Starting phenix.real_space_refine on Fri Sep 19 07:02:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b27_44099/09_2025/9b27_44099.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b27_44099/09_2025/9b27_44099.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b27_44099/09_2025/9b27_44099.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b27_44099/09_2025/9b27_44099.map" model { file = "/net/cci-nas-00/data/ceres_data/9b27_44099/09_2025/9b27_44099.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b27_44099/09_2025/9b27_44099.cif" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.020 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 12 5.49 5 Mg 6 5.21 5 S 163 5.16 5 C 15057 2.51 5 N 4024 2.21 5 O 4566 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23828 Number of models: 1 Model: "" Number of chains: 14 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: 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: "C" 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: "D" 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: "E" 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: "F" 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: "G" Number of atoms: 3259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3259 Classifications: {'peptide': 397} Link IDs: {'PTRANS': 13, 'TRANS': 383} Chain breaks: 1 Chain: "H" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 3001 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 14, 'TRANS': 353} 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} Time building chain proxies: 6.26, per 1000 atoms: 0.26 Number of scatterers: 23828 At special positions: 0 Unit cell: (132.84, 140.4, 232.2, 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 163 16.00 P 12 15.00 Mg 6 11.99 O 4566 8.00 N 4024 7.00 C 15057 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.91 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5612 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 37 sheets defined 53.3% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 112 through 126 removed outlier: 4.157A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 removed outlier: 3.845A pdb=" N GLY A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.724A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 202 through 216 removed outlier: 3.554A pdb=" N ARG A 206 " --> pdb=" O THR A 202 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.695A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 267 removed outlier: 3.747A pdb=" N PHE A 266 " --> pdb=" O GLN A 263 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE A 267 " --> pdb=" O PRO A 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 263 through 267' Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.761A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 306 removed outlier: 4.245A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 removed outlier: 3.725A pdb=" N ARG A 312 " --> pdb=" O GLY A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.614A pdb=" N GLN A 353 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.767A pdb=" N GLU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 97 through 101' Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.143A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.794A pdb=" N GLY B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 204 through 217 removed outlier: 4.156A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 removed outlier: 3.583A pdb=" N GLU B 226 " --> pdb=" O ASP B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.709A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.603A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 306 removed outlier: 3.573A pdb=" N MET B 305 " --> pdb=" O GLY B 302 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 302 through 306' Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.945A pdb=" N ARG B 312 " --> pdb=" O GLY B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 348 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.613A pdb=" N PHE B 352 " --> pdb=" O LEU B 349 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN B 353 " --> pdb=" O SER B 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 349 through 353' Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.528A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.710A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 4.017A 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: 4.054A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.746A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.960A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 removed outlier: 3.535A pdb=" N GLU C 226 " --> pdb=" O ASP C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.586A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.765A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 306 removed outlier: 4.027A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 303 through 306' Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.809A pdb=" N ARG C 312 " --> pdb=" O GLY C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.533A pdb=" N PHE C 352 " --> pdb=" O LEU C 349 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN C 353 " --> pdb=" O SER C 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 349 through 353' Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 369 through 374 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 removed outlier: 3.600A pdb=" N MET D 82 " --> pdb=" O ASN D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.616A pdb=" N GLU D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.886A 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: 4.027A 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 removed outlier: 3.684A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.547A pdb=" N ARG D 206 " --> pdb=" O THR D 202 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N CYS D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 removed outlier: 3.568A pdb=" N GLU D 226 " --> pdb=" O ASP D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.683A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 260 No H-bonds generated for 'chain 'D' and resid 258 through 260' Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.548A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 306 removed outlier: 3.960A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.567A pdb=" N ARG D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 347 Processing helix chain 'D' and resid 349 through 355 removed outlier: 3.619A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.673A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 126 removed outlier: 4.076A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 Processing helix chain 'E' and resid 181 through 193 Processing helix chain 'E' and resid 202 through 217 removed outlier: 3.904A pdb=" N GLU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS E 217 " --> pdb=" O LYS E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 257 removed outlier: 3.661A pdb=" N CYS E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 290 through 295 removed outlier: 3.682A pdb=" N ALA E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 305 removed outlier: 3.866A pdb=" N MET E 305 " --> pdb=" O GLY E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 337 through 347 removed outlier: 3.983A pdb=" N GLY E 343 " --> pdb=" O VAL E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 348 through 349 No H-bonds generated for 'chain 'E' and resid 348 through 349' Processing helix chain 'E' and resid 350 through 354 removed outlier: 3.719A pdb=" N GLN E 353 " --> pdb=" O SER E 350 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 350 through 354' Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 368 through 374 removed outlier: 3.919A 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: 3.676A pdb=" N MET F 82 " --> pdb=" O ASN