Starting phenix.real_space_refine on Thu Jun 19 16:52:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f8t_28936/06_2025/8f8t_28936.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f8t_28936/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8f8t_28936/06_2025/8f8t_28936.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f8t_28936/06_2025/8f8t_28936.map" model { file = "/net/cci-nas-00/data/ceres_data/8f8t_28936/06_2025/8f8t_28936.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f8t_28936/06_2025/8f8t_28936.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.67, per 1000 atoms: 0.66 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: 5.21 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 3.40 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: 8.59 Time building geometry restraints manager: 6.26 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 375 or resid 401 through 402)) selection = (chain 'C' and (resid 5 through 375 or resid 401 through 402)) selection = (chain 'D' and (resid 5 through 375 or resid 401 through 402)) selection = (chain 'E' and (resid 5 through 375 or resid 401 through 402)) selection = (chain 'F' and (resid 5 through 375 or resid 401 through 402)) selection = (chain 'G' and (resid 5 through 375 or resid 401 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: 4.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.830 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 52.990 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.120 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: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.800 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.025 0.003 TRP A 356 HIS 0.011 0.001 HIS A 87 PHE 0.020 0.002 PHE A 90 TYR 0.024 0.002 TYR A 362 ARG 0.006 0.001 ARG A 210 Details of bonding type rmsd hydrogen bonds : bond 0.16582 ( 1082) hydrogen bonds : angle 6.60609 ( 2871) covalent geometry : bond 0.00498 (22871) covalent geometry : angle 0.92613 (31027) *********************** 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 : 2.631 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: 0.4059 time to fit residues: 235.8097 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 : 2.480 ------------------------------------------------------------------------------- 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 238 optimal weight: 20.0000 chunk 213 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 144 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 221 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 164 optimal weight: 0.3980 chunk 256 optimal weight: 10.0000 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN B 121 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 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 = 0.3285 r_free = 0.3285 target = 0.069775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.051496 restraints weight = 69543.337| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 3.31 r_work: 0.2720 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2725 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2725 r_free = 0.2725 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 = 0.2719 r_free = 0.2719 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.2719 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22871 Z= 0.162 Angle : 0.613 9.660 31027 Z= 0.302 Chirality : 0.045 0.160 3449 Planarity : 0.004 0.054 3975 Dihedral : 9.824 158.322 3217 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.66 % Allowed : 9.94 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.16), residues: 2794 helix: 0.72 (0.15), residues: 1217 sheet: 0.58 (0.23), residues: 490 loop : 0.34 (0.20), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 356 HIS 0.009 0.001 HIS B 161 PHE 0.016 0.001 PHE C 127 TYR 0.024 0.001 TYR T 242 ARG 0.007 0.000 ARG D 372 Details of bonding type rmsd hydrogen bonds : bond 0.03495 ( 1082) hydrogen bonds : angle 4.74673 ( 2871) covalent geometry : bond 0.00370 (22871) covalent geometry : angle 0.61308 (31027) *********************** 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 217 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 177 time to evaluate : 2.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.5452 (tpp) cc_final: 0.5182 (pmm) REVERT: A 82 MET cc_start: 0.8891 (tpt) cc_final: 0.8305 (tpp) REVERT: A 118 LYS cc_start: 0.9315 (tptt) cc_final: 0.9038 (tppt) REVERT: A 132 MET cc_start: 0.9442 (ppp) cc_final: 0.9037 (ppp) REVERT: B 50 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8515 (mmmt) REVERT: B 59 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.8598 (tm-30) REVERT: B 119 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8426 (mtm) REVERT: B 176 MET cc_start: 0.8603 (mmm) cc_final: 0.8003 (mtt) REVERT: C 303 THR cc_start: 0.9323 (OUTLIER) cc_final: 0.8922 (p) REVERT: E 132 MET cc_start: 0.9174 (ppp) cc_final: 0.8781 (ppp) REVERT: E 176 MET cc_start: 0.9033 (mmm) cc_final: 0.8759 (mtp) REVERT: F 64 ILE cc_start: 0.9381 (OUTLIER) cc_final: 0.9094 (pp) REVERT: F 147 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.8581 (ptp-170) REVERT: F 355 MET cc_start: 0.9236 (mtt) cc_final: 0.8917 (mtm) REVERT: G 149 THR cc_start: 0.9146 (OUTLIER) cc_final: 0.8474 (m) REVERT: G 292 ASP cc_start: 0.9318 (m-30) cc_final: 0.8917 (t0) REVERT: G 325 MET cc_start: 0.7992 (mmt) cc_final: 0.7694 (mmp) REVERT: T 182 ASP cc_start: 0.9150 (t70) cc_final: 0.8811 (t70) REVERT: T 185 GLU cc_start: 0.9267 (OUTLIER) cc_final: 0.9064 (pp20) REVERT: T 242 TYR cc_start: 0.7883 (m-80) cc_final: 0.7304 (m-80) REVERT: T 274 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8267 (mt-10) REVERT: T 288 ASP cc_start: 0.8578 (t0) cc_final: 0.8236 (t0) REVERT: T 305 MET cc_start: 0.8876 (mmm) cc_final: 0.8420 (mmm) REVERT: T 317 TYR cc_start: 0.8366 (t80) cc_final: 0.7968 (t80) outliers start: 40 outliers final: 18 residues processed: 210 average time/residue: 0.3370 time to fit residues: 111.2716 Evaluate side-chains 182 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 2.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL 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 45 optimal weight: 5.9990 chunk 47 optimal weight: 0.2980 chunk 76 optimal weight: 1.9990 chunk 157 optimal weight: 0.8980 chunk 278 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 226 optimal weight: 5.9990 chunk 127 optimal weight: 0.0970 chunk 198 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 GLN D 41 GLN D 49 GLN D 115 ASN E 12 ASN T 318 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.068825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.050418 restraints weight = 69214.070| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 3.31 r_work: 0.2711 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.2717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22871 Z= 0.124 Angle : 0.562 9.143 31027 Z= 0.273 Chirality : 0.044 0.165 3449 Planarity : 0.004 0.052 3975 Dihedral : 7.744 124.201 3186 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.17), residues: 2794 helix: 1.05 (0.16), residues: 1212 sheet: 0.68 (0.23), residues: 495 loop : 0.41 (0.21), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 79 HIS 0.018 0.001 HIS T 318 PHE 0.021 0.001 PHE T 229 TYR 0.018 0.001 TYR T 242 ARG 0.006 0.000 ARG A 39 Details of bonding type rmsd hydrogen bonds : bond 0.03005 ( 1082) hydrogen bonds : angle 4.43220 ( 2871) covalent geometry : bond 0.00285 (22871) covalent geometry : angle 0.56183 (31027) *********************** 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 193 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 2.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.5362 (tpp) cc_final: 0.5040 (pmm) REVERT: A 82 MET cc_start: 0.8941 (tpt) cc_final: 0.8387 (tpp) REVERT: A 118 LYS cc_start: 0.9342 (tptt) cc_final: 0.8984 (tppt) REVERT: A 132 MET cc_start: 0.9443 (ppp) cc_final: 0.9101 (ppp) REVERT: A 355 MET cc_start: 0.9255 (mmp) cc_final: 0.9048 (mmm) REVERT: B 50 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8469 (ptpt) REVERT: B 59 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.8594 (tm-30) REVERT: B 176 MET cc_start: 0.8583 (mmm) cc_final: 0.7864 (mtt) REVERT: C 303 THR cc_start: 0.9296 (OUTLIER) cc_final: 0.8892 (p) REVERT: D 305 MET cc_start: 0.9555 (mmm) cc_final: 0.9316 (mmm) REVERT: E 119 MET cc_start: 0.8818 (ttm) cc_final: 0.8592 (ttm) REVERT: F 64 ILE cc_start: 0.9363 (OUTLIER) cc_final: 0.9070 (pp) REVERT: G 149 THR cc_start: 0.9158 (OUTLIER) cc_final: 0.8507 (m) REVERT: G 292 ASP cc_start: 0.9338 (m-30) cc_final: 0.8996 (t0) REVERT: G 325 MET cc_start: 0.7931 (mmt) cc_final: 0.7659 (mmp) REVERT: T 182 ASP cc_start: 0.9118 (t70) cc_final: 0.8803 (t70) REVERT: T 185 GLU cc_start: 0.9326 (OUTLIER) cc_final: 0.9108 (pp20) REVERT: T 188 GLU cc_start: 0.9117 (tt0) cc_final: 0.8806 (tp30) REVERT: T 274 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8174 (mp0) REVERT: T 288 ASP cc_start: 0.8462 (t0) cc_final: 0.8074 (t0) REVERT: T 305 MET cc_start: 0.8914 (mmm) cc_final: 0.8711 (mmm) REVERT: T 317 TYR cc_start: 0.8278 (t80) cc_final: 0.7923 (t80) REVERT: T 318 HIS cc_start: 0.7997 (OUTLIER) cc_final: 0.7631 (m90) outliers start: 31 outliers final: 17 residues processed: 188 average time/residue: 0.3176 time to fit residues: 97.4888 Evaluate side-chains 178 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 2.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 SER 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 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 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 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 Chi-restraints excluded: chain T residue 318 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 172 optimal weight: 5.9990 chunk 217 optimal weight: 6.9990 chunk 164 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 278 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 273 optimal weight: 0.0980 overall best weight: 2.4188 ------------------------------------------------------------------------------- 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** C 59 GLN D 12 ASN D 41 GLN D 49 GLN D 115 ASN E 12 ASN F 115 ASN T 318 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.066514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.048011 restraints weight = 70073.802| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 3.39 r_work: 0.2633 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2636 