O2A ADP D 401 " ideal model delta sinusoidal sigma weight residual 300.00 123.42 176.58 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP F 401 " pdb=" O5' ADP F 401 " pdb=" PA ADP F 401 " pdb=" O2A ADP F 401 " ideal model delta sinusoidal sigma weight residual 300.00 123.76 176.25 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 13811 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2662 0.065 - 0.130: 671 0.130 - 0.195: 105 0.195 - 0.260: 9 0.260 - 0.325: 2 Chirality restraints: 3449 Sorted by residual: chirality pdb=" CB ILE A 151 " pdb=" CA ILE A 151 " pdb=" CG1 ILE A 151 " pdb=" CG2 ILE A 151 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CA CYS A 257 " pdb=" N CYS A 257 " pdb=" C CYS A 257 " pdb=" CB CYS A 257 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CB ILE T 231 " pdb=" CA ILE T 231 " pdb=" CG1 ILE T 231 " pdb=" CG2 ILE T 231 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 3446 not shown) Planarity restraints: 3975 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 335 " 0.023 2.00e-02 2.50e+03 4.63e-02 2.14e+01 pdb=" C ARG B 335 " -0.080 2.00e-02 2.50e+03 pdb=" O ARG B 335 " 0.030 2.00e-02 2.50e+03 pdb=" N LYS B 336 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 49 " 0.022 2.00e-02 2.50e+03 4.51e-02 2.03e+01 pdb=" CD GLN A 49 " -0.078 2.00e-02 2.50e+03 pdb=" OE1 GLN A 49 " 0.030 2.00e-02 2.50e+03 pdb=" NE2 GLN A 49 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 291 " 0.022 2.00e-02 2.50e+03 4.39e-02 1.93e+01 pdb=" C LYS A 291 " -0.076 2.00e-02 2.50e+03 pdb=" O LYS A 291 " 0.029 2.00e-02 2.50e+03 pdb=" N ASP A 292 " 0.025 2.00e-02 2.50e+03 ... (remaining 3972 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 260 2.66 - 3.22: 18930 3.22 - 3.78: 34486 3.78 - 4.34: 48590 4.34 - 4.90: 80243 Nonbonded interactions: 182509 Sorted by model distance: nonbonded pdb=" O1B ADP A 401 " pdb="MG MG A 402 " model vdw 2.105 2.170 nonbonded pdb=" O1B ADP C 401 " pdb="MG MG C 402 " model vdw 2.110 2.170 nonbonded pdb=" O1B ADP F 401 " pdb="MG MG F 402 " model vdw 2.110 2.170 nonbonded pdb=" O1B ADP G 401 " pdb="MG MG G 402 " model vdw 2.112 2.170 nonbonded pdb=" O1B ADP E 401 " pdb="MG MG E 402 " model vdw 2.123 2.170 ... (remaining 182504 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' selection = (chain 'B' and resid 5 through 402) selection = (chain 'C' and resid 5 through 402) selection = (chain 'D' and resid 5 through 402) selection = (chain 'E' and resid 5 through 402) selection = (chain 'F' and resid 5 through 402) selection = (chain 'G' and resid 5 through 402) } 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=0.38 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 24.190 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 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 : 0.005 0.078 22871 Z= 0.263 Angle : 0.926 9.113 31027 Z= 0.525 Chirality : 0.057 0.325 3449 Planarity : 0.008 0.068 3975 Dihedral : 15.119 176.815 8558 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.58 % Allowed : 6.65 % Favored : 89.77 % 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 aren not related in a simple way. whole: -0.20 (0.16), residues: 2794 helix: -0.24 (0.15), residues: 1161 sheet: 0.31 (0.23), residues: 502 loop : 0.01 (0.20), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 210 TYR 0.024 0.002 TYR A 362 PHE 0.020 0.002 PHE A 90 TRP 0.025 0.003 TRP A 356 HIS 0.011 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00498 (22871) covalent geometry : angle 0.92613 (31027) hydrogen bonds : bond 0.16582 ( 1082) hydrogen bonds : angle 6.60609 ( 2871) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 317 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 VAL cc_start: -0.2890 (OUTLIER) cc_final: -0.3233 (t) REVERT: A 82 MET cc_start: 0.8998 (tpt) cc_final: 0.8337 (tpp) REVERT: A 118 LYS cc_start: 0.9268 (tptt) cc_final: 0.8982 (tppt) REVERT: A 121 GLN cc_start: 0.9387 (tt0) cc_final: 0.8905 (tm-30) REVERT: A 132 MET cc_start: 0.9014 (ppp) cc_final: 0.8770 (ppp) REVERT: A 142 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.9032 (tp) REVERT: A 270 GLU cc_start: 0.7019 (mm-30) cc_final: 0.6571 (mt-10) REVERT: A 367 PRO cc_start: 0.8881 (OUTLIER) cc_final: 0.8591 (Cg_endo) REVERT: B 43 VAL cc_start: 0.7363 (OUTLIER) cc_final: 0.6903 (m) REVERT: B 50 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8362 (ptpt) REVERT: B 184 ASP cc_start: 0.9055 (m-30) cc_final: 0.8765 (m-30) REVERT: C 82 MET cc_start: 0.9235 (tpt) cc_final: 0.9019 (tpt) REVERT: D 47 MET cc_start: 0.5180 (ptm) cc_final: 0.4940 (ppp) REVERT: D 147 ARG cc_start: 0.9244 (OUTLIER) cc_final: 0.9040 (ptp90) REVERT: E 57 GLU cc_start: 0.8621 (tt0) cc_final: 0.8348 (tp30) REVERT: E 59 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8261 (tp-100) REVERT: F 117 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8327 (mp0) REVERT: F 147 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.8570 (ptp-170) REVERT: F 269 MET cc_start: 0.9529 (mtm) cc_final: 0.9316 (mtm) REVERT: G 59 GLN cc_start: 0.9391 (OUTLIER) cc_final: 0.9190 (tp40) REVERT: G 149 THR cc_start: 0.9187 (OUTLIER) cc_final: 0.8331 (m) REVERT: G 292 ASP cc_start: 0.9122 (m-30) cc_final: 0.8877 (t0) REVERT: G 325 MET cc_start: 0.7986 (mmt) cc_final: 0.7783 (mmp) REVERT: G 359 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.8761 (tptm) REVERT: T 71 LEU cc_start: 0.8689 (mt) cc_final: 0.8484 (mp) REVERT: T 73 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8451 (pttm) REVERT: T 182 ASP cc_start: 0.8107 (t70) cc_final: 0.7564 (t70) REVERT: T 210 ILE cc_start: 0.8525 (mm) cc_final: 0.8306 (tt) REVERT: T 305 MET cc_start: 0.7912 (mmm) cc_final: 0.7222 (mmm) outliers start: 86 outliers final: 6 residues processed: 392 average time/residue: 0.1816 time to fit residues: 105.5762 Evaluate side-chains 194 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 176 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 367 PRO Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain D residue 147 ARG Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain E residue 59 GLN Chi-restraints excluded: chain F residue 147 ARG Chi-restraints excluded: chain G residue 59 GLN Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 359 LYS Chi-restraints excluded: chain T residue 73 LYS Chi-restraints excluded: chain T residue 173 VAL Chi-restraints excluded: chain T residue 177 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.0170 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 overall best weight: 1.3622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN C 59 GLN D 41 GLN D 59 GLN D 115 ASN E 12 ASN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 GLN E 115 ASN E 296 ASN F 371 HIS G 41 GLN G 59 GLN ** T 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 318 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.069982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.051697 restraints weight = 69578.518| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 3.32 r_work: 0.2726 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2732 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.2727 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22871 Z= 0.153 Angle : 0.609 9.858 31027 Z= 0.299 Chirality : 0.045 0.161 3449 Planarity : 0.004 0.054 3975 Dihedral : 9.728 156.495 3217 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.62 % Allowed : 10.02 % Favored : 88.36 % 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 aren not related in a simple way. whole: 0.73 (0.16), residues: 2794 helix: 0.73 (0.15), residues: 1217 sheet: 0.58 (0.23), residues: 490 loop : 0.37 (0.20), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 372 TYR 0.024 0.001 TYR T 242 PHE 0.016 0.001 PHE C 127 TRP 0.019 0.001 TRP A 356 HIS 0.009 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00350 (22871) covalent geometry : angle 0.60910 (31027) hydrogen bonds : bond 0.03511 ( 1082) hydrogen bonds : angle 4.73628 ( 2871) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 179 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.5479 (tpp) cc_final: 0.5195 (pmm) REVERT: A 82 MET cc_start: 0.8884 (tpt) cc_final: 0.8294 (tpp) REVERT: A 118 LYS cc_start: 0.9312 (tptt) cc_final: 0.9033 (tppt) REVERT: A 132 MET cc_start: 0.9443 (ppp) cc_final: 0.9050 (ppp) REVERT: B 50 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8561 (mmmt) REVERT: B 59 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.8610 (tm-30) REVERT: B 119 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8410 (mtm) REVERT: B 176 MET cc_start: 0.8601 (mmm) cc_final: 0.8022 (mtt) REVERT: C 303 THR cc_start: 0.9315 (OUTLIER) cc_final: 0.8906 (p) REVERT: E 132 MET cc_start: 0.9169 (ppp) cc_final: 0.8778 (ppp) REVERT: E 176 MET cc_start: 0.9028 (mmm) cc_final: 0.8769 (mtp) REVERT: F 64 ILE cc_start: 0.9377 (OUTLIER) cc_final: 0.9091 (pp) REVERT: F 147 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8584 (ptp-170) REVERT: F 355 MET cc_start: 0.9233 (mtt) cc_final: 0.8915 (mtm) REVERT: G 149 THR cc_start: 0.9142 (OUTLIER) cc_final: 0.8479 (m) REVERT: G 292 ASP cc_start: 0.9316 (m-30) cc_final: 0.8912 (t0) REVERT: G 325 MET cc_start: 0.7990 (mmt) cc_final: 0.7693 (mmp) REVERT: T 70 HIS cc_start: 0.6889 (m90) cc_final: 0.6679 (t70) REVERT: T 182 ASP cc_start: 0.9168 (t70) cc_final: 0.8844 (t70) REVERT: T 185 GLU cc_start: 0.9269 (OUTLIER) cc_final: 0.9060 (pp20) REVERT: T 242 TYR cc_start: 0.7879 (m-80) cc_final: 0.7272 (m-80) REVERT: T 274 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8272 (mt-10) REVERT: T 288 ASP cc_start: 0.8581 (t0) cc_final: 0.8256 (t0) REVERT: T 305 MET cc_start: 0.8896 (mmm) cc_final: 0.8439 (mmm) outliers start: 39 outliers final: 17 residues processed: 211 average time/residue: 0.1539 time to fit residues: 51.3195 Evaluate side-chains 181 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain E residue 12 ASN Chi-restraints excluded: chain E residue 359 LYS Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 147 ARG Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain T residue 173 VAL Chi-restraints excluded: chain T residue 185 GLU Chi-restraints excluded: chain T residue 318 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 275 optimal weight: 10.0000 chunk 132 optimal weight: 0.8980 chunk 263 optimal weight: 0.0270 chunk 65 optimal weight: 4.9990 chunk 160 optimal weight: 0.9990 chunk 241 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 257 optimal weight: 7.9990 chunk 131 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 overall best weight: 0.