F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 101 removed outlier: 3.721A pdb=" N GLU F 100 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N HIS F 101 " --> pdb=" O PRO F 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 97 through 101' Processing helix chain 'F' and resid 112 through 126 removed outlier: 4.048A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 144 Processing helix chain 'F' and resid 181 through 193 Processing helix chain 'F' and resid 194 through 196 No H-bonds generated for 'chain 'F' and resid 194 through 196' Processing helix chain 'F' and resid 202 through 217 removed outlier: 3.501A pdb=" N ARG F 206 " --> pdb=" O THR F 202 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU F 207 " --> pdb=" O THR F 203 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N CYS F 217 " --> pdb=" O LYS F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 233 Processing helix chain 'F' and resid 252 through 257 removed outlier: 3.660A pdb=" N CYS F 257 " --> pdb=" O GLU F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 261 removed outlier: 3.541A pdb=" N LEU F 261 " --> pdb=" O PRO F 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 258 through 261' Processing helix chain 'F' and resid 273 through 284 Processing helix chain 'F' and resid 289 through 295 removed outlier: 3.586A pdb=" N LEU F 293 " --> pdb=" O ILE F 289 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA F 295 " --> pdb=" O LYS F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 306 removed outlier: 4.116A pdb=" N TYR F 306 " --> pdb=" O THR F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 321 removed outlier: 3.707A pdb=" N ARG F 312 " --> pdb=" O GLY F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 348 removed outlier: 3.668A pdb=" N SER F 348 " --> pdb=" O SER F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 354 removed outlier: 3.704A pdb=" N GLN F 353 " --> pdb=" O SER F 350 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLN F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 366 Processing helix chain 'F' and resid 368 through 374 removed outlier: 4.213A pdb=" N ARG F 372 " --> pdb=" O SER F 368 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS F 374 " --> pdb=" O VAL F 370 " (cutoff:3.500A) Processing helix chain 'G' and resid 785 through 790 Processing helix chain 'G' and resid 791 through 802 Processing helix chain 'G' and resid 836 through 851 Processing helix chain 'G' and resid 853 through 864 Processing helix chain 'G' and resid 870 through 880 removed outlier: 3.577A pdb=" N ILE G 874 " --> pdb=" O THR G 870 " (cutoff:3.500A) Processing helix chain 'G' and resid 883 through 892 Processing helix chain 'G' and resid 893 through 900 removed outlier: 3.725A pdb=" N GLU G 896 " --> pdb=" O LEU G 893 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR G 897 " --> pdb=" O LYS G 894 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ASP G 898 " --> pdb=" O GLU G 895 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU G 900 " --> pdb=" O TYR G 897 " (cutoff:3.500A) Processing helix chain 'G' and resid 901 through 913 removed outlier: 3.776A pdb=" N VAL G 913 " --> pdb=" O VAL G 909 " (cutoff:3.500A) Processing helix chain 'G' and resid 916 through 952 removed outlier: 4.526A pdb=" N SER G 930 " --> pdb=" O LYS G 926 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N GLU G 931 " --> pdb=" O LEU G 927 " (cutoff:3.500A) Proline residue: G 938 - end of helix Processing helix chain 'G' and resid 954 through 971 Processing helix chain 'G' and resid 984 through 991 removed outlier: 3.990A pdb=" N CYS G 988 " --> pdb=" O SER G 985 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG G 991 " --> pdb=" O CYS G 988 " (cutoff:3.500A) Processing helix chain 'G' and resid 1001 through 1013 Processing helix chain 'G' and resid 1016 through 1018 No H-bonds generated for 'chain 'G' and resid 1016 through 1018' Processing helix chain 'G' and resid 1019 through 1024 removed outlier: 3.514A pdb=" N GLU G1023 " --> pdb=" O LYS G1019 " (cutoff:3.500A) Processing helix chain 'G' and resid 1026 through 1031 Processing helix chain 'G' and resid 1034 through 1058 Processing helix chain 'G' and resid 1068 through 1105 removed outlier: 3.712A pdb=" N LYS G1072 " --> pdb=" O LYS G1068 " (cutoff:3.500A) Processing helix chain 'G' and resid 1114 through 1166 Processing helix chain 'H' and resid 746 through 750 removed outlier: 3.949A pdb=" N GLY H 749 " --> pdb=" O LEU H 746 " (cutoff:3.500A) Processing helix chain 'H' and resid 785 through 790 Processing helix chain 'H' and resid 791 through 802 Processing helix chain 'H' and resid 837 through 851 Processing helix chain 'H' and resid 853 through 864 Processing helix chain 'H' and resid 870 through 880 removed outlier: 3.514A pdb=" N ILE H 874 " --> pdb=" O THR H 870 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN H 880 " --> pdb=" O ASN H 876 " (cutoff:3.500A) Processing helix chain 'H' and resid 883 through 892 Processing helix chain 'H' and resid 893 through 897 removed outlier: 3.688A pdb=" N GLU H 896 " --> pdb=" O LEU H 893 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR H 897 " --> pdb=" O LYS H 894 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 893 through 897' Processing helix chain 'H' and resid 901 through 912 removed outlier: 3.620A pdb=" N THR H 912 " --> pdb=" O VAL H 908 " (cutoff:3.500A) Processing helix chain 'H' and resid 916 through 928 Processing helix chain 'H' and resid 928 through 953 Proline residue: H 938 - end of helix removed outlier: 3.778A pdb=" N LYS H 952 " --> pdb=" O GLU H 948 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER H 953 " --> pdb=" O GLU H 949 " (cutoff:3.500A) Processing helix chain 'H' and resid 953 through 971 Processing helix chain 'H' and resid 983 through 991 removed outlier: 4.189A pdb=" N CYS H 988 " --> pdb=" O SER H 985 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG H 991 " --> pdb=" O CYS H 988 " (cutoff:3.500A) Processing helix chain 'H' and resid 1001 through 1013 Processing helix chain 'H' and resid 1016 through 1020 removed outlier: 3.977A pdb=" N LYS H1019 " --> pdb=" O GLU H1016 " (cutoff:3.500A) Processing helix chain 'H' and resid 1029 through 1033 removed outlier: 4.201A pdb=" N ARG H1032 " --> pdb=" O LYS H1029 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL H1033 " --> pdb=" O ALA H1030 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 1029 through 1033' Processing helix chain 'H' and resid 1034 through 1059 Processing helix chain 'H' and resid 1068 through 1105 removed outlier: 3.505A pdb=" N GLU H1082 " --> pdb=" O LYS H1078 " (cutoff:3.500A) Processing helix chain 'H' and resid 1113 through 1143 removed outlier: 3.655A pdb=" N ASP H1120 " --> pdb=" O GLU H1116 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.795A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 3.527A 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 169 through 170 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.468A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (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: 6.793A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (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 169 through 170 Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.326A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (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: 6.534A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (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: 6.189A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.250A 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: 3.827A 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: 6.725A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (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: 3.705A pdb=" N SER D 155 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 176 through 178 removed outlier: 3.985A 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: 6.493A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N THR E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N ALA E 135 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (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 169 through 170 Processing sheet with id=AD2, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.301A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (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: 6.636A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR F 103 " --> pdb=" O TYR F 133 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ALA F 135 " --> pdb=" O THR F 103 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU F 105 " --> pdb=" O ALA F 135 " (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: 6.080A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) removed outlier: 6.096A 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 981 through 982 1167 hydrogen bonds defined for protein. 