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2636 r_free = 0.2636 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2636 r_free = 0.2636 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.2636 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2846 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= 0.231 Angle : 0.623 9.144 31027 Z= 0.304 Chirality : 0.046 0.148 3449 Planarity : 0.004 0.050 3975 Dihedral : 6.591 90.686 3181 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.70 % Allowed : 10.69 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.17), residues: 2794 helix: 1.08 (0.16), residues: 1219 sheet: 0.62 (0.23), residues: 497 loop : 0.29 (0.21), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 79 HIS 0.007 0.001 HIS T 318 PHE 0.012 0.001 PHE D 31 TYR 0.016 0.001 TYR T 242 ARG 0.004 0.000 ARG T 340 Details of bonding type rmsd hydrogen bonds : bond 0.03478 ( 1082) hydrogen bonds : angle 4.50976 ( 2871) covalent geometry : bond 0.00530 (22871) covalent geometry : angle 0.62336 (31027) *********************** 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 199 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 158 time to evaluate : 2.521 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.5587 (tpp) cc_final: 0.5217 (pmm) REVERT: A 82 MET cc_start: 0.8934 (tpt) cc_final: 0.8364 (tpp) REVERT: A 118 LYS cc_start: 0.9360 (tptt) cc_final: 0.9124 (tppt) REVERT: A 132 MET cc_start: 0.9431 (ppp) cc_final: 0.9088 (ppp) REVERT: A 355 MET cc_start: 0.9355 (mmp) cc_final: 0.9135 (mmm) REVERT: B 50 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8427 (ptpt) REVERT: B 59 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.8481 (tm-30) REVERT: B 176 MET cc_start: 0.8621 (mmm) cc_final: 0.7601 (mtt) REVERT: B 372 ARG cc_start: 0.8711 (mtm-85) cc_final: 0.8243 (mtm180) REVERT: C 176 MET cc_start: 0.9159 (mmm) cc_final: 0.8857 (mtp) REVERT: D 305 MET cc_start: 0.9592 (mmm) cc_final: 0.9360 (mmm) REVERT: E 283 MET cc_start: 0.9120 (mmm) cc_final: 0.8714 (mmm) REVERT: F 64 ILE cc_start: 0.9432 (OUTLIER) cc_final: 0.9126 (pp) REVERT: F 227 MET cc_start: 0.9318 (tpp) cc_final: 0.9056 (mtp) REVERT: G 149 THR cc_start: 0.9184 (OUTLIER) cc_final: 0.8604 (m) REVERT: G 292 ASP cc_start: 0.9337 (m-30) cc_final: 0.9005 (t0) REVERT: G 325 MET cc_start: 0.7923 (mmt) cc_final: 0.7664 (mmp) REVERT: G 359 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.8915 (tptm) REVERT: T 71 LEU cc_start: 0.8019 (mp) cc_final: 0.7788 (mt) REVERT: T 182 ASP cc_start: 0.9065 (t70) cc_final: 0.8834 (t70) REVERT: T 185 GLU cc_start: 0.9327 (pt0) cc_final: 0.9109 (pp20) REVERT: T 188 GLU cc_start: 0.9145 (tt0) cc_final: 0.8867 (tp30) REVERT: T 288 ASP cc_start: 0.8363 (t0) cc_final: 0.7835 (t0) REVERT: T 317 TYR cc_start: 0.8442 (t80) cc_final: 0.8007 (t80) REVERT: T 333 MET cc_start: 0.7613 (tpp) cc_final: 0.7298 (ttm) outliers start: 41 outliers final: 29 residues processed: 194 average time/residue: 0.3180 time to fit residues: 101.1465 Evaluate side-chains 185 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 2.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 SER 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 59 GLN 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 12 ASN Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 149 THR 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 12 ASN 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 149 THR Chi-restraints excluded: chain F residue 151 ILE 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 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 320 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 177 optimal weight: 3.9990 chunk 278 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 143 optimal weight: 0.7980 chunk 160 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 133 optimal weight: 0.9980 chunk 257 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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** C 59 GLN D 12 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 = 0.3218 r_free = 0.3218 target = 0.066850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.048328 restraints weight = 69756.154| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 3.41 r_work: 0.2642 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2645 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2645 r_free = 0.2645 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2645 r_free = 0.2645 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.2645 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22871 Z= 0.175 Angle : 0.580 10.089 31027 Z= 0.279 Chirality : 0.045 0.143 3449 Planarity : 0.004 0.051 3975 Dihedral : 6.335 82.106 3181 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.70 % Allowed : 11.23 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.17), residues: 2794 helix: 1.23 (0.16), residues: 1215 sheet: 0.51 (0.23), residues: 502 loop : 0.39 (0.21), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 79 HIS 0.005 0.001 HIS A 371 PHE 0.012 0.001 PHE D 31 TYR 0.009 0.001 TYR A 294 ARG 0.005 0.000 ARG T 340 Details of bonding type rmsd hydrogen bonds : bond 0.03120 ( 1082) hydrogen bonds : angle 4.37376 ( 2871) covalent geometry : bond 0.00402 (22871) covalent geometry : angle 0.57965 (31027) *********************** 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 196 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 155 time to evaluate : 2.