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 GLN D 49 GLN D 115 ASN T 318 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.069020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.050583 restraints weight = 69010.500| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 3.32 r_work: 0.2717 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.2722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22871 Z= 0.121 Angle : 0.560 9.777 31027 Z= 0.271 Chirality : 0.043 0.151 3449 Planarity : 0.004 0.052 3975 Dihedral : 7.841 126.770 3185 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.29 % Allowed : 10.64 % Favored : 88.07 % 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 aren not related in a simple way. whole: 1.01 (0.17), residues: 2794 helix: 1.05 (0.16), residues: 1212 sheet: 0.68 (0.23), residues: 495 loop : 0.43 (0.21), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 39 TYR 0.018 0.001 TYR T 242 PHE 0.024 0.001 PHE T 229 TRP 0.011 0.001 TRP A 356 HIS 0.012 0.001 HIS T 318 Details of bonding type rmsd covalent geometry : bond 0.00275 (22871) covalent geometry : angle 0.56044 (31027) hydrogen bonds : bond 0.02971 ( 1082) hydrogen bonds : angle 4.43336 ( 2871) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 159 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.5413 (tpp) cc_final: 0.5052 (pmm) REVERT: A 82 MET cc_start: 0.8928 (tpt) cc_final: 0.8388 (tpp) REVERT: A 118 LYS cc_start: 0.9340 (tptt) cc_final: 0.8972 (tppt) REVERT: A 132 MET cc_start: 0.9447 (ppp) cc_final: 0.9013 (ppp) REVERT: B 50 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8481 (ptpt) REVERT: B 59 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.8594 (tm-30) REVERT: B 176 MET cc_start: 0.8582 (mmm) cc_final: 0.7940 (mtt) REVERT: C 303 THR cc_start: 0.9308 (OUTLIER) cc_final: 0.8910 (p) REVERT: D 47 MET cc_start: 0.5316 (tmm) cc_final: 0.5067 (ppp) REVERT: D 305 MET cc_start: 0.9547 (mmm) cc_final: 0.9310 (mmm) REVERT: E 12 ASN cc_start: 0.8998 (OUTLIER) cc_final: 0.8731 (m-40) REVERT: E 176 MET cc_start: 0.9065 (mmm) cc_final: 0.8783 (mtp) REVERT: F 64 ILE cc_start: 0.9366 (OUTLIER) cc_final: 0.9075 (pp) REVERT: F 147 ARG cc_start: 0.9060 (OUTLIER) cc_final: 0.8751 (ptp-170) REVERT: G 149 THR cc_start: 0.9145 (OUTLIER) cc_final: 0.8523 (m) REVERT: G 292 ASP cc_start: 0.9340 (m-30) cc_final: 0.8966 (t0) REVERT: G 325 MET cc_start: 0.7920 (mmt) cc_final: 0.7645 (mmp) REVERT: T 182 ASP cc_start: 0.9127 (t70) cc_final: 0.8801 (t70) REVERT: T 185 GLU cc_start: 0.9321 (OUTLIER) cc_final: 0.9099 (pp20) REVERT: T 188 GLU cc_start: 0.9116 (tt0) cc_final: 0.8813 (tp30) REVERT: T 274 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8174 (mp0) REVERT: T 288 ASP cc_start: 0.8473 (t0) cc_final: 0.8105 (t0) REVERT: T 305 MET cc_start: 0.8883 (mmm) cc_final: 0.8682 (mmm) outliers start: 31 outliers final: 14 residues processed: 186 average time/residue: 0.1259 time to fit residues: 38.0583 Evaluate side-chains 175 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 12 ASN Chi-restraints excluded: chain E residue 359 LYS Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 147 ARG Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain T residue 173 VAL Chi-restraints excluded: chain T residue 185 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 57 optimal weight: 0.6980 chunk 258 optimal weight: 0.0570 chunk 10 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 164 optimal weight: 0.0670 chunk 236 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 78 optimal weight: 0.1980 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 173 HIS D 173 HIS E 115 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.070307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.051775 restraints weight = 68595.058| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 3.40 r_work: 0.2744 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2747 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| r_final: 0.2748 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22871 Z= 0.085 Angle : 0.532 9.149 31027 Z= 0.251 Chirality : 0.042 0.147 3449 Planarity : 0.004 0.050 3975 Dihedral : 6.177 82.845 3185 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.96 % Allowed : 11.27 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.17), residues: 2794 helix: 1.24 (0.16), residues: 1222 sheet: 0.74 (0.23), residues: 491 loop : 0.54 (0.21), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 39 TYR 0.014 0.001 TYR T 242 PHE 0.012 0.001 PHE T 229 TRP 0.014 0.001 TRP A 356 HIS 0.006 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00196 (22871) covalent geometry : angle 0.53248 (31027) hydrogen bonds : bond 0.02501 ( 1082) hydrogen bonds : angle 4.19677 ( 2871) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 171 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.5417 (tpp) cc_final: 0.5108 (pmm) REVERT: A 82 MET cc_start: 0.8874 (tpt) cc_final: 0.8217 (tpp) REVERT: A 118 LYS cc_start: 0.9334 (tptt) cc_final: 0.8947 (tppt) REVERT: A 132 MET cc_start: 0.9389 (ppp) cc_final: 0.9032 (ppp) REVERT: B 50 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8509 (ptpt) REVERT: B 59 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.8602 (tm-30) REVERT: B 119 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8288 (mtm) REVERT: B 176 MET cc_start: 0.8594 (mmm) cc_final: 0.7849 (mtt) REVERT: C 237 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8669 (mm-30) REVERT: C 303 THR cc_start: 0.9257 (OUTLIER) cc_final: 0.8842 (p) REVERT: E 132 MET cc_start: 0.9100 (ppp) cc_final: 0.8773 (ppp) REVERT: E 176 MET cc_start: 0.9072 (mmm) cc_final: 0.8821 (mtp) REVERT: F 64 ILE cc_start: 0.9401 (OUTLIER) cc_final: 0.9175 (pp) REVERT: F 147 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8704 (ptp-170) REVERT: G 292 ASP cc_start: 0.9305 (m-30) cc_final: 0.8922 (t0) REVERT: T 182 ASP cc_start: 0.9111 (t70) cc_final: 0.8798 (t70) REVERT: T 185 GLU cc_start: 0.9358 (pt0) cc_final: 0.9105 (pp20) REVERT: T 188 GLU cc_start: 0.9128 (tt0) cc_final: 0.8843 (tp30) REVERT: T 288 ASP cc_start: 0.8329 (t0) cc_final: 0.7864 (t0) outliers start: 23 outliers final: 14 residues processed: 190 average time/residue: 0.1298 time to fit residues: 40.4701 Evaluate side-chains 174 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 154 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 359 LYS Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 147 ARG Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain T residue 173 VAL Chi-restraints excluded: chain T residue 304 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 82 optimal weight: 0.9990 chunk 127 optimal weight: 0.5980 chunk 21 optimal weight: 4.9990 chunk 231 optimal weight: 8.9990 chunk 76 optimal weight: 0.1980 chunk 66 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 253 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 181 optimal weight: 0.6980 chunk 276 optimal weight: 9.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 ASN E 12 ASN E 115 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.068683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.050206 restraints weight = 69137.815| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 3.35 r_work: 0.2701 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2706 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2706 r_free = 0.2706 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2705 r_free = 0.2705 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.2705 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22871 Z= 0.123 Angle : 0.553 9.367 31027 Z= 0.262 Chirality : 0.043 0.142 3449 Planarity : 0.004 0.050 3975 Dihedral : 5.880 75.478 3183 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.54 % Allowed : 11.60 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.17), residues: 2794 helix: 1.39 (0.16), residues: 1217 sheet: 0.72 (0.23), residues: 497 loop : 0.57 (0.21), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG T 340 TYR 0.010 0.001 TYR T 317 PHE 0.010 0.001 PHE A 255 TRP 0.010 0.001 TRP A 79 HIS 0.004 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00286 (22871) covalent geometry : angle 0.55301 (31027) hydrogen bonds : bond 0.02734 ( 1082) hydrogen bonds : angle 4.13653 ( 2871) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 156 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.5631 (tpp) cc_final: 0.5174 (pmm) REVERT: A 82 MET cc_start: 0.8974 (tpt) cc_final: 0.8396 (tpp) REVERT: A 118 LYS cc_start: 0.9327 (tptt) cc_final: 0.9088 (tppt) REVERT: A 132 MET cc_start: 0.9394 (ppp) cc_final: 0.9063 (ppp) REVERT: B 50 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8539 (ptpt) REVERT: B 59 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.8605 (tm-30) REVERT: B 176 MET cc_start: 0.8625 (mmm) cc_final: 0.7530 (mtt) REVERT: B 372 ARG cc_start: 0.8697 (mtm-85) cc_final: 0.8383 (mtm180) REVERT: C 176 MET cc_start: 0.9192 (mmm) cc_final: 0.8865 (mtp) REVERT: C 303 THR cc_start: 0.9232 (OUTLIER) cc_final: 0.8785 (p) REVERT: D 283 MET cc_start: 0.9057 (mmm) cc_final: 0.8735 (mmm) REVERT: E 176 MET cc_start: 0.9079 (mmm) cc_final: 0.8808 (mtp) REVERT: F 64 ILE cc_start: 0.9398 (OUTLIER) cc_final: 0.9105 (pp) REVERT: F 147 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.7939 (ptm160) REVERT: F 283 MET cc_start: 0.9015 (mmt) cc_final: 0.8296 (mpp) REVERT: G 292 ASP cc_start: 0.9320 (m-30) cc_final: 0.8947 (t0) REVERT: G 305 MET cc_start: 0.9417 (mmt) cc_final: 0.9185 (mmt) REVERT: G 325 MET cc_start: 0.8806 (mmp) cc_final: 0.8382 (mmt) REVERT: G 359 LYS cc_start: 0.9322 (OUTLIER) cc_final: 0.8897 (tptm) REVERT: T 182 ASP cc_start: 0.9107 (t70) cc_final: 0.8822 (t70) REVERT: T 185 GLU cc_start: 0.9332 (pt0) cc_final: 0.9094 (pp20) REVERT: T 188 GLU cc_start: 0.9135 (tt0) cc_final: 0.8856 (tp30) REVERT: T 288 ASP cc_start: 0.8300 (t0) cc_final: 0.7804 (t0) REVERT: T 305 MET cc_start: 0.8673 (mmm) cc_final: 0.8053 (tpp) outliers start: 37 outliers final: 20 residues