3210 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.21 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 6318 1.33 - 1.45: 4178 1.45 - 1.57: 13516 1.57 - 1.69: 18 1.69 - 1.81: 288 Bond restraints: 24318 Sorted by residual: bond pdb=" CE1 HIC E 73 " pdb=" NE2 HIC E 73 " ideal model delta sigma weight residual 1.347 1.404 -0.057 2.00e-02 2.50e+03 8.15e+00 bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.404 -0.057 2.00e-02 2.50e+03 8.04e+00 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 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 7.87e+00 bond pdb=" CE1 HIC F 73 " pdb=" NE2 HIC F 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.80e+00 ... (remaining 24313 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 31966 2.20 - 4.40: 783 4.40 - 6.60: 122 6.60 - 8.80: 27 8.80 - 11.00: 10 Bond angle restraints: 32908 Sorted by residual: angle pdb=" C PHE H1105 " pdb=" N VAL H1106 " pdb=" CA VAL H1106 " ideal model delta sigma weight residual 121.97 131.27 -9.30 1.80e+00 3.09e-01 2.67e+01 angle pdb=" C LYS H 952 " pdb=" N SER H 953 " pdb=" CA SER H 953 " ideal model delta sigma weight residual 122.36 129.01 -6.65 1.42e+00 4.96e-01 2.19e+01 angle pdb=" C LEU A 110 " pdb=" N ASN A 111 " pdb=" CA ASN A 111 " ideal model delta sigma weight residual 120.49 126.99 -6.50 1.42e+00 4.96e-01 2.10e+01 angle pdb=" CA VAL H1106 " pdb=" CB VAL H1106 " pdb=" CG1 VAL H1106 " ideal model delta sigma weight residual 110.40 117.78 -7.38 1.70e+00 3.46e-01 1.88e+01 angle pdb=" C GLY A 46 " pdb=" N MET A 47 " pdb=" CA MET A 47 " ideal model delta sigma weight residual 122.08 128.38 -6.30 1.47e+00 4.63e-01 1.84e+01 ... (remaining 32903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.66: 14506 35.66 - 71.32: 241 71.32 - 106.97: 15 106.97 - 142.63: 8 142.63 - 178.29: 9 Dihedral angle restraints: 14779 sinusoidal: 6076 harmonic: 8703 Sorted by residual: dihedral pdb=" CD ARG G 915 " pdb=" NE ARG G 915 " pdb=" CZ ARG G 915 " pdb=" NH1 ARG G 915 " ideal model delta sinusoidal sigma weight residual 0.00 -82.84 82.84 1 1.00e+01 1.00e-02 8.40e+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 300.00 121.71 178.29 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O1B ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PB ADP D 401 " pdb=" PA ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 106.12 -166.12 1 2.00e+01 2.50e-03 4.73e+01 ... (remaining 14776 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 3235 0.082 - 0.164: 360 0.164 - 0.246: 32 0.246 - 0.328: 13 0.328 - 0.410: 1 Chirality restraints: 3641 Sorted by residual: chirality pdb=" CB VAL H1106 " pdb=" CA VAL H1106 " pdb=" CG1 VAL H1106 " pdb=" CG2 VAL H1106 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" CB ILE B 151 " pdb=" CA ILE B 151 " pdb=" CG1 ILE B 151 " pdb=" CG2 ILE B 151 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.66e+00 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 2.35 0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 3638 not shown) Planarity restraints: 4227 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 915 " -1.081 9.50e-02 1.11e+02 4.84e-01 1.41e+02 pdb=" NE ARG G 915 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG G 915 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG G 915 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG G 915 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 111 " 0.060 5.00e-02 4.00e+02 9.13e-02 1.33e+01 pdb=" N PRO B 112 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO B 112 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 112 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 111 " 0.052 5.00e-02 4.00e+02 7.95e-02 1.01e+01 pdb=" N PRO D 112 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO D 112 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 112 " 0.043 5.00e-02 4.00e+02 ... (remaining 4224 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.20: 12 2.20 - 2.87: 8180 2.87 - 3.55: 30284 3.55 - 4.22: 55941 4.22 - 4.90: 95472 Nonbonded interactions: 189889 Sorted by model distance: nonbonded pdb=" NH1 ARG G 915 " pdb=" N ARG G 917 " model vdw 1.519 3.200 nonbonded pdb=" NH1 ARG G 915 " pdb=" CB ARG G 917 " model vdw 2.007 3.520 nonbonded pdb=" NH1 ARG G 915 " pdb=" CA ARG G 917 " model vdw 2.092 3.550 nonbonded pdb=" O3A ADP D 401 " pdb="MG MG D 402 " model vdw 2.093 2.170 nonbonded pdb=" O2A ADP E 401 " pdb="MG MG E 402 " model vdw 2.104 2.170 ... (remaining 189884 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' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'G' and (resid 750 through 803 or resid 836 through 1143)) selection = (chain 'H' and (resid 750 through 803 or resid 836 through 1143)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.010 Normalize map: mean=0, sd=1: 5.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 24.220 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 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 : 0.004 0.074 24323 Z= 0.220 Angle : 0.819 11.004 32908 Z= 0.441 Chirality : 0.053 0.410 3641 Planarity : 0.011 0.484 4227 Dihedral : 15.443 178.291 9167 Min Nonbonded Distance : 1.519 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.73 % Favored : 96.14 % Rotamer: Outliers : 0.23 % Allowed : 0.27 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.27 (0.13), residues: 2953 helix: -3.33 (0.08), residues: 1378 sheet: -0.42 (0.25), residues: 396 loop : -0.97 (0.17), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 116 TYR 0.015 0.001 TYR H1104 PHE 0.029 0.002 PHE G1020 TRP 0.021 0.002 TRP H 767 HIS 0.005 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00439 (24318) covalent geometry : angle 0.81912 (32908) hydrogen bonds : bond 0.17412 ( 1151) hydrogen bonds : angle 7.61321 ( 3210) Misc. bond : bond 0.00306 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 362 time to evaluate : 1.029 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: symmetry clash REVERT: A 34 ILE cc_start: 0.8877 (pt) cc_final: 0.8538 (tp) REVERT: A 51 ASP cc_start: 0.8659 (p0) cc_final: 0.8449 (t0) REVERT: A 225 ASN cc_start: 0.8689 (m-40) cc_final: 0.8455 (t0) REVERT: A 269 MET cc_start: 0.8561 (mtp) cc_final: 0.8267 (mtt) REVERT: A 305 MET cc_start: 0.8701 (mmm) cc_final: 0.8499 (mmm) REVERT: B 123 MET cc_start: 0.8599 (mmt) cc_final: 0.8156 (mmm) REVERT: B 257 CYS cc_start: 0.8991 (t) cc_final: 0.8751 (p) REVERT: B 283 MET cc_start: 0.7367 (mmm) cc_final: 0.6840 (tmm) REVERT: D 25 ASP cc_start: 0.7489 (m-30) cc_final: 0.7077 (p0) REVERT: D 82 MET cc_start: 0.8832 (tpt) cc_final: 0.8305 (mmm) REVERT: D 190 MET cc_start: 0.7896 (mtp) cc_final: 0.7545 (mtt) REVERT: D 299 MET cc_start: 0.8200 (mtm) cc_final: 0.7627 (mtt) REVERT: D 363 ASP cc_start: 0.8911 (m-30) cc_final: 0.8562 (p0) REVERT: E 10 CYS cc_start: 0.8374 (t) cc_final: 0.7899 (t) REVERT: E 12 ASN cc_start: 0.7608 (m110) cc_final: 0.6933 (m-40) REVERT: E 121 GLN cc_start: 0.9280 (tt0) cc_final: 0.8969 (tm-30) REVERT: E 132 MET cc_start: 0.8322 (ppp) cc_final: 0.8024 (ptt) REVERT: E 142 LEU cc_start: 0.7239 (tp) cc_final: 0.6852 (tp) REVERT: E 149 THR cc_start: 0.8340 (t) cc_final: 0.8131 (m) REVERT: E 325 MET cc_start: 0.8172 (mmm) cc_final: 0.7840 (mpp) REVERT: E 354 GLN cc_start: 0.9245 (pt0) cc_final: 0.9011 (pp30) REVERT: E 355 MET cc_start: 0.8388 (mtp) cc_final: 0.7943 (mtp) REVERT: F 119 MET cc_start: 0.8625 (mtp) cc_final: 0.8359 (mtm) REVERT: F 191 LYS cc_start: 0.9092 (tttm) cc_final: 0.8864 (ttmt) REVERT: F 340 TRP cc_start: 0.7089 (t60) cc_final: 0.6318 (t60) REVERT: G 869 LEU cc_start: 0.7166 (mt) cc_final: 0.6931 (mt) REVERT: G 1019 LYS cc_start: 0.9596 (mttt) cc_final: 0.9306 (mtmm) REVERT: G 1026 HIS cc_start: 0.8657 (m90) cc_final: 0.8354 (m-70) REVERT: G 1090 MET cc_start: 0.8786 (mtp) cc_final: 0.8307 (mmm) REVERT: G 1118 PHE cc_start: 0.9349 (m-80) cc_final: 0.9120 (m-80) REVERT: G 1143 GLU cc_start: 0.9012 (tt0) cc_final: 0.8590 (pt0) REVERT: H 889 MET cc_start: 0.8166 (mtm) cc_final: 0.7852 (tmm) REVERT: H 1071 GLU cc_start: 0.8417 (tt0) cc_final: 0.7871 (mp0) outliers start: 6 outliers final: 2 residues processed: 368 average time/residue: 0.1813 time to fit residues: 103.8705 Evaluate side-chains 211 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 209 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 915 ARG Chi-restraints excluded: chain G residue 1113 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 GLN B 12 ASN D 12 ASN D 162 ASN E 162 ASN F 41 GLN F 59 GLN ** F 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.080488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.059433 restraints weight = 102699.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.061153 restraints weight = 46108.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.062261 restraints weight = 26499.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.063048 restraints weight = 18013.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.063478 restraints weight = 13874.048| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24323 Z= 0.127 Angle : 0.597 6.978 32908 Z= 0.298 Chirality : 0.042 0.189 3641 Planarity : 0.005 0.074 4227 Dihedral : 11.304 179.176 3318 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.78 % Allowed : 6.01 % Favored : 93.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.14), residues: 2953 helix: -0.60 (0.12), residues: 1386 sheet: -0.10 (0.27), residues: 396 loop : -0.52 (0.18), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 95 TYR 0.018 0.001 TYR G 969 PHE 0.020 0.001 PHE G1107 TRP 0.013 0.001 TRP G 767 HIS 0.007 0.001 HIS H1122 Details of bonding type rmsd covalent geometry : bond 0.00287 (24318) covalent geometry : angle 0.59685 (32908) hydrogen bonds : bond 0.03457 ( 1151) hydrogen bonds : angle 4.46529 ( 3210) Misc. bond : bond 0.00159 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 214 time to evaluate : 0.888 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 176 MET cc_start: 0.8447 (mmm) cc_final: 0.8042 (mtp) REVERT: A 269 MET cc_start: 0.8418 (mtp) cc_final: 0.8159 (mtt) REVERT: B 44 MET cc_start: 0.8164 (mmp) cc_final: 0.7508 (ptp) REVERT: B 123 MET cc_start: 0.8582 (mmt) cc_final: 0.8337 (mmm) REVERT: B 283 MET cc_start: 0.7203 (mmm) cc_final: 0.6761 (tmm) REVERT: C 47 MET cc_start: 0.5701 (ppp) cc_final: 0.5501 (ppp) REVERT: D 25 ASP cc_start: 0.7209 (m-30) cc_final: 0.6997 (p0) REVERT: D 82 MET cc_start: 0.8801 (tpt) cc_final: 0.7992 (mmm) REVERT: D 190 MET cc_start: 0.8169 (mtp) cc_final: 0.7818 (mtt) REVERT: D 299 MET cc_start: 0.8251 (mtm) cc_final: 0.7741 (mtt) REVERT: D 361 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8249 (mp0) REVERT: E 132 MET cc_start: 0.7883 (ppp) cc_final: 0.7660 (ptt) REVERT: E 142 LEU cc_start: 0.7307 (tp) cc_final: 0.7011 (tp) REVERT: E 227 MET cc_start: 0.7322 (mmm) cc_final: 0.6845 (mmm) REVERT: E 325 MET cc_start: 0.8128 (mmm) cc_final: 0.7845 (mpp) REVERT: E 355 MET cc_start: 0.8330 (mtp) cc_final: 0.7908 (mtp) REVERT: F 191 LYS cc_start: 0.9164 (tttm) cc_final: 0.8960 (ttmt) REVERT: F 369 ILE cc_start: 0.7553 (OUTLIER) cc_final: 0.7268 (tt) REVERT: G 1019 LYS cc_start: 0.9612 (mttt) cc_final: 0.9369 (mtmm) REVERT: G 1026 HIS cc_start: 0.8658 (m90) cc_final: 0.8328 (m-70) REVERT: G 1143 GLU cc_start: 0.8832 (tt0) cc_final: 0.8475 (pt0) REVERT: H 889 MET cc_start: 0.8064 (mtm) cc_final: 0.7798 (tmm) REVERT: H 1071 GLU cc_start: 0.8621 (tt0) cc_final: 0.8254 (pm20) REVERT: H 1089 MET cc_start: 0.8577 (ptt) cc_final: 0.8217 (mmp) outliers start: 20 outliers final: 8 residues processed: 228 average time/residue: 0.1461 time to fit residues: 54.4461 Evaluate side-chains 198 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 189 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain F residue 369 ILE Chi-restraints excluded: chain G residue 762 LEU Chi-restraints excluded: chain H residue 1065 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 212 optimal weight: 0.1980 chunk 233 optimal weight: 0.6980 chunk 167 optimal weight: 0.3980 chunk 294 optimal weight: 6.9990 chunk 232 optimal weight: 0.9980 chunk 200 optimal weight: 0.9980 chunk 291 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 275 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 270 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 40 HIS ** E 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H1091 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.080351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.059224 restraints weight = 103455.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.060998 restraints weight = 45382.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.062123 restraints weight = 25649.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.062831 restraints weight = 17347.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.063378 restraints weight = 13383.896| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 24323 Z= 0.101 Angle : 0.553 9.721 32908 Z= 0.268 Chirality : 0.041 0.146 3641 Planarity : 0.004 0.065 4227 Dihedral : 10.255 176.477 3313 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.78 % Allowed : 6.79 % Favored : 92.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.15), residues: 2953 helix: 0.50 (0.14), residues: 1423 sheet: 0.08 (0.27), residues: 396 loop : -0.25 (0.19), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 95 TYR 0.014 0.001 TYR A 143 PHE 0.017 0.001 PHE G1107 TRP 0.009 0.001 TRP G 781 HIS 0.004 0.001 HIS H1122 Details of bonding type rmsd covalent geometry : bond 0.00227 (24318) covalent geometry : angle 0.55269 (32908) hydrogen bonds : bond 0.02929 ( 1151) hydrogen bonds : angle 4.11621 ( 3210) Misc. bond : bond 0.00100 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 201 time to evaluate : 1.140 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: symmetry clash REVERT: A 123 MET cc_start: 0.8557 (tpp) cc_final: 0.8255 (mmm) REVERT: A 269 MET cc_start: 0.8378 (mtp) cc_final: 0.8111 (mtt) REVERT: B 44 MET cc_start: 0.8067 (mmp) cc_final: 0.7476 (ptp) REVERT: B 82 MET cc_start: 0.8870 (tpt) cc_final: 0.7963 (tmm) REVERT: B 283 MET cc_start: 0.7186 (mmm) cc_final: 0.6816 (tmm) REVERT: D 299 MET cc_start: 0.8287 (mtm) cc_final: 0.7764 (mtt) REVERT: D 361 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8131 (mp0) REVERT: E 44 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7953 (tpp) REVERT: E 132 MET cc_start: 0.7974 (ppp) cc_final: 0.7690 (ptt) REVERT: E 142 LEU cc_start: 0.7448 (tp) cc_final: 0.7083 (tp) REVERT: E 227 MET cc_start: 0.7410 (mmm) cc_final: 0.6986 (mmm) REVERT: F 119 MET cc_start: 0.8782 (mtm) cc_final: 0.8577 (mtp) REVERT: F 191 LYS cc_start: 0.9189 (tttm) cc_final: 0.8980 (ttmt) REVERT: G 1000 MET cc_start: 0.8921 (ppp) cc_final: 0.7868 (ppp) REVERT: G 1019 LYS cc_start: 0.9607 (mttt) cc_final: 0.9351 (mtmm) REVERT: G 1026 HIS cc_start: 0.8723 (m90) cc_final: 0.8351 (m-70) REVERT: G 1143 GLU cc_start: 0.8759 (tt0) cc_final: 0.8432 (pt0) REVERT: H 854 TYR cc_start: 0.5328 (m-80) cc_final: 