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.5652 (tpp) cc_final: 0.5279 (pmm) REVERT: A 82 MET cc_start: 0.8931 (tpt) cc_final: 0.8325 (tpp) REVERT: A 118 LYS cc_start: 0.9365 (tptt) cc_final: 0.9011 (tppt) REVERT: A 132 MET cc_start: 0.9413 (ppp) cc_final: 0.9090 (ppp) REVERT: A 355 MET cc_start: 0.9366 (mmp) cc_final: 0.9099 (mmm) REVERT: B 50 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8453 (ptpt) REVERT: B 59 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8444 (tm-30) REVERT: B 132 MET cc_start: 0.8777 (ppp) cc_final: 0.8526 (ppp) REVERT: B 372 ARG cc_start: 0.8736 (mtm-85) cc_final: 0.8243 (mtm180) REVERT: C 176 MET cc_start: 0.9134 (mmm) cc_final: 0.8845 (mtp) REVERT: D 47 MET cc_start: 0.5891 (OUTLIER) cc_final: 0.5565 (ppp) REVERT: D 305 MET cc_start: 0.9574 (mmm) cc_final: 0.9354 (mmm) REVERT: E 176 MET cc_start: 0.9140 (mmm) cc_final: 0.8857 (mtp) REVERT: E 283 MET cc_start: 0.9150 (mmm) cc_final: 0.8787 (mmm) REVERT: E 305 MET cc_start: 0.9424 (mmm) cc_final: 0.9146 (mmm) REVERT: F 64 ILE cc_start: 0.9431 (OUTLIER) cc_final: 0.9115 (pp) REVERT: F 227 MET cc_start: 0.9320 (tpp) cc_final: 0.9054 (mtp) REVERT: G 292 ASP cc_start: 0.9317 (m-30) cc_final: 0.8993 (t0) REVERT: G 305 MET cc_start: 0.9476 (mmt) cc_final: 0.9128 (mmt) REVERT: G 325 MET cc_start: 0.7658 (mmt) cc_final: 0.7432 (mmp) REVERT: G 359 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.8866 (tptm) REVERT: T 71 LEU cc_start: 0.8024 (mp) cc_final: 0.7758 (mt) REVERT: T 182 ASP cc_start: 0.9066 (t70) cc_final: 0.8826 (t70) REVERT: T 185 GLU cc_start: 0.9355 (pt0) cc_final: 0.9109 (pp20) REVERT: T 188 GLU cc_start: 0.9149 (tt0) cc_final: 0.8858 (tp30) REVERT: T 288 ASP cc_start: 0.8332 (t0) cc_final: 0.7655 (t0) REVERT: T 317 TYR cc_start: 0.8594 (t80) cc_final: 0.8291 (t80) REVERT: T 322 GLN cc_start: 0.8265 (mp10) cc_final: 0.7618 (pt0) outliers start: 41 outliers final: 24 residues processed: 189 average time/residue: 0.3022 time to fit residues: 93.7049 Evaluate side-chains 180 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 2.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 145 SER 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 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 12 ASN Chi-restraints excluded: chain D residue 47 MET 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 349 LEU Chi-restraints excluded: chain D residue 374 CYS 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 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 208 ILE Chi-restraints excluded: chain T residue 320 THR 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 138 optimal weight: 2.9990 chunk 117 optimal weight: 0.0170 chunk 33 optimal weight: 3.9990 chunk 132 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 253 optimal weight: 6.9990 chunk 269 optimal weight: 10.0000 chunk 221 optimal weight: 0.4980 chunk 88 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.0422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 HIS D 12 ASN D 115 ASN ** T 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.067665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.049446 restraints weight = 68464.493| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 3.36 r_work: 0.2666 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2671 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2671 r_free = 0.2671 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2671 r_free = 0.2671 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.2671 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22871 Z= 0.119 Angle : 0.549 10.782 31027 Z= 0.261 Chirality : 0.043 0.145 3449 Planarity : 0.004 0.050 3975 Dihedral : 5.993 78.731 3179 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.62 % Allowed : 11.48 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.17), residues: 2794 helix: 1.37 (0.16), residues: 1216 sheet: 0.56 (0.23), residues: 502 loop : 0.48 (0.21), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 79 HIS 0.004 0.001 HIS A 371 PHE 0.011 0.001 PHE D 31 TYR 0.014 0.001 TYR T 242 ARG 0.005 0.000 ARG T 340 Details of bonding type rmsd hydrogen bonds : bond 0.02799 ( 1082) hydrogen bonds : angle 4.22050 ( 2871) covalent geometry : bond 0.00276 (22871) covalent geometry : angle 0.54878 (31027) *********************** 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 199 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 160 time to evaluate : 2.