processed: 187 average time/residue: 0.1462 time to fit residues: 44.6775 Evaluate side-chains 180 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 359 LYS Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 147 ARG Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 359 LYS Chi-restraints excluded: chain T residue 173 VAL Chi-restraints excluded: chain T residue 304 SER Chi-restraints excluded: chain T residue 339 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 249 optimal weight: 0.8980 chunk 246 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 173 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 232 optimal weight: 0.5980 chunk 137 optimal weight: 0.0170 chunk 237 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 188 optimal weight: 4.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 ASN E 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.069213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.050744 restraints weight = 69180.289| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 3.39 r_work: 0.2719 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2723 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.2723 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 22871 Z= 0.095 Angle : 0.536 10.357 31027 Z= 0.251 Chirality : 0.043 0.142 3449 Planarity : 0.003 0.050 3975 Dihedral : 5.617 68.129 3183 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.37 % Allowed : 11.89 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.17), residues: 2794 helix: 1.43 (0.16), residues: 1228 sheet: 0.76 (0.23), residues: 488 loop : 0.62 (0.21), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG T 340 TYR 0.009 0.001 TYR T 317 PHE 0.008 0.001 PHE T 315 TRP 0.009 0.001 TRP C 79 HIS 0.005 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00221 (22871) covalent geometry : angle 0.53627 (31027) hydrogen bonds : bond 0.02490 ( 1082) hydrogen bonds : angle 4.06667 ( 2871) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 163 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8975 (tpt) cc_final: 0.8382 (tpp) REVERT: A 118 LYS cc_start: 0.9310 (tptt) cc_final: 0.8948 (tppt) REVERT: A 132 MET cc_start: 0.9386 (ppp) cc_final: 0.8982 (ppp) REVERT: A 352 PHE cc_start: 0.8608 (t80) cc_final: 0.8029 (t80) REVERT: B 50 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8506 (ptpt) REVERT: B 59 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8626 (tm-30) REVERT: B 176 MET cc_start: 0.8606 (mmm) cc_final: 0.7464 (mtt) REVERT: C 176 MET cc_start: 0.9167 (mmm) cc_final: 0.8848 (mtp) REVERT: C 303 THR cc_start: 0.9179 (OUTLIER) cc_final: 0.8695 (p) REVERT: D 283 MET cc_start: 0.9009 (mmm) cc_final: 0.8668 (mmm) REVERT: E 176 MET cc_start: 0.9068 (mmm) cc_final: 0.8788 (mtp) REVERT: F 64 ILE cc_start: 0.9384 (OUTLIER) cc_final: 0.9082 (pp) REVERT: F 147 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.8818 (ptp-170) REVERT: G 292 ASP cc_start: 0.9320 (m-30) cc_final: 0.8959 (t0) REVERT: G 325 MET cc_start: 0.8710 (mmp) cc_final: 0.8436 (tpp) REVERT: T 182 ASP cc_start: 0.9105 (t70) cc_final: 0.8809 (t70) REVERT: T 185 GLU cc_start: 0.9327 (pt0) cc_final: 0.9087 (pp20) REVERT: T 188 GLU cc_start: 0.9135 (tt0) cc_final: 0.8856 (tp30) REVERT: T 288 ASP cc_start: 0.8255 (t0) cc_final: 0.7732 (t0) REVERT: T 305 MET cc_start: 0.8669 (mmm) cc_final: 0.8132 (tpp) REVERT: T 332 MET cc_start: 0.8929 (mmm) cc_final: 0.8589 (mmm) outliers start: 33 outliers final: 17 residues processed: 192 average time/residue: 0.1288 time to fit residues: 40.5710 Evaluate side-chains 179 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 359 LYS Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 147 ARG Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain T residue 173 VAL Chi-restraints excluded: chain T residue 320 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 236 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 252 optimal weight: 7.9990 chunk 210 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 277 optimal weight: 4.9990 chunk 170 optimal weight: 0.9980 chunk 172 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN D 115 ASN E 12 ASN E 296 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.067986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.049757 restraints weight = 68669.467| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 3.36 r_work: 0.2672 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2677 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2677 r_free = 0.2677 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2677 r_free = 0.2677 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.2677 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 22871 Z= 0.155 Angle : 0.578 12.927 31027 Z= 0.271 Chirality : 0.044 0.267 3449 Planarity : 0.004 0.049 3975 Dihedral : 5.669 75.252 3182 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.54 % Allowed : 12.31 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.17), residues: 2794 helix: 1.52 (0.16), residues: 1217 sheet: 0.58 (0.23), residues: 502 loop : 0.62 (0.21), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG T 340 TYR 0.010 