0.5023 (m-10) REVERT: H 889 MET cc_start: 0.8024 (mtm) cc_final: 0.7748 (tmm) REVERT: H 1071 GLU cc_start: 0.8661 (tt0) cc_final: 0.8270 (pm20) REVERT: H 1089 MET cc_start: 0.8548 (ptt) cc_final: 0.8163 (mmp) REVERT: H 1090 MET cc_start: 0.7104 (mmt) cc_final: 0.6896 (mmt) outliers start: 20 outliers final: 12 residues processed: 213 average time/residue: 0.1539 time to fit residues: 54.6982 Evaluate side-chains 198 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 185 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 762 LEU Chi-restraints excluded: chain H residue 1094 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 231 optimal weight: 4.9990 chunk 172 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 259 optimal weight: 9.9990 chunk 196 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 220 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 26 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 HIS ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS D 137 GLN ** E 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 ASN F 161 HIS F 162 ASN G1093 ASN ** G1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1123 ASN H1130 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.076191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.055044 restraints weight = 106191.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.056646 restraints weight = 48795.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.057695 restraints weight = 28543.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.058429 restraints weight = 19814.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.058882 restraints weight = 15416.104| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 24323 Z= 0.273 Angle : 0.690 11.874 32908 Z= 0.344 Chirality : 0.046 0.168 3641 Planarity : 0.005 0.057 4227 Dihedral : 9.724 170.274 3313 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.01 % Allowed : 8.46 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.16), residues: 2953 helix: 0.83 (0.14), residues: 1416 sheet: -0.45 (0.27), residues: 372 loop : -0.06 (0.19), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 372 TYR 0.020 0.002 TYR B 306 PHE 0.021 0.002 PHE E 255 TRP 0.010 0.002 TRP F 79 HIS 0.006 0.001 HIS E 87 Details of bonding type rmsd covalent geometry : bond 0.00621 (24318) covalent geometry : angle 0.69006 (32908) hydrogen bonds : bond 0.03606 ( 1151) hydrogen bonds : angle 4.45099 ( 3210) Misc. bond : bond 0.00254 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 176 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.8578 (tpp) cc_final: 0.8374 (mmm) REVERT: A 176 MET cc_start: 0.8489 (mmm) cc_final: 0.8277 (mtt) REVERT: B 44 MET cc_start: 0.8104 (mmp) cc_final: 0.7290 (ptp) REVERT: B 283 MET cc_start: 0.7234 (mmm) cc_final: 0.6797 (tmm) REVERT: C 82 MET cc_start: 0.8586 (mtp) cc_final: 0.8221 (mtp) REVERT: D 82 MET cc_start: 0.8584 (tpp) cc_final: 0.7869 (mmm) REVERT: D 299 MET cc_start: 0.8438 (mtm) cc_final: 0.8113 (mtm) REVERT: D 361 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8151 (mp0) REVERT: E 44 MET cc_start: 0.8532 (tpp) cc_final: 0.8093 (tpp) REVERT: E 132 MET cc_start: 0.8283 (ppp) cc_final: 0.7766 (ppp) REVERT: E 142 LEU cc_start: 0.7418 (tp) cc_final: 0.7074 (tp) REVERT: E 346 LEU cc_start: 0.9417 (tp) cc_final: 0.9214 (tt) REVERT: F 82 MET cc_start: 0.8545 (tpt) cc_final: 0.8235 (tpt) REVERT: F 119 MET cc_start: 0.8899 (mtm) cc_final: 0.8671 (mtp) REVERT: F 191 LYS cc_start: 0.9271 (tttm) cc_final: 0.8880 (ttmm) REVERT: G 1019 LYS cc_start: 0.9621 (mttt) cc_final: 0.9381 (mtmm) REVERT: G 1026 HIS cc_start: 0.8752 (m90) cc_final: 0.8384 (m-70) REVERT: G 1127 MET cc_start: 0.9565 (mtm) cc_final: 0.9204 (mtm) REVERT: H 852 MET cc_start: 0.6463 (ttm) cc_final: 0.6207 (ttp) REVERT: H 889 MET cc_start: 0.8128 (mtm) cc_final: 0.7806 (tmm) REVERT: H 1026 HIS cc_start: 0.7465 (OUTLIER) cc_final: 0.6991 (t-90) REVERT: H 1071 GLU cc_start: 0.8763 (tt0) cc_final: 0.8327 (pm20) REVERT: H 1089 MET cc_start: 0.8346 (ptt) cc_final: 0.7964 (mmp) REVERT: H 1090 MET cc_start: 0.7216 (mmt) cc_final: 0.7008 (mmt) outliers start: 26 outliers final: 21 residues processed: 196 average time/residue: 0.1606 time to fit residues: 51.6594 Evaluate side-chains 190 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain G residue 859 ASN Chi-restraints excluded: chain G residue 1113 SER Chi-restraints excluded: chain H residue 1026 HIS Chi-restraints excluded: chain H residue 1066 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 99 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 152 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 256 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 267 optimal weight: 10.0000 chunk 115 optimal weight: 0.1980 chunk 111 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS E 354 GLN ** G1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.078355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.057393 restraints weight = 103264.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.059045 restraints weight = 46947.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.060071 restraints weight = 27186.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.060822 restraints weight = 18828.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.061250 restraints weight = 14588.927| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 24323 Z= 0.101 Angle : 0.554 10.378 32908 Z= 0.268 Chirality : 0.041 0.143 3641 Planarity : 0.004 0.061 4227 Dihedral : 8.899 164.598 3313 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.78 % Allowed : 9.43 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.16), residues: 2953 helix: 1.18 (0.14), residues: 1418 sheet: -0.22 (0.28), residues: 366 loop : 0.08 (0.19), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 372 TYR 0.024 0.001 TYR A 143 PHE 0.016 0.001 PHE G1107 TRP 0.011 0.001 TRP E 79 HIS 0.003 0.001 HIS E 87 Details of bonding type rmsd covalent geometry : bond 0.00230 (24318) covalent geometry : angle 0.55442 (32908) hydrogen bonds : bond 0.02857 ( 1151) hydrogen bonds : angle 4.05732 ( 3210) Misc. bond : bond 0.00114 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 178 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8838 (tpp) cc_final: 0.8609 (tpp) REVERT: A 123 MET cc_start: 0.8568 (tpp) cc_final: 0.8359 (mmm) REVERT: B 82 MET cc_start: 0.9101 (mmm) cc_final: 0.8823 (mmm) REVERT: B 132 MET cc_start: 0.8149 (tmm) cc_final: 0.7900 (tmm) REVERT: B 283 MET cc_start: 0.7187 (mmm) cc_final: 0.6802 (tmm) REVERT: C 82 MET cc_start: 0.8507 (mtp) cc_final: 0.8241 (mtp) REVERT: C 299 MET cc_start: 0.8444 (mtm) cc_final: 0.8171 (mtp) REVERT: D 82 MET cc_start: 0.8461 (tpp) cc_final: 0.8218 (mmm) REVERT: D 299 MET cc_start: 0.8437 (mtm) cc_final: 0.7877 (mtt) REVERT: D 361 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8065 (mp0) REVERT: E 44 MET cc_start: 0.8465 (tpp) cc_final: 0.8060 (tpp) REVERT: E 132 MET cc_start: 0.8202 (ppp) cc_final: 0.7779 (ppp) REVERT: E 142 LEU cc_start: 0.7302 (tp) cc_final: 0.6941 (tp) REVERT: E 227 MET cc_start: 0.7448 (mmm) cc_final: 0.7107 (mmm) REVERT: F 82 MET cc_start: 0.8424 (tpt) cc_final: 0.8161 (tpt) REVERT: F 119 MET cc_start: 0.8911 (mtm) cc_final: 0.8672 (mtp) REVERT: F 191 LYS cc_start: 0.9203 (tttm) cc_final: 0.8854 (ttmm) REVERT: F 369 ILE cc_start: 0.7783 (OUTLIER) cc_final: 0.7355 (tt) REVERT: G 1019 LYS cc_start: 0.9604 (mttt) cc_final: 0.9363 (mtmm) REVERT: G 1026 HIS cc_start: 0.8870 (m90) cc_final: 0.8508 (m-70) REVERT: G 1094 MET cc_start: 0.8941 (ttp) cc_final: 0.8709 (mtm) REVERT: G 1119 MET cc_start: 0.9171 (mtt) cc_final: 0.8890 (mmm) REVERT: H 889 MET cc_start: 0.7957 (mtm) cc_final: 0.7609 (tmm) REVERT: H 1066 LYS cc_start: 0.6168 (OUTLIER) cc_final: 0.5785 (tmtt) REVERT: H 1071 GLU cc_start: 0.8759 (tt0) cc_final: 0.8385 (pm20) REVERT: H 1089 MET cc_start: 0.8359 (ptt) cc_final: 0.7995 (mmp) outliers start: 20 outliers final: 10 residues processed: 194 average time/residue: 0.1465 time to fit residues: 47.6772 Evaluate side-chains 184 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 172 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 369 ILE Chi-restraints excluded: chain G residue 859 ASN Chi-restraints excluded: chain H residue 1066 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 219 optimal weight: 2.9990 chunk 286 optimal weight: 50.0000 chunk 96 optimal weight: 3.9990 chunk 165 optimal weight: 0.9980 chunk 195 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 chunk 176 optimal weight: 3.9990 chunk 201 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 276 optimal weight: 6.9990 chunk 135 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 ASN E 354 GLN ** G1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.077805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.056786 restraints weight = 104056.