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.5645 (tpp) cc_final: 0.5308 (pmm) REVERT: A 82 MET cc_start: 0.8973 (tpt) cc_final: 0.8349 (tpp) REVERT: A 118 LYS cc_start: 0.9361 (tptt) cc_final: 0.8997 (tppt) REVERT: A 132 MET cc_start: 0.9406 (ppp) cc_final: 0.9087 (ppp) REVERT: A 227 MET cc_start: 0.8843 (mmm) cc_final: 0.8637 (mmm) REVERT: A 305 MET cc_start: 0.9207 (mmm) cc_final: 0.8977 (mmt) REVERT: B 50 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8434 (ptpt) REVERT: B 59 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8451 (tm-30) REVERT: B 176 MET cc_start: 0.8655 (mmm) cc_final: 0.7846 (mtt) REVERT: B 372 ARG cc_start: 0.8760 (mtm-85) cc_final: 0.8231 (mtm180) REVERT: C 176 MET cc_start: 0.9122 (mmm) cc_final: 0.8822 (mtp) REVERT: D 47 MET cc_start: 0.5923 (OUTLIER) cc_final: 0.5568 (ppp) REVERT: D 305 MET cc_start: 0.9564 (mmm) cc_final: 0.9347 (mmm) REVERT: E 132 MET cc_start: 0.9190 (ppp) cc_final: 0.8840 (ppp) REVERT: E 176 MET cc_start: 0.9124 (mmm) cc_final: 0.8860 (mtp) REVERT: E 283 MET cc_start: 0.9139 (mmm) cc_final: 0.8744 (mmm) REVERT: E 305 MET cc_start: 0.9431 (mmm) cc_final: 0.9137 (mmm) REVERT: F 64 ILE cc_start: 0.9434 (OUTLIER) cc_final: 0.9108 (pp) REVERT: F 227 MET cc_start: 0.9316 (tpp) cc_final: 0.9039 (mtp) REVERT: G 149 THR cc_start: 0.9203 (OUTLIER) cc_final: 0.8642 (m) REVERT: G 292 ASP cc_start: 0.9321 (m-30) cc_final: 0.9002 (t0) REVERT: T 71 LEU cc_start: 0.8021 (mp) cc_final: 0.7752 (mt) REVERT: T 81 ARG cc_start: 0.6027 (OUTLIER) cc_final: 0.5326 (mmp-170) REVERT: T 182 ASP cc_start: 0.9084 (t70) cc_final: 0.8877 (t70) REVERT: T 185 GLU cc_start: 0.9346 (pt0) cc_final: 0.9061 (pp20) REVERT: T 288 ASP cc_start: 0.8347 (t0) cc_final: 0.7642 (t0) REVERT: T 305 MET cc_start: 0.8784 (mmm) cc_final: 0.8238 (tpp) REVERT: T 317 TYR cc_start: 0.8564 (t80) cc_final: 0.8331 (t80) outliers start: 39 outliers final: 23 residues processed: 193 average time/residue: 0.3201 time to fit residues: 102.2433 Evaluate side-chains 181 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 2.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN 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 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 64 ILE Chi-restraints excluded: chain D residue 94 LEU 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 359 LYS 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 47 MET Chi-restraints excluded: chain G residue 149 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 304 SER 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 73 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 278 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 172 optimal weight: 5.9990 chunk 216 optimal weight: 5.9990 chunk 270 optimal weight: 5.9990 chunk 156 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 231 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 F 115 ASN ** T 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.066487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.048092 restraints weight = 70050.048| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 3.38 r_work: 0.2636 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2640 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2640 r_free = 0.2640 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2640 r_free = 0.2640 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.2640 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 22871 Z= 0.196 Angle : 0.595 11.273 31027 Z= 0.283 Chirality : 0.045 0.217 3449 Planarity : 0.004 0.049 3975 Dihedral : 6.016 82.130 3178 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.75 % Allowed : 11.60 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.17), residues: 2794 helix: 1.36 (0.16), residues: 1220 sheet: 0.52 (0.23), residues: 502 loop : 0.38 (0.21), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 79 HIS 0.004 0.001 HIS A 371 PHE 0.012 0.001 PHE D 31 TYR 0.008 0.001 TYR A 294 ARG 0.005 0.000 ARG T 340 Details of bonding type rmsd hydrogen bonds : bond 0.03109 ( 1082) hydrogen bonds : angle 4.29298 ( 2871) covalent geometry : bond 0.00452 (22871) covalent geometry : angle 0.59461 (31027) *********************** 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 194 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 152 time to evaluate : 2.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8958 (tpt) cc_final: 0.8346 (tpp) REVERT: A 118 LYS cc_start: 0.9365 (tptt) cc_final: 0.9011 (tppt) REVERT: A 132 MET cc_start: 0.9396 (ppp) cc_final: 0.9068 (ppp) REVERT: B 50 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8469 (ptpt) REVERT: B 59 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8473 (tm-30) REVERT: B 176 MET cc_start: 0.8641 (mmm) cc_final: 0.8227 (mtt) REVERT: B 372 ARG cc_start: 0.8826 (mtm-85) cc_final: 0.8620 (mtm-85) REVERT: C 176 MET cc_start: 0.9141 (mmm) cc_final: 0.8883 (mtp) REVERT: D 47 MET cc_start: 0.5946 (OUTLIER) cc_final: 0.5524 (ppp) REVERT: D 305 MET cc_start: 0.9586 (mmm) cc_final: 0.9377 (mmm) REVERT: E 176 MET cc_start: 0.9141 (mmm) cc_final: 0.8866 (mtp) REVERT: E 305 MET cc_start: 0.9449 (mmm) cc_final: 0.9149 (mmm) REVERT: E 325 MET cc_start: 0.9019 (mmt) cc_final: 0.8740 (mmp) REVERT: F 64 ILE cc_start: 0.9453 (OUTLIER) cc_final: 0.9129 (pp) REVERT: G 149 THR cc_start: 0.9176 (OUTLIER) cc_final: 0.8649 (m) REVERT: G 292 ASP cc_start: 0.9310 (m-30) cc_final: 0.9000 (t0) REVERT: G 305 MET cc_start: 0.9465 (mmt) cc_final: 0.9159 (mmt) REVERT: G 359 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.8838 (tptm) REVERT: T 71 LEU cc_start: 0.8036 (mp) cc_final: 0.7776 (mt) REVERT: T 81 ARG cc_start: 0.5903 (OUTLIER) cc_final: 0.5153 (mmp-170) REVERT: T 185 GLU cc_start: 0.9333 (pt0) cc_final: 0.9091 (pp20) REVERT: T 288 ASP cc_start: 0.8345 (t0) cc_final: 0.7605 (t0) REVERT: T 317 TYR cc_start: 0.8593 (t80) cc_final: 0.8377 (t80) REVERT: T 322 GLN cc_start: 0.8284 (mp10) cc_final: 0.7715 (pt0) outliers start: 42 outliers final: 29 residues processed: 188 average time/residue: 0.3175 time to fit residues: 97.4073 Evaluate side-chains 187 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 2.