0.001 TYR E 279 PHE 0.011 0.001 PHE D 31 TRP 0.011 0.001 TRP A 79 HIS 0.005 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00358 (22871) covalent geometry : angle 0.57819 (31027) hydrogen bonds : bond 0.02863 ( 1082) hydrogen bonds : angle 4.12978 ( 2871) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 158 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.5265 (tpp) cc_final: 0.4836 (pmm) REVERT: A 82 MET cc_start: 0.9001 (tpt) cc_final: 0.8392 (tpp) REVERT: A 118 LYS cc_start: 0.9367 (tptt) cc_final: 0.9036 (tppt) REVERT: A 132 MET cc_start: 0.9415 (ppp) cc_final: 0.9069 (ppp) REVERT: B 50 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8512 (ptpt) REVERT: B 59 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8533 (tm-30) REVERT: B 176 MET cc_start: 0.8622 (mmm) cc_final: 0.7654 (mtt) REVERT: C 176 MET cc_start: 0.9155 (mmm) cc_final: 0.8843 (mtp) REVERT: C 303 THR cc_start: 0.9226 (OUTLIER) cc_final: 0.8739 (p) REVERT: D 283 MET cc_start: 0.9046 (mmm) cc_final: 0.8651 (mmm) REVERT: E 283 MET cc_start: 0.9058 (mmt) cc_final: 0.8605 (mmm) REVERT: F 64 ILE cc_start: 0.9408 (OUTLIER) cc_final: 0.9104 (pp) REVERT: F 147 ARG cc_start: 0.9083 (OUTLIER) cc_final: 0.8042 (ptm160) REVERT: F 227 MET cc_start: 0.9349 (tpp) cc_final: 0.9101 (mtp) REVERT: G 292 ASP cc_start: 0.9338 (m-30) cc_final: 0.9002 (t0) REVERT: G 305 MET cc_start: 0.9422 (mmt) cc_final: 0.9199 (mmt) REVERT: G 325 MET cc_start: 0.8690 (mmp) cc_final: 0.8412 (tpp) REVERT: G 359 LYS cc_start: 0.9318 (OUTLIER) cc_final: 0.8848 (tptm) REVERT: T 81 ARG cc_start: 0.5808 (OUTLIER) cc_final: 0.5110 (mmp-170) REVERT: T 182 ASP cc_start: 0.9096 (t70) cc_final: 0.8819 (t70) REVERT: T 185 GLU cc_start: 0.9343 (pt0) cc_final: 0.9078 (pp20) REVERT: T 242 TYR cc_start: 0.8162 (m-10) cc_final: 0.7776 (m-10) REVERT: T 288 ASP cc_start: 0.8321 (t0) cc_final: 0.7613 (t0) REVERT: T 305 MET cc_start: 0.8709 (mmm) cc_final: 0.8181 (tpp) outliers start: 37 outliers final: 26 residues processed: 190 average time/residue: 0.1326 time to fit residues: 40.5383 Evaluate side-chains 188 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 155 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 359 LYS Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 147 ARG Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 269 MET Chi-restraints excluded: chain G residue 359 LYS Chi-restraints excluded: chain T residue 81 ARG Chi-restraints excluded: chain T residue 173 VAL Chi-restraints excluded: chain T residue 304 SER Chi-restraints excluded: chain T residue 320 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 71 optimal weight: 0.3980 chunk 136 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 274 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 257 optimal weight: 0.8980 chunk 216 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 ASN E 12 ASN G 12 ASN T 321 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.068234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.049730 restraints weight = 69247.673| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 3.40 r_work: 0.2682 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2686 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.2686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22871 Z= 0.129 Angle : 0.557 11.987 31027 Z= 0.262 Chirality : 0.044 0.209 3449 Planarity : 0.003 0.049 3975 Dihedral : 5.568 73.166 3182 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.46 % Allowed : 12.39 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.17), residues: 2794 helix: 1.53 (0.16), residues: 1217 sheet: 0.60 (0.23), residues: 502 loop : 0.62 (0.21), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG T 340 TYR 0.010 0.001 TYR T 317 PHE 0.010 0.001 PHE D 31 TRP 0.010 0.001 TRP A 79 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00300 (22871) covalent geometry : angle 0.55704 (31027) hydrogen bonds : bond 0.02677 ( 1082) hydrogen bonds : angle 4.08852 ( 2871) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.5190 (tpp) cc_final: 0.4908 (pmm) REVERT: A 82 MET cc_start: 0.8947 (tpt) cc_final: 0.8322 (tpp) REVERT: A 118 LYS cc_start: 0.9368 (tptt) cc_final: 0.9045 (tppt) REVERT: A 132 MET cc_start: 0.9343 (ppp) cc_final: 0.9004 (ppp) REVERT: B 50 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8427 (ptpt) REVERT: B 59 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8589 (tm-30) REVERT: B 132 MET cc_start: 0.8836 (ppp) cc_final: 0.8356 (ppp) REVERT: C 176 MET cc_start: 0.9149 (mmm) cc_final: 0.8832 (mtp) REVERT: C 303 THR cc_start: 0.9227 (OUTLIER) cc_final: 0.8735 (p) REVERT: D 283 MET cc_start: 0.9047 (mmm) cc_final: 0.8653 (mmm) REVERT: E 176 MET cc_start: 0.9118 (mmm) cc_final: 0.8875 (mtp) REVERT: F 64 ILE cc_start: 0.9399 (OUTLIER) cc_final: 0.9090 (pp) REVERT: F 227 MET cc_start: 0.9350 (tpp) cc_final: 0.9052 (mtp) REVERT: G 292 ASP cc_start: 0.9344 (m-30) cc_final: 0.9017 (t0) REVERT: G 299 MET cc_start: 0.9028 (mtt) cc_final: 0.8807 (mtp) REVERT: G 305 MET cc_start: 0.9440 (mmt) cc_final: 0.9087 (mmt) REVERT: G 325 MET cc_start: 0.8681 (mmp) cc_final: 0.8391 (tpp) REVERT: T 81 ARG cc_start: 