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.058400 restraints weight = 47534.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.059445 restraints weight = 27743.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.060240 restraints weight = 19236.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.060643 restraints weight = 14859.352| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24323 Z= 0.128 Angle : 0.571 10.731 32908 Z= 0.275 Chirality : 0.042 0.161 3641 Planarity : 0.004 0.054 4227 Dihedral : 8.636 165.480 3313 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.97 % Allowed : 10.01 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.16), residues: 2953 helix: 1.28 (0.14), residues: 1426 sheet: -0.26 (0.28), residues: 366 loop : 0.23 (0.19), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 372 TYR 0.029 0.001 TYR A 143 PHE 0.016 0.001 PHE G1107 TRP 0.024 0.001 TRP E 86 HIS 0.004 0.001 HIS E 87 Details of bonding type rmsd covalent geometry : bond 0.00295 (24318) covalent geometry : angle 0.57078 (32908) hydrogen bonds : bond 0.02885 ( 1151) hydrogen bonds : angle 4.01708 ( 3210) Misc. bond : bond 0.00109 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 177 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8858 (tpp) cc_final: 0.8625 (tpp) REVERT: A 143 TYR cc_start: 0.8218 (m-80) cc_final: 0.8002 (m-80) REVERT: B 44 MET cc_start: 0.8194 (mmp) cc_final: 0.7422 (ptp) REVERT: B 82 MET cc_start: 0.9108 (mmm) cc_final: 0.8846 (mmm) REVERT: B 132 MET cc_start: 0.8144 (tmm) cc_final: 0.7934 (tmm) REVERT: B 283 MET cc_start: 0.7191 (mmm) cc_final: 0.6759 (tmm) REVERT: C 82 MET cc_start: 0.8600 (mtp) cc_final: 0.8231 (mtp) REVERT: C 299 MET cc_start: 0.8530 (mtm) cc_final: 0.8236 (mtp) REVERT: C 325 MET cc_start: 0.6202 (mmt) cc_final: 0.5916 (mmt) REVERT: D 82 MET cc_start: 0.8493 (tpp) cc_final: 0.7465 (mmm) REVERT: D 299 MET cc_start: 0.8480 (mtm) cc_final: 0.7916 (mtt) REVERT: D 361 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8124 (mp0) REVERT: E 44 MET cc_start: 0.8488 (tpp) cc_final: 0.8102 (tpp) REVERT: E 123 MET cc_start: 0.8999 (mmt) cc_final: 0.8795 (mmm) REVERT: E 132 MET cc_start: 0.8198 (ppp) cc_final: 0.7813 (ppp) REVERT: E 142 LEU cc_start: 0.7344 (tp) cc_final: 0.7019 (tp) REVERT: E 227 MET cc_start: 0.7590 (mmm) cc_final: 0.7227 (mmm) REVERT: E 325 MET cc_start: 0.8106 (mmm) cc_final: 0.6687 (mmm) REVERT: F 82 MET cc_start: 0.8458 (tpt) cc_final: 0.7933 (tpt) REVERT: F 119 MET cc_start: 0.8955 (mtm) cc_final: 0.8710 (mtp) REVERT: F 191 LYS cc_start: 0.9187 (tttm) cc_final: 0.8849 (ttmm) REVERT: F 369 ILE cc_start: 0.7790 (OUTLIER) cc_final: 0.7395 (tt) REVERT: G 1019 LYS cc_start: 0.9622 (mttt) cc_final: 0.9374 (mtmm) REVERT: G 1026 HIS cc_start: 0.8824 (m90) cc_final: 0.8463 (m90) REVERT: G 1094 MET cc_start: 0.8956 (ttp) cc_final: 0.8722 (mtm) REVERT: H 852 MET cc_start: 0.6171 (ttp) cc_final: 0.5952 (ttp) REVERT: H 889 MET cc_start: 0.7936 (mtm) cc_final: 0.7588 (tmm) REVERT: H 1066 LYS cc_start: 0.6001 (OUTLIER) cc_final: 0.5633 (tmtt) REVERT: H 1071 GLU cc_start: 0.8779 (tt0) cc_final: 0.8352 (pm20) REVERT: H 1089 MET cc_start: 0.8322 (ptt) cc_final: 0.7907 (mmp) REVERT: H 1090 MET cc_start: 0.6845 (mmt) cc_final: 0.6474 (mmt) REVERT: H 1119 MET cc_start: 0.7173 (ptt) cc_final: 0.6812 (mmm) outliers start: 25 outliers final: 16 residues processed: 195 average time/residue: 0.1508 time to fit residues: 48.5128 Evaluate side-chains 191 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 173 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 326 LYS Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 369 ILE Chi-restraints excluded: chain G residue 762 LEU Chi-restraints excluded: chain G residue 859 ASN Chi-restraints excluded: chain H residue 1066 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 120 optimal weight: 5.9990 chunk 170 optimal weight: 5.9990 chunk 55 optimal weight: 0.3980 chunk 185 optimal weight: 10.0000 chunk 243 optimal weight: 5.9990 chunk 238 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 246 optimal weight: 0.2980 chunk 102 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 242 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.077077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.056141 restraints weight = 104542.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.057733 restraints weight = 47894.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.058724 restraints weight = 28026.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.059475 restraints weight = 19463.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.059878 restraints weight = 15097.036| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24323 Z= 0.150 Angle : 0.581 10.744 32908 Z= 0.282 Chirality : 0.043 0.159 3641 Planarity : 0.004 0.064 4227 Dihedral : 8.477 166.030 3313 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.97 % Allowed : 10.12 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.16), residues: 2953 helix: 1.32 (0.14), residues: 1424 sheet: -0.32 (0.28), residues: 366 loop : 0.28 (0.20), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G1088 TYR 0.024 0.001 TYR A 143 PHE 0.016 0.001 PHE G1107 TRP 0.016 0.001 TRP E 86 HIS 0.004 0.001 HIS E 87 Details of bonding type rmsd covalent geometry : bond 0.00346 (24318) covalent geometry : angle 0.58137 (32908) hydrogen bonds : bond 0.02959 ( 1151) hydrogen bonds : angle 4.05139 ( 3210) Misc. bond : bond 0.00138 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.8674 (tpp) cc_final: 0.8228 (tmm) REVERT: A 176 MET cc_start: 0.8480 (mmm) cc_final: 0.8258 (mmt) REVERT: A 362 TYR cc_start: 0.8992 (t80) cc_final: 0.8470 (t80) REVERT: B 44 MET cc_start: 0.8123 (mmp) cc_final: 0.7339 (ptt) REVERT: B 82 MET cc_start: 0.9121 (mmm) cc_final: 0.8848 (mmm) REVERT: B 283 MET cc_start: 0.7198 (mmm) cc_final: 0.6767 (tmm) REVERT: C 82 MET cc_start: 0.8707 (mtp) cc_final: 0.8324 (mtp) REVERT: C 123 MET cc_start: 0.8454 (tpp) cc_final: 0.8128 (tpp) REVERT: C 299 MET cc_start: 0.8554 (mtm) cc_final: 0.8259 (mtp) REVERT: D 82 MET cc_start: 0.8545 (tpp) cc_final: 0.7898 (mmm) REVERT: D 299 MET cc_start: 0.8461 (mtm) cc_final: 0.7899 (mtt) REVERT: E 44 MET cc_start: 0.8486 (tpp) cc_final: 0.8119 (tpp) REVERT: E 132 MET cc_start: 0.8272 (ppp) cc_final: 0.7894 (ppp) REVERT: E 142 LEU cc_start: 0.7362 (tp) cc_final: 0.7035 (tp) REVERT: E 227 MET cc_start: 0.7611 (mmm) cc_final: 0.7247 (mmm) REVERT: F 44 MET cc_start: 0.9165 (mmm) cc_final: 0.8640 (mmm) REVERT: F 82 MET cc_start: 0.8500 (tpt) cc_final: 0.7976 (tpt) REVERT: F 119 MET cc_start: 0.9001 (mtm) cc_final: 0.8742 (mtp) REVERT: F 191 LYS cc_start: 0.9181 (tttm) cc_final: 0.8852 (ttmm) REVERT: F 325 MET cc_start: 0.7638 (tpp) cc_final: 0.7410 (tpp) REVERT: F 369 ILE cc_start: 0.7799 (OUTLIER) cc_final: 0.7455 (tt) REVERT: G 1019 LYS cc_start: 0.9625 (mttt) cc_final: 0.9379 (mtmm) REVERT: G 1026 HIS cc_start: 0.8858 (m90) cc_final: 0.8456 (m90) REVERT: G 1089 MET cc_start: 0.9188 (ppp) cc_final: 0.8914 (ppp) REVERT: G 1090 MET cc_start: 0.8672 (mmm) cc_final: 