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN 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 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 64 ILE Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 216 LEU 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 236 LEU 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 151 ILE Chi-restraints excluded: chain F residue 269 MET 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 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 139 optimal weight: 3.9990 chunk 214 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 4 optimal weight: 30.0000 chunk 126 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 213 optimal weight: 4.9990 chunk 240 optimal weight: 0.9980 chunk 279 optimal weight: 3.9990 chunk 198 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 ** T 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.065801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.047760 restraints weight = 69332.931| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 3.28 r_work: 0.2621 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2625 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.2625 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 22871 Z= 0.231 Angle : 0.618 11.809 31027 Z= 0.297 Chirality : 0.046 0.194 3449 Planarity : 0.004 0.049 3975 Dihedral : 6.118 84.316 3178 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.79 % Allowed : 11.98 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.17), residues: 2794 helix: 1.29 (0.16), residues: 1220 sheet: 0.56 (0.23), residues: 485 loop : 0.26 (0.20), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 79 HIS 0.005 0.001 HIS A 371 PHE 0.013 0.001 PHE D 31 TYR 0.017 0.001 TYR T 242 ARG 0.005 0.000 ARG T 340 Details of bonding type rmsd hydrogen bonds : bond 0.03326 ( 1082) hydrogen bonds : angle 4.37966 ( 2871) covalent geometry : bond 0.00530 (22871) covalent geometry : angle 0.61786 (31027) *********************** 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 196 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 153 time to evaluate : 2.655 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8970 (tpt) cc_final: 0.8388 (tpp) REVERT: A 118 LYS cc_start: 0.9375 (tptt) cc_final: 0.9021 (tppt) REVERT: A 132 MET cc_start: 0.9381 (ppp) cc_final: 0.9035 (ppp) REVERT: B 50 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8351 (ptpt) REVERT: B 59 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8404 (tm-30) REVERT: B 132 MET cc_start: 0.8876 (ppp) cc_final: 0.8438 (ppp) REVERT: B 176 MET cc_start: 0.8626 (mmm) cc_final: 0.8221 (mtt) REVERT: C 176 MET cc_start: 0.9147 (mmm) cc_final: 0.8903 (mtp) REVERT: D 283 MET cc_start: 0.9058 (mmm) cc_final: 0.8744 (mmm) REVERT: D 305 MET cc_start: 0.9587 (mmm) cc_final: 0.9374 (mmm) REVERT: E 47 MET cc_start: 0.6929 (ppp) cc_final: 0.6717 (ppp) REVERT: E 305 MET cc_start: 0.9477 (mmm) cc_final: 0.9177 (mmm) REVERT: E 325 MET cc_start: 0.9050 (mmt) cc_final: 0.8764 (mmp) REVERT: F 64 ILE cc_start: 0.9478 (OUTLIER) cc_final: 0.9142 (pp) REVERT: G 149 THR cc_start: 0.9208 (OUTLIER) cc_final: 0.8720 (m) REVERT: G 292 ASP cc_start: 0.9340 (m-30) cc_final: 0.9071 (t70) REVERT: G 305 MET cc_start: 0.9477 (mmt) cc_final: 0.8992 (mmt) REVERT: G 359 LYS cc_start: 0.9333 (OUTLIER) cc_final: 0.8851 (tptm) REVERT: T 71 LEU cc_start: 0.8070 (mp) cc_final: 0.7801 (mt) REVERT: T 81 ARG cc_start: 0.5557 (OUTLIER) cc_final: 0.4818 (mmp-170) REVERT: T 185 GLU cc_start: 0.9363 (pt0) cc_final: 0.9120 (pp20) REVERT: T 288 ASP cc_start: 0.8389 (t0) cc_final: 0.7587 (t0) REVERT: T 317 TYR cc_start: 0.8640 (t80) cc_final: 0.8422 (t80) REVERT: T 319 PHE cc_start: 0.8512 (m-80) cc_final: 0.8276 (m-80) REVERT: T 322 GLN cc_start: 0.8340 (mp10) cc_final: 0.7792 (pt0) outliers start: 43 outliers final: 33 residues processed: 187 average time/residue: 0.3260 time to fit residues: 100.2044 Evaluate side-chains 189 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 150 time to evaluate : 2.541 ------------------------------------------------------------------------------- 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 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 355 MET 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 94 LEU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 216 LEU 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 236 LEU 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 151 ILE Chi-restraints excluded: chain F residue 269 MET 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 269 MET Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 359 LYS Chi-restraints excluded: chain T residue 81 ARG Chi-restraints excluded: chain T residue 170 TYR Chi-restraints excluded: chain T residue 173 VAL Chi-restraints excluded: chain T residue 208 ILE Chi-restraints excluded: chain T residue 304 SER Chi-restraints excluded: chain T residue 320 THR Chi-restraints excluded: chain T residue 339 