0.5966 (OUTLIER) cc_final: 0.5190 (mmp-170) REVERT: T 182 ASP cc_start: 0.9081 (t70) cc_final: 0.8804 (t70) REVERT: T 185 GLU cc_start: 0.9326 (pt0) cc_final: 0.9065 (pp20) REVERT: T 288 ASP cc_start: 0.8279 (t0) cc_final: 0.7547 (t0) REVERT: T 305 MET cc_start: 0.8707 (mmm) cc_final: 0.8202 (tpp) outliers start: 35 outliers final: 22 residues processed: 183 average time/residue: 0.1295 time to fit residues: 38.6283 Evaluate side-chains 181 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 12 ASN Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 359 LYS Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain G residue 269 MET Chi-restraints excluded: chain T residue 81 ARG Chi-restraints excluded: chain T residue 173 VAL Chi-restraints excluded: chain T residue 208 ILE Chi-restraints excluded: chain T residue 304 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 194 optimal weight: 1.9990 chunk 237 optimal weight: 9.9990 chunk 41 optimal weight: 0.0980 chunk 259 optimal weight: 2.9990 chunk 250 optimal weight: 5.9990 chunk 179 optimal weight: 2.9990 chunk 271 optimal weight: 0.9990 chunk 180 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 278 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN E 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.068458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.049979 restraints weight = 69257.321| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 3.40 r_work: 0.2688 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2693 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2693 r_free = 0.2693 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2693 r_free = 0.2693 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.2693 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22871 Z= 0.113 Angle : 0.562 12.521 31027 Z= 0.260 Chirality : 0.043 0.208 3449 Planarity : 0.003 0.050 3975 Dihedral : 5.380 72.663 3178 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.25 % Allowed : 12.47 % Favored : 86.28 % 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 aren not related in a simple way. whole: 1.49 (0.17), residues: 2794 helix: 1.58 (0.16), residues: 1217 sheet: 0.61 (0.23), residues: 502 loop : 0.68 (0.21), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG T 340 TYR 0.016 0.001 TYR T 225 PHE 0.009 0.001 PHE D 31 TRP 0.009 0.001 TRP A 79 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00264 (22871) covalent geometry : angle 0.56215 (31027) hydrogen bonds : bond 0.02600 ( 1082) hydrogen bonds : angle 4.03531 ( 2871) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 157 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.5204 (tpp) cc_final: 0.4917 (pmm) REVERT: A 82 MET cc_start: 0.8947 (tpt) cc_final: 0.8319 (tpp) REVERT: A 118 LYS cc_start: 0.9383 (tptt) cc_final: 0.9067 (tppt) REVERT: A 132 MET cc_start: 0.9352 (ppp) cc_final: 0.9022 (ppp) REVERT: B 50 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8458 (ptpt) REVERT: B 59 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8571 (tm-30) REVERT: B 132 MET cc_start: 0.8842 (ppp) cc_final: 0.8358 (ppp) REVERT: B 176 MET cc_start: 0.8624 (mmm) cc_final: 0.7868 (mtt) REVERT: C 176 MET cc_start: 0.9147 (mmm) cc_final: 0.8831 (mtp) REVERT: D 283 MET cc_start: 0.9037 (mmm) cc_final: 0.8653 (mmm) REVERT: E 176 MET cc_start: 0.9121 (mmm) cc_final: 0.8876 (mtp) REVERT: F 64 ILE cc_start: 0.9397 (OUTLIER) cc_final: 0.9090 (pp) REVERT: F 227 MET cc_start: 0.9356 (tpp) cc_final: 0.9052 (mtp) REVERT: G 292 ASP cc_start: 0.9329 (m-30) cc_final: 0.9006 (t0) REVERT: G 305 MET cc_start: 0.9433 (mmt) cc_final: 0.9134 (mmt) REVERT: G 325 MET cc_start: 0.8683 (mmp) cc_final: 0.8372 (tpp) REVERT: T 81 ARG cc_start: 0.5891 (OUTLIER) cc_final: 0.5058 (mmp-170) REVERT: T 182 ASP cc_start: 0.9083 (t70) cc_final: 0.8813 (t70) REVERT: T 185 GLU cc_start: 0.9341 (pt0) cc_final: 0.9081 (pp20) REVERT: T 238 ASP cc_start: 0.8860 (m-30) cc_final: 0.8630 (t0) REVERT: T 288 ASP cc_start: 0.8287 (t0) cc_final: 0.7552 (t0) REVERT: T 305 MET cc_start: 0.8661 (mmm) cc_final: 0.8154 (tpp) outliers start: 30 outliers final: 20 residues processed: 181 average time/residue: 0.1436 time to fit residues: 42.0759 Evaluate side-chains 180 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 359 LYS Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain G residue 269 MET Chi-restraints excluded: chain T residue 81 ARG Chi-restraints excluded: chain T residue 173 VAL Chi-restraints excluded: chain T residue 208 ILE Chi-restraints excluded: chain T residue 304 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 281 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 chunk 153 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 204 optimal weight: 4.9990 chunk 218 optimal weight: 0.7980 chunk 145 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN D 115 ASN E 12 ASN F 115 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.066309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.048164 restraints weight = 69402.290| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 3.33 r_work: 0.2633 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2641 