0.8280 (mtt) REVERT: G 1127 MET cc_start: 0.9592 (mtm) cc_final: 0.9216 (mtm) REVERT: H 756 TYR cc_start: 0.5172 (m-80) cc_final: 0.3803 (m-10) REVERT: H 889 MET cc_start: 0.8061 (mtm) cc_final: 0.7666 (tmm) REVERT: H 1066 LYS cc_start: 0.6034 (OUTLIER) cc_final: 0.5679 (tmtt) REVERT: H 1071 GLU cc_start: 0.8804 (tt0) cc_final: 0.8374 (pm20) REVERT: H 1089 MET cc_start: 0.8342 (ptt) cc_final: 0.7917 (mmp) REVERT: H 1090 MET cc_start: 0.6936 (mmt) cc_final: 0.6667 (mmt) outliers start: 25 outliers final: 16 residues processed: 195 average time/residue: 0.1501 time to fit residues: 48.5198 Evaluate side-chains 189 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 171 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 326 LYS Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 369 ILE Chi-restraints excluded: chain G residue 859 ASN Chi-restraints excluded: chain G residue 1113 SER Chi-restraints excluded: chain H residue 1066 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 167 optimal weight: 0.0370 chunk 108 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 chunk 180 optimal weight: 4.9990 chunk 220 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 196 optimal weight: 0.7980 chunk 269 optimal weight: 4.9990 chunk 271 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 354 GLN ** G1136 GLN ** 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 = 0.3884 r_free = 0.3884 target = 0.078321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.057373 restraints weight = 103668.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.059002 restraints weight = 47148.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.060058 restraints weight = 27368.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.060696 restraints weight = 18919.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.061243 restraints weight = 14872.095| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24323 Z= 0.096 Angle : 0.568 11.493 32908 Z= 0.270 Chirality : 0.041 0.209 3641 Planarity : 0.003 0.052 4227 Dihedral : 8.242 165.097 3313 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.89 % Allowed : 10.59 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.16), residues: 2953 helix: 1.42 (0.15), residues: 1432 sheet: 0.03 (0.27), residues: 402 loop : 0.33 (0.20), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 372 TYR 0.032 0.001 TYR A 143 PHE 0.016 0.001 PHE G1107 TRP 0.009 0.001 TRP E 79 HIS 0.003 0.001 HIS D 40 Details of bonding type rmsd covalent geometry : bond 0.00222 (24318) covalent geometry : angle 0.56760 (32908) hydrogen bonds : bond 0.02705 ( 1151) hydrogen bonds : angle 3.93994 ( 3210) Misc. bond : bond 0.00114 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 181 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.8642 (mm) cc_final: 0.8427 (pp) REVERT: A 82 MET cc_start: 0.8709 (tpp) cc_final: 0.8470 (tpp) REVERT: A 123 MET cc_start: 0.8578 (tpp) cc_final: 0.8181 (tmm) REVERT: A 362 TYR cc_start: 0.8958 (t80) cc_final: 0.8519 (t80) REVERT: B 44 MET cc_start: 0.8066 (mmp) cc_final: 0.7195 (ptt) REVERT: B 82 MET cc_start: 0.9096 (mmm) cc_final: 0.8861 (mmm) REVERT: B 283 MET cc_start: 0.7165 (mmm) cc_final: 0.6794 (tmm) REVERT: C 82 MET cc_start: 0.8685 (mtp) cc_final: 0.8295 (mtp) REVERT: C 299 MET cc_start: 0.8495 (mtm) cc_final: 0.8172 (mtp) REVERT: C 325 MET cc_start: 0.5910 (mmt) cc_final: 0.5674 (mmm) REVERT: D 82 MET cc_start: 0.8451 (tpp) cc_final: 0.7414 (mmm) REVERT: D 132 MET cc_start: 0.8515 (tmm) cc_final: 0.8262 (tmm) REVERT: D 299 MET cc_start: 0.8446 (mtm) cc_final: 0.7946 (mtt) REVERT: D 361 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8307 (mp0) REVERT: E 47 MET cc_start: 0.5925 (OUTLIER) cc_final: 0.5724 (ptt) REVERT: E 132 MET cc_start: 0.8167 (ppp) cc_final: 0.7812 (ppp) REVERT: E 142 LEU cc_start: 0.7323 (tp) cc_final: 0.6945 (tp) REVERT: E 227 MET cc_start: 0.7552 (mmm) cc_final: 0.7164 (mmm) REVERT: E 325 MET cc_start: 0.7919 (mmm) cc_final: 0.6796 (mmm) REVERT: F 82 MET cc_start: 0.8426 (tpt) cc_final: 0.7907 (tpt) REVERT: F 119 MET cc_start: 0.8986 (mtm) cc_final: 0.8738 (mtp) REVERT: F 191 LYS cc_start: 0.9175 (tttm) cc_final: 0.8841 (ttmm) REVERT: F 325 MET cc_start: 0.7591 (tpp) cc_final: 0.7343 (tpp) REVERT: F 369 ILE cc_start: 0.7758 (OUTLIER) cc_final: 0.7519 (tt) REVERT: G 1019 LYS cc_start: 0.9611 (mttt) cc_final: 0.9358 (mtmm) REVERT: G 1026 HIS cc_start: 0.8893 (m90) cc_final: 0.8539 (m-70) REVERT: G 1089 MET cc_start: 0.9173 (ppp) cc_final: 0.8894 (ppp) REVERT: G 1090 MET cc_start: 0.8655 (mmm) cc_final: 0.8223 (mtt) REVERT: H 756 TYR cc_start: 0.5141 (m-80) cc_final: 0.3782 (m-10) REVERT: H 852 MET cc_start: 0.6021 (ttp) cc_final: 0.5269 (tmm) REVERT: H 889 MET cc_start: 0.8006 (mtm) cc_final: 0.7609 (tmm) REVERT: H 1071 GLU cc_start: 0.8762 (tt0) cc_final: 0.8335 (pm20) REVERT: H 1089 MET cc_start: 0.8323 (ptt) cc_final: 0.7890 (mmp) REVERT: H 1090 MET cc_start: 0.7148 (mmt) cc_final: 0.6946 (mmt) outliers start: 23 outliers final: 16 residues processed: 197 average time/residue: 0.1549 time to fit residues: 50.5338 Evaluate side-chains 191 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 173 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 326 LYS Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 294 TYR Chi-restraints excluded: chain F residue 369 ILE Chi-restraints excluded: chain G residue 762 LEU Chi-restraints excluded: chain G residue 859 ASN Chi-restraints excluded: chain G residue 1113 SER Chi-restraints excluded: chain H residue 1066 LYS Chi-restraints excluded: chain H residue 1094 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 205 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 167 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 267 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN E 354 GLN ** G1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.076588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.055722 restraints weight = 105437.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.057299 restraints weight = 48403.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.058336 restraints weight = 28368.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.058989 restraints weight = 19651.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.059516 restraints weight = 15322.974| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 24323 Z= 0.181 Angle : 0.626 10.246 32908 Z= 0.304 Chirality : 0.044 0.204 3641 Planarity : 0.004 0.073 4227 Dihedral : 8.417 163.088 3313 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.93 % Allowed : 10.82 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.16), residues: 2953 helix: 1.38 (0.14), residues: 1420 sheet: -0.40 (0.27), residues: 366 loop : 0.28 (0.20), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 372 TYR 0.036 0.001 TYR A 143 PHE 0.018 0.002 PHE G1107 TRP 0.011 0.001 TRP H 767 HIS 0.005 0.001 HIS E 88 Details of bonding type rmsd covalent geometry : bond 0.00415 (24318) covalent geometry : angle 0.62598 (32908) hydrogen bonds : bond 0.03114 ( 1151) hydrogen bonds : angle 4.15647 ( 3210) Misc. bond : bond 0.00159 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.8666 (mm) cc_final: 0.8388 (pp) REVERT: A 123 MET cc_start: 0.8621 (tpp) cc_final: 0.8229 (tmm) REVERT: A 362 TYR cc_start: 0.9009 (t80) cc_final: 0.8385 (t80) REVERT: B 99 GLU cc_start: 0.9007 (OUTLIER) cc_final: 0.8795 (pm20) REVERT: B 107 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6136 (tm-30) REVERT: B 283 MET cc_start: 0.7215 (mmm) cc_final: 0.6779 (tmm) REVERT: C 82 MET cc_start: 0.8685 (mtp) cc_final: 0.8258 (mtp) REVERT: C 123 MET cc_start: 0.8558 (tpp) cc_final: 0.8217 (tpp) REVERT: C 299 MET cc_start: 0.8604 (mtm) cc_final: 0.8315 (mtp) REVERT: C 325 MET cc_start: 0.6239 (mmt) cc_final: 0.5911 (mmm) REVERT: D 82 MET cc_start: 0.8559 (tpp) cc_final: 0.7857 (mmm) REVERT: D 132 MET cc_start: 0.8598 (tmm) cc_final: 0.8323 (tmm) REVERT: D 299 MET cc_start: 0.8465 (mtm) cc_final: 0.7902 (mtt) REVERT: D 361 GLU cc_start: 0.8941 (mt-10) cc_final: 0.8366 (mp0) REVERT: E 132 MET cc_start: 0.8184 (ppp) cc_final: 0.7796 (ppp) REVERT: E 142 LEU cc_start: 0.7346 (tp) cc_final: 0.7064 (tp) REVERT: E 294 TYR cc_start: 0.8379 (OUTLIER) cc_final: 0.7401 (m-80) REVERT: E 325 MET cc_start: 0.7955 (mmm) cc_final: 0.6573 (tpt) REVERT: F 82 MET cc_start: 0.8544 (tpt) cc_final: 0.8000 (tpt) REVERT: F 119 MET cc_start: 0.9030 (mtm) cc_final: 0.8688 (mtp) REVERT: F 191 LYS cc_start: 0.9204 (tttm) cc_final: 0.8856 (ttmm) REVERT: F 325 MET cc_start: 0.7711 (tpp) cc_final: 0.7450 (tpp) REVERT: G 1019 LYS cc_start: 0.9631 (mttt) cc_final: 0.9377 (mtmm) REVERT: G 1026 HIS cc_start: 0.8919 (m90) cc_final: 0.8509 (m90) REVERT: G 1089 MET cc_start: 0.9216 (ppp) cc_final: 0.8975 (ppp) REVERT: G 1090 MET cc_start: 0.8727 (mmm) cc_final: 0.8274 (mtt) REVERT: H 756 TYR cc_start: 0.5277 (m-80) cc_final: 0.3857 (m-10) REVERT: H 889 MET cc_start: 0.8261 (mtm) cc_final: 0.7917 (tmm) REVERT: H 1066 LYS cc_start: 0.6065 (OUTLIER) cc_final: 0.5755 (tmtt) REVERT: H 1071 GLU cc_start: 0.8640 (tt0) cc_final: 0.8290 (pm20) REVERT: H 1089 MET cc_start: 0.8303 (ptt) cc_final: 0.7851 (mmp) outliers start: 24 outliers final: 16 residues processed: 188 average time/residue: 0.1530 time to fit residues: 47.4617 Evaluate side-chains 186 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 294 TYR Chi-restraints excluded: chain E residue 326 LYS Chi-restraints excluded: chain E residue 354 GLN Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 294 TYR Chi-restraints excluded: chain G residue 859 ASN Chi-restraints excluded: chain G residue 1113 SER Chi-restraints excluded: chain H residue 1066 LYS Chi-restraints excluded: chain H residue 1094 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 220 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 258 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 223 optimal weight: 20.0000 chunk 70 optimal weight: 2.9990 chunk 244 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 chunk 162 optimal weight: 3.9990 chunk 214 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 ASN C 297 ASN D 297 ASN D 354 GLN ** E 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 761 GLN ** G1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 761 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.074133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.053280 restraints weight = 107925.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.054782 restraints weight = 50415.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.055804 restraints weight = 30025.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.056400 restraints weight = 20968.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.056930 restraints weight = 16736.033| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.117 24323 Z= 0.330 Angle : 0.808 17.756 32908 Z= 0.402 Chirality : 0.049 0.195 3641 Planarity : 0.005 0.066 4227 Dihedral : 8.959 158.634 3313 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.93 % Allowed : 11.02 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.16), residues: 2953 helix: 0.77 (0.14), residues: 1423 sheet: -0.94 (0.26), residues: 372 loop : -0.12 (0.20), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 372 TYR 0.024 0.002 TYR E 337 PHE 0.027 0.002 PHE E 255 TRP 0.019 0.002 TRP H 767 HIS 0.010 0.002 HIS E 87 Details of bonding type rmsd covalent geometry : bond 0.00751 (24318) covalent geometry : angle 0.80817 (32908) hydrogen bonds : bond 0.03995 ( 1151) hydrogen bonds : angle 4.78153 ( 3210) Misc. bond : bond 0.00319 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.8612 (mm) cc_final: 0.8336 (pp) REVERT: A 119 MET cc_start: 0.8457 (ttm) cc_final: 0.7984 (mtp) REVERT: A 362 TYR cc_start: 0.9138 (t80) cc_final: 0.8387 (t80) REVERT: B 82 MET cc_start: 0.9114 (mmm) cc_final: 0.8811 (mmm) REVERT: B 107 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.6572 (tm-30) REVERT: B 283 MET cc_start: 0.7312 (mmm) cc_final: 0.6837 (tmm) REVERT: C 82 MET cc_start: 0.8765 (mtp) cc_final: 0.8311 (mtp) REVERT: C 123 MET cc_start: 0.8659 (tpp) cc_final: 0.8394 (tpp) REVERT: C 299 MET cc_start: 0.8648 (mtm) cc_final: 0.8380 (mtp) REVERT: C 325 MET cc_start: 0.6609 (mmt) cc_final: 0.6327 (mmt) REVERT: D 82 MET cc_start: 0.8542 (tpp) cc_final: 0.7850 (mmm) REVERT: D 299 MET cc_start: 0.8565 (mtm) cc_final: 0.8212 (mtm) REVERT: D 361 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8758 (tt0) REVERT: E 47 MET cc_start: 0.6244 (ptt) cc_final: 0.5635 (ptp) REVERT: E 132 MET cc_start: 0.8264 (ppp) cc_final: 0.7887 (ppp) REVERT: E 142 LEU cc_start: 0.7295 (tp) cc_final: 0.7060 (tp) REVERT: E 294 TYR cc_start: 0.8519 (OUTLIER) cc_final: 0.7555 (m-80) REVERT: E 325 MET cc_start: 0.7984 (mmm) cc_final: 0.6681 (tpt) REVERT: F 82 MET cc_start: 0.8625 (tpt) cc_final: 0.8388 (tpt) REVERT: F 119 MET cc_start: 0.9121 (mtm) cc_final: 0.8779 (mtp) REVERT: F 191 LYS cc_start: 0.9268 (tttm) cc_final: 0.8907 (ttmm) REVERT: G 1019 LYS cc_start: 0.9590 (mttt) cc_final: 0.9366 (mtmm) REVERT: G 1026 HIS cc_start: 0.9035 (m90) cc_final: 0.8684 (m-70) REVERT: G 1119 MET cc_start: 0.9281 (mtt) cc_final: 0.8915 (mmm) REVERT: G 1127 MET cc_start: 0.9618 (mtm) cc_final: 0.9190 (mtm) REVERT: H 756 TYR cc_start: 0.5395 (m-80) cc_final: 0.3921 (m-10) REVERT: H 852 MET cc_start: 0.6174 (tmm) cc_final: 0.5254 (tmm) REVERT: H 889 MET cc_start: 0.8350 (mtm) cc_final: 0.7893 (tmm) REVERT: H 1071 GLU cc_start: 0.8598 (tt0) cc_final: 0.8369 (pm20) REVERT: H 1089 MET cc_start: 0.8367 (ptt) cc_final: 0.7773 (mmp) outliers start: 24 outliers final: 17 residues processed: 185 average time/residue: 0.1632 time to fit residues: 49.7490 Evaluate side-chains 179 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 294 TYR Chi-restraints excluded: chain E residue 326 LYS Chi-restraints excluded: chain F residue 294 TYR Chi-restraints excluded: chain G residue 859 ASN Chi-restraints excluded: chain G residue 1113 SER Chi-restraints excluded: chain H residue 1094 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 182 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 chunk 156 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 296 optimal weight: 10.0000 chunk 235 optimal weight: 0.9980 chunk 209 optimal weight: 0.8980 chunk 285 optimal weight: 0.0370 chunk 181 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 HIS ** G 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1136 GLN ** 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 = 0.3859 r_free = 0.3859 target = 0.077184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.056338 restraints weight = 104015.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.057933 restraints weight = 47615.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.058999 restraints weight = 27880.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.059631 restraints weight = 19239.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.060146 restraints weight = 15149.966| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24323 Z= 0.111 Angle : 0.611 13.150 32908 Z= 0.294 Chirality : 0.043 0.201 3641 Planarity : 0.004 0.070 4227 Dihedral : 8.384 162.675 3313 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.66 % Allowed : 11.37 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.16), residues: 2953 helix: 1.35 (0.14), residues: 1430 sheet: -0.45 (0.27), residues: 360 loop : 0.26 (0.20), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G1088 TYR 0.039 0.001 TYR A 143 PHE 0.017 0.001 PHE G1117 TRP 0.014 0.002 TRP B 356 HIS 0.004 0.001 HIS F 161 Details of bonding type rmsd covalent geometry : bond 0.00251 (24318) covalent geometry : angle 0.61067 (32908) hydrogen bonds : bond 0.02935 ( 1151) hydrogen bonds : angle 4.16969 ( 3210) Misc. bond : bond 0.00113 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4586.12 seconds wall clock time: 79 minutes 54.50 seconds (4794.50 seconds total)