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 41 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 chunk 16 optimal weight: 0.5980 chunk 109 optimal weight: 0.1980 chunk 149 optimal weight: 4.9990 chunk 267 optimal weight: 5.9990 chunk 234 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 242 optimal weight: 1.9990 chunk 275 optimal weight: 5.9990 chunk 218 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 ** T 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.066442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.048108 restraints weight = 69695.305| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 3.35 r_work: 0.2634 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2637 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2637 r_free = 0.2637 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2637 r_free = 0.2637 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.2637 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22871 Z= 0.172 Angle : 0.588 12.441 31027 Z= 0.280 Chirality : 0.045 0.191 3449 Planarity : 0.004 0.049 3975 Dihedral : 5.986 81.774 3178 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.75 % Allowed : 12.18 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.17), residues: 2794 helix: 1.34 (0.16), residues: 1220 sheet: 0.57 (0.23), residues: 486 loop : 0.30 (0.21), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 79 HIS 0.010 0.001 HIS A 371 PHE 0.011 0.001 PHE D 31 TYR 0.018 0.001 TYR T 225 ARG 0.005 0.000 ARG T 340 Details of bonding type rmsd hydrogen bonds : bond 0.03067 ( 1082) hydrogen bonds : angle 4.28330 ( 2871) covalent geometry : bond 0.00397 (22871) covalent geometry : angle 0.58751 (31027) *********************** 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 194 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 152 time to evaluate : 2.777 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8974 (tpt) cc_final: 0.8356 (tpp) REVERT: A 118 LYS cc_start: 0.9355 (tptt) cc_final: 0.9137 (tppt) REVERT: A 132 MET cc_start: 0.9366 (ppp) cc_final: 0.9038 (ppp) REVERT: A 305 MET cc_start: 0.9196 (mmm) cc_final: 0.8949 (mmt) REVERT: B 44 MET cc_start: 0.5182 (tpp) cc_final: 0.4765 (tpt) REVERT: B 50 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8323 (ptpt) REVERT: B 59 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8415 (tm-30) REVERT: B 118 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8803 (mmtm) REVERT: B 132 MET cc_start: 0.8859 (ppp) cc_final: 0.8428 (ppp) REVERT: B 176 MET cc_start: 0.8623 (mmm) cc_final: 0.8200 (mtt) REVERT: C 176 MET cc_start: 0.9129 (mmm) cc_final: 0.8868 (mtp) REVERT: D 283 MET cc_start: 0.9047 (mmm) cc_final: 0.8738 (mmm) REVERT: D 305 MET cc_start: 0.9564 (mmm) cc_final: 0.9348 (mmm) REVERT: E 176 MET cc_start: 0.9135 (mmm) cc_final: 0.8870 (mtp) REVERT: E 305 MET cc_start: 0.9463 (mmm) cc_final: 0.9157 (mmm) REVERT: F 64 ILE cc_start: 0.9466 (OUTLIER) cc_final: 0.9133 (pp) REVERT: F 227 MET cc_start: 0.9356 (tpp) cc_final: 0.9087 (mtp) REVERT: G 149 THR cc_start: 0.9157 (OUTLIER) cc_final: 0.8646 (m) REVERT: G 292 ASP cc_start: 0.9343 (m-30) cc_final: 0.9051 (t70) REVERT: G 305 MET cc_start: 0.9461 (mmt) cc_final: 0.9052 (mmt) REVERT: T 71 LEU cc_start: 0.8063 (mp) cc_final: 0.7798 (mt) REVERT: T 81 ARG cc_start: 0.5220 (OUTLIER) cc_final: 0.4561 (mmp-170) REVERT: T 185 GLU cc_start: 0.9355 (pt0) cc_final: 0.9110 (pp20) REVERT: T 288 ASP cc_start: 0.8315 (t0) cc_final: 0.7549 (t0) REVERT: T 317 TYR cc_start: 0.8669 (t80) cc_final: 0.8438 (t80) REVERT: T 319 PHE cc_start: 0.8500 (m-80) cc_final: 0.8267 (m-80) REVERT: T 322 GLN cc_start: 0.8280 (mp10) cc_final: 0.7723 (pt0) outliers start: 42 outliers final: 29 residues processed: 187 average time/residue: 0.3176 time to fit residues: 97.6474 Evaluate side-chains 186 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 151 time to evaluate : 2.712 ------------------------------------------------------------------------------- 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 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 64 ILE Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 216 LEU 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 236 LEU 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 269 MET Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 269 MET Chi-restraints excluded: chain G residue 303 THR 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 Chi-restraints excluded: chain T residue 320 THR Chi-restraints excluded: chain T residue 339 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 208 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 221 optimal weight: 3.9990 chunk 231 optimal weight: 0.8980 chunk 145 optimal weight: 0.9980 chunk 217 optimal weight: 1.9990 chunk 180 optimal weight: 0.4980 chunk 203 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 212 optimal weight: 0.6980 chunk 112 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 F 115 ASN ** T 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.068000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.049588 restraints weight = 69471.971| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 3.39 r_work: 0.2676 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2679 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 