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2641 r_free = 0.2641 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2641 r_free = 0.2641 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.2641 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 22871 Z= 0.229 Angle : 0.640 12.960 31027 Z= 0.304 Chirality : 0.046 0.203 3449 Planarity : 0.004 0.048 3975 Dihedral : 5.670 81.484 3177 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.29 % Allowed : 12.52 % Favored : 86.20 % 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 aren not related in a simple way. whole: 1.29 (0.17), residues: 2794 helix: 1.44 (0.16), residues: 1220 sheet: 0.52 (0.23), residues: 501 loop : 0.52 (0.21), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG T 340 TYR 0.018 0.001 TYR T 225 PHE 0.015 0.001 PHE D 31 TRP 0.014 0.001 TRP A 79 HIS 0.004 0.001 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.00526 (22871) covalent geometry : angle 0.64025 (31027) hydrogen bonds : bond 0.03297 ( 1082) hydrogen bonds : angle 4.28284 ( 2871) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.9004 (tpt) cc_final: 0.8353 (tpp) REVERT: A 118 LYS cc_start: 0.9415 (tptt) cc_final: 0.9055 (tppt) REVERT: A 132 MET cc_start: 0.9392 (ppp) cc_final: 0.9043 (ppp) REVERT: A 325 MET cc_start: 0.8664 (mmt) cc_final: 0.8416 (mmt) REVERT: B 50 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8420 (ptpt) REVERT: B 59 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8414 (tm-30) REVERT: B 118 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8853 (mmtm) REVERT: B 132 MET cc_start: 0.8822 (ppp) cc_final: 0.8420 (ppp) REVERT: B 176 MET cc_start: 0.8607 (mmm) cc_final: 0.7917 (mtt) REVERT: B 299 MET cc_start: 0.9256 (mtp) cc_final: 0.8988 (mtp) REVERT: C 176 MET cc_start: 0.9164 (mmm) cc_final: 0.8891 (mtp) REVERT: D 283 MET cc_start: 0.9084 (mmm) cc_final: 0.8703 (mmm) REVERT: E 176 MET cc_start: 0.9147 (mmm) cc_final: 0.8885 (mtp) REVERT: E 305 MET cc_start: 0.9425 (mmm) cc_final: 0.9137 (mmm) REVERT: F 64 ILE cc_start: 0.9455 (OUTLIER) cc_final: 0.9130 (pp) REVERT: G 292 ASP cc_start: 0.9335 (m-30) cc_final: 0.9034 (t70) REVERT: G 305 MET cc_start: 0.9477 (mmt) cc_final: 0.8945 (mmt) REVERT: G 325 MET cc_start: 0.8717 (mmp) cc_final: 0.8448 (tpp) REVERT: G 359 LYS cc_start: 0.9337 (OUTLIER) cc_final: 0.8834 (tptm) REVERT: T 81 ARG cc_start: 0.5560 (OUTLIER) cc_final: 0.4796 (mmp-170) REVERT: T 182 ASP cc_start: 0.9076 (t70) cc_final: 0.8827 (t70) REVERT: T 185 GLU cc_start: 0.9361 (pt0) cc_final: 0.9116 (pp20) REVERT: T 288 ASP cc_start: 0.8348 (t0) cc_final: 0.7516 (t0) REVERT: T 305 MET cc_start: 0.8614 (mmm) cc_final: 0.8161 (tpp) REVERT: T 321 GLN cc_start: 0.9169 (mm-40) cc_final: 0.8898 (mm110) REVERT: T 322 GLN cc_start: 0.8240 (mp-120) cc_final: 0.7782 (pt0) outliers start: 31 outliers final: 22 residues processed: 175 average time/residue: 0.1565 time to fit residues: 44.4786 Evaluate side-chains 177 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 359 LYS Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain G residue 269 MET Chi-restraints excluded: chain G residue 359 LYS Chi-restraints excluded: chain T residue 81 ARG Chi-restraints excluded: chain T residue 173 VAL Chi-restraints excluded: chain T residue 208 ILE Chi-restraints excluded: chain T residue 304 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 23 optimal weight: 0.9980 chunk 201 optimal weight: 0.0470 chunk 131 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 228 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 242 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 129 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 ASN F 115 ASN T 321 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.067898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.049757 restraints weight = 68394.407| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 3.32 r_work: 0.2676 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2683 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2683 r_free = 0.2683 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2683 r_free = 0.2683 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.2683 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22871 Z= 0.115 Angle : 0.571 13.058 31027 Z= 0.266 Chirality : 0.043 0.199 3449 Planarity : 0.003 0.048 3975 Dihedral : 5.439 73.716 3177 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.08 % Allowed : 12.93 % Favored : 85.99 % 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 aren not related in a simple way. whole: 1.44 (0.17), residues: 2794 helix: 1.57 (0.16), residues: 1217 sheet: 0.51 (0.23), residues: 502 loop : 0.65 (0.21), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG T 340 TYR 0.016 0.001 TYR T 225 PHE 0.010 0.001 PHE D 31 TRP 0.010 0.001 TRP C 79 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00270 (22871) covalent geometry : angle 0.57109 (31027) hydrogen bonds : bond 0.02706 ( 1082) hydrogen bonds : angle 4.09320 ( 2871) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4226.80 seconds wall clock time: 73 minutes 25.87 seconds (4405.87 seconds total)