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 = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.2678 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 22871 Z= 0.101 Angle : 0.553 12.606 31027 Z= 0.260 Chirality : 0.043 0.184 3449 Planarity : 0.004 0.051 3975 Dihedral : 5.658 73.694 3178 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.33 % Allowed : 12.43 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.17), residues: 2794 helix: 1.47 (0.16), residues: 1221 sheet: 0.52 (0.23), residues: 502 loop : 0.49 (0.21), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 79 HIS 0.005 0.001 HIS A 371 PHE 0.010 0.001 PHE D 31 TYR 0.016 0.001 TYR T 225 ARG 0.008 0.000 ARG A 372 Details of bonding type rmsd hydrogen bonds : bond 0.02620 ( 1082) hydrogen bonds : angle 4.10949 ( 2871) covalent geometry : bond 0.00236 (22871) covalent geometry : angle 0.55269 (31027) ********************** 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 189 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 2.632 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8967 (tpt) cc_final: 0.8334 (tpp) REVERT: A 118 LYS cc_start: 0.9351 (tptt) cc_final: 0.9030 (tppt) REVERT: A 132 MET cc_start: 0.9368 (ppp) cc_final: 0.9061 (ppp) REVERT: A 305 MET cc_start: 0.9174 (mmm) cc_final: 0.8965 (mmt) REVERT: B 50 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8279 (ptpt) REVERT: B 59 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8504 (tm-30) REVERT: B 118 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8804 (mmtm) REVERT: B 132 MET cc_start: 0.8809 (ppp) cc_final: 0.8390 (ppp) REVERT: B 176 MET cc_start: 0.8595 (mmm) cc_final: 0.7771 (mtt) REVERT: C 176 MET cc_start: 0.9092 (mmm) cc_final: 0.8813 (mtp) REVERT: D 47 MET cc_start: 0.6177 (OUTLIER) cc_final: 0.5813 (ppp) REVERT: D 283 MET cc_start: 0.9010 (mmm) cc_final: 0.8678 (mmm) REVERT: D 305 MET cc_start: 0.9538 (mmm) cc_final: 0.9326 (mmm) REVERT: E 119 MET cc_start: 0.8894 (ttm) cc_final: 0.8693 (ttp) REVERT: E 176 MET cc_start: 0.9122 (mmm) cc_final: 0.8868 (mtp) REVERT: E 305 MET cc_start: 0.9450 (mmm) cc_final: 0.9143 (mmm) REVERT: F 64 ILE cc_start: 0.9461 (OUTLIER) cc_final: 0.9136 (pp) REVERT: F 227 MET cc_start: 0.9351 (tpp) cc_final: 0.9083 (mtp) REVERT: G 292 ASP cc_start: 0.9347 (m-30) cc_final: 0.9004 (t0) REVERT: G 305 MET cc_start: 0.9432 (mmt) cc_final: 0.9163 (mmt) REVERT: T 71 LEU cc_start: 0.8119 (mp) cc_final: 0.7871 (mt) REVERT: T 81 ARG cc_start: 0.5234 (OUTLIER) cc_final: 0.4509 (mmp-170) REVERT: T 185 GLU cc_start: 0.9351 (pt0) cc_final: 0.9109 (pp20) REVERT: T 288 ASP cc_start: 0.8312 (t0) cc_final: 0.7557 (t0) REVERT: T 317 TYR cc_start: 0.8642 (t80) cc_final: 0.8415 (t80) REVERT: T 319 PHE cc_start: 0.8534 (m-80) cc_final: 0.8289 (m-80) REVERT: T 322 GLN cc_start: 0.8221 (mp10) cc_final: 0.7654 (pt0) outliers start: 32 outliers final: 17 residues processed: 182 average time/residue: 0.3098 time to fit residues: 92.4208 Evaluate side-chains 179 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 2.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 HIS 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 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 216 LEU 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 269 MET 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 Chi-restraints excluded: chain T residue 320 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 214 optimal weight: 4.9990 chunk 4 optimal weight: 20.0000 chunk 167 optimal weight: 2.9990 chunk 259 optimal weight: 0.1980 chunk 238 optimal weight: 2.9990 chunk 218 optimal weight: 0.4980 chunk 71 optimal weight: 0.0770 chunk 230 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 260 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- 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 ** T 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.067514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.049085 restraints weight = 69439.426| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 3.40 r_work: 0.2663 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2666 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2666 r_free = 0.2666 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 = 0.2666 r_free = 0.2666 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.2666 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22871 Z= 0.127 Angle : 0.568 12.488 31027 Z= 0.266 Chirality : 0.044 0.181 3449 Planarity : 0.004 0.051 3975 Dihedral : 5.580 75.514 3178 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.16 % Allowed : 12.77 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.17), residues: 2794 helix: 1.50 (0.16), residues: 1221 sheet: 0.51 (0.23), residues: 502 loop : 0.51 (0.21), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 79 HIS 0.004 0.001 HIS A 371 PHE 0.011 0.001 PHE D 31 TYR 0.016 0.001 TYR T 225 ARG 0.005 0.000 ARG T 340 Details of bonding type rmsd hydrogen bonds : bond 0.02739 ( 1082) hydrogen bonds : angle 4.10430 ( 2871) covalent geometry : bond 0.00295 (22871) covalent geometry : angle 0.56843 (31027) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10240.96 seconds wall clock time: 176 minutes 48.20 seconds (10608.20 seconds total)