Starting phenix.real_space_refine on Fri Jun 20 19:09:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b27_44099/06_2025/9b27_44099.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b27_44099/06_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_44099/06_2025/9b27_44099.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b27_44099/06_2025/9b27_44099.map" model { file = "/net/cci-nas-00/data/ceres_data/9b27_44099/06_2025/9b27_44099.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b27_44099/06_2025/9b27_44099.cif" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.020 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.43, per 1000 atoms: 0.61 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: 5.34 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 2.90 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: 9.24 Time building geometry restraints manager: 6.46 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: 0.000 Normalize map: mean=0, sd=1: 5.200 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: 0.870 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 53.620 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.210 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.021 0.002 TRP H 767 HIS 0.005 0.001 HIS C 161 PHE 0.029 0.002 PHE G1020 TYR 0.015 0.001 TYR H1104 ARG 0.007 0.000 ARG B 116 Details of bonding type rmsd hydrogen bonds : bond 0.17412 ( 1151) hydrogen bonds : angle 7.61321 ( 3210) covalent geometry : bond 0.00439 (24318) covalent geometry : angle 0.81912 (32908) 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 : 2.627 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 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: 0.8752 (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: 0.6932 (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: 0.8132 (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: 0.9121 (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) REVERT: H 1127 MET cc_start: 0.6912 (mtt) cc_final: 0.6620 (ptp) outliers start: 6 outliers final: 2 residues processed: 368 average time/residue: 0.3938 time to fit residues: 228.1263 Evaluate side-chains 210 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 208 time to evaluate : 2.790 ------------------------------------------------------------------------------- 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 250 optimal weight: 2.9990 chunk 225 optimal weight: 8.9990 chunk 124 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 151 optimal weight: 8.9990 chunk 120 optimal weight: 2.9990 chunk 232 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 141 optimal weight: 0.9990 chunk 173 optimal weight: 2.9990 chunk 269 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.080528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.059427 restraints weight = 103853.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.061155 restraints weight = 46673.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.062299 restraints weight = 26825.087| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24323 Z= 0.123 Angle : 0.593 7.125 32908 Z= 0.295 Chirality : 0.042 0.183 3641 Planarity : 0.005 0.074 4227 Dihedral : 11.266 178.427 3318 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.78 % Allowed : 6.13 % Favored : 93.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.15), residues: 2953 helix: -0.55 (0.12), residues: 1386 sheet: -0.09 (0.27), residues: 396 loop : -0.51 (0.18), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 767 HIS 0.006 0.001 HIS H1122 PHE 0.018 0.001 PHE G1076 TYR 0.018 0.001 TYR H 854 ARG 0.007 0.000 ARG E 95 Details of bonding type rmsd hydrogen bonds : bond 0.03392 ( 1151) hydrogen bonds : angle 4.45584 ( 3210) covalent geometry : bond 0.00280 (24318) covalent geometry : angle 0.59287 (32908) Misc. bond : bond 0.00152 ( 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 : 2.535 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 269 MET cc_start: 0.8436 (mtp) cc_final: 0.8176 (mtt) REVERT: B 44 MET cc_start: 0.8234 (mmp) cc_final: 0.7520 (ptp) REVERT: B 123 MET cc_start: 0.8610 (mmt) cc_final: 0.8351 (mmm) REVERT: B 283 MET cc_start: 0.7248 (mmm) cc_final: 0.6806 (tmm) REVERT: C 47 MET cc_start: 0.5761 (ppp) cc_final: 0.5525 (ppp) REVERT: D 25 ASP cc_start: 0.7257 (m-30) cc_final: 0.7004 (p0) REVERT: D 82 MET cc_start: 0.8830 (tpt) cc_final: 0.7990 (mmm) REVERT: D 190 MET cc_start: 0.8169 (mtp) cc_final: 0.7820 (mtt) REVERT: D 299 MET cc_start: 0.8262 (mtm) cc_final: 0.7767 (mtt) REVERT: D 361 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8286 (mp0) REVERT: E 132 MET cc_start: 0.7848 (ppp) cc_final: 0.7627 (ptt) REVERT: E 142 LEU cc_start: 0.7324 (tp) cc_final: 0.7023 (tp) REVERT: E 227 MET cc_start: 0.7313 (mmm) cc_final: 0.6853 (mmm) REVERT: E 325 MET cc_start: 0.8142 (mmm) cc_final: 0.7886 (mpp) REVERT: E 355 MET cc_start: 0.8369 (mtp) cc_final: 0.7957 (mtp) REVERT: F 191 LYS cc_start: 0.9184 (tttm) cc_final: 0.8973 (ttmt) REVERT: F 369 ILE cc_start: 0.7530 (OUTLIER) cc_final: 0.7259 (tt) REVERT: G 1019 LYS cc_start: 0.9616 (mttt) cc_final: 0.9374 (mtmm) REVERT: G 1026 HIS cc_start: 0.8671 (m90) cc_final: 0.8341 (m-70) REVERT: G 1143 GLU cc_start: 0.8867 (tt0) cc_final: 0.8509 (pt0) REVERT: H 889 MET cc_start: 0.8119 (mtm) cc_final: 0.7828 (tmm) REVERT: H 1071 GLU cc_start: 0.8645 (tt0) cc_final: 0.8271 (pm20) REVERT: H 1089 MET cc_start: 0.8590 (ptt) cc_final: 0.8240 (mmp) outliers start: 20 outliers final: 8 residues processed: 228 average time/residue: 0.3480 time to fit residues: 128.8152 Evaluate side-chains 197 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 188 time to evaluate : 2.812 ------------------------------------------------------------------------------- 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 261 optimal weight: 0.0170 chunk 231 optimal weight: 9.9990 chunk 252 optimal weight: 5.9990 chunk 205 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 206 optimal weight: 2.9990 chunk 289 optimal weight: 7.9990 chunk 278 optimal weight: 5.9990 overall best weight: 3.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS B 12 ASN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 ASN C 371 HIS D 40 HIS D 137 GLN D 162 ASN ** 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** H1091 HIS H1130 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.076519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.055434 restraints weight = 105784.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.057038 restraints weight = 48588.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.058047 restraints weight = 28565.163| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 24323 Z= 0.263 Angle : 0.697 10.721 32908 Z= 0.350 Chirality : 0.046 0.175 3641 Planarity : 0.005 0.063 4227 Dihedral : 10.525 172.164 3313 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.01 % Allowed : 8.03 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.16), residues: 2953 helix: 0.51 (0.14), residues: 1410 sheet: -0.35 (0.32), residues: 282 loop : -0.30 (0.18), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 79 HIS 0.006 0.001 HIS E 87 PHE 0.021 0.002 PHE E 255 TYR 0.019 0.002 TYR C 306 ARG 0.006 0.001 ARG B 177 Details of bonding type rmsd hydrogen bonds : bond 0.03690 ( 1151) hydrogen bonds : angle 4.54376 ( 3210) covalent geometry : bond 0.00595 (24318) covalent geometry : angle 0.69750 (32908) Misc. bond : bond 0.00319 ( 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 214 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 188 time to evaluate : 5.219 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: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.8615 (tpp) cc_final: 0.8384 (mmm) REVERT: B 44 MET cc_start: 0.8249 (mmp) cc_final: 0.7419 (ptp) REVERT: B 107 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6981 (tt0) REVERT: B 123 MET cc_start: 0.8853 (mmt) cc_final: 0.8585 (mmm) REVERT: B 283 MET cc_start: 0.7348 (mmm) cc_final: 0.6898 (tmm) REVERT: C 82 MET cc_start: 0.8626 (mtp) cc_final: 0.8261 (mtp) REVERT: C 299 MET cc_start: 0.8705 (mtp) cc_final: 0.8504 (mtm) REVERT: D 25 ASP cc_start: 0.7570 (m-30) cc_final: 0.7348 (p0) REVERT: D 299 MET cc_start: 0.8359 (mtm) cc_final: 0.7997 (mtm) REVERT: D 361 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8251 (mp0) REVERT: E 44 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8170 (tpp) REVERT: E 132 MET cc_start: 0.8261 (ppp) cc_final: 0.7734 (ppp) REVERT: E 142 LEU cc_start: 0.7399 (tp) cc_final: 0.7046 (tp) REVERT: F 119 MET cc_start: 0.8981 (mtm) cc_final: 0.8744 (mtp) REVERT: F 191 LYS cc_start: 0.9295 (tttm) cc_final: 0.8886 (ttmm) REVERT: G 1000 MET cc_start: 0.9097 (ptm) cc_final: 0.8678 (ptm) REVERT: G 1019 LYS cc_start: 0.9626 (mttt) cc_final: 0.9388 (mtmm) REVERT: G 1026 HIS cc_start: 0.8825 (m90) cc_final: 0.8504 (m-70) REVERT: G 1127 MET cc_start: 0.9562 (mtm) cc_final: 0.9270 (mtm) REVERT: H 889 MET cc_start: 0.8215 (mtm) cc_final: 0.7864 (tmm) REVERT: H 1071 GLU cc_start: 0.8779 (tt0) cc_final: 0.8384 (pm20) REVERT: H 1089 MET cc_start: 0.8485 (ptt) cc_final: 0.8057 (mmp) REVERT: H 1090 MET cc_start: 0.7205 (mmt) cc_final: 0.6989 (mmt) outliers start: 26 outliers final: 15 residues processed: 206 average time/residue: 0.4416 time to fit residues: 148.1906 Evaluate side-chains 190 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 173 time to evaluate : 4.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain C residue 159 VAL 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 44 MET Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain G residue 1113 SER Chi-restraints excluded: chain H residue 1066 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 230 optimal weight: 0.0770 chunk 215 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 263 optimal weight: 5.9990 chunk 293 optimal weight: 6.9990 chunk 168 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 239 optimal weight: 3.9990 chunk 214 optimal weight: 0.8980 chunk 111 optimal weight: 6.9990 overall best weight: 1.1342 ------------------------------------------------------------------------------- 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** B 12 ASN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS ** E 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 928 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.077739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.056606 restraints weight = 105321.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.058313 restraints weight = 46781.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.059417 restraints weight = 26881.138| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24323 Z= 0.118 Angle : 0.562 9.629 32908 Z= 0.274 Chirality : 0.042 0.158 3641 Planarity : 0.004 0.057 4227 Dihedral : 9.496 165.678 3313 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.74 % Allowed : 9.04 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.16), residues: 2953 helix: 0.98 (0.14), residues: 1416 sheet: -0.40 (0.28), residues: 360 loop : -0.06 (0.19), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 79 HIS 0.004 0.001 HIS D 40 PHE 0.016 0.001 PHE G1107 TYR 0.020 0.001 TYR A 143 ARG 0.006 0.000 ARG F 372 Details of bonding type rmsd hydrogen bonds : bond 0.02980 ( 1151) hydrogen bonds : angle 4.14447 ( 3210) covalent geometry : bond 0.00269 (24318) covalent geometry : angle 0.56195 (32908) Misc. bond : bond 0.00128 ( 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 203 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 184 time to evaluate : 2.588 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 269 MET cc_start: 0.8474 (mtp) cc_final: 0.8212 (mtt) REVERT: B 44 MET cc_start: 0.8166 (mmp) cc_final: 0.7340 (ptp) REVERT: B 82 MET cc_start: 0.8976 (mmm) cc_final: 0.8231 (mmm) REVERT: B 107 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6780 (tt0) REVERT: B 283 MET cc_start: 0.7191 (mmm) cc_final: 0.6781 (tmm) REVERT: C 82 MET cc_start: 0.8567 (mtp) cc_final: 0.8162 (mtp) REVERT: C 299 MET cc_start: 0.8590 (mtp) cc_final: 0.8317 (mtm) REVERT: D 82 MET cc_start: 0.8484 (tpp) cc_final: 0.7532 (mmm) REVERT: D 299 MET cc_start: 0.8431 (mtm) cc_final: 0.7858 (mtt) REVERT: D 361 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8110 (mp0) REVERT: E 44 MET cc_start: 0.8602 (tpp) cc_final: 0.8178 (tpp) REVERT: E 132 MET cc_start: 0.8187 (ppp) cc_final: 0.7747 (ppp) REVERT: E 142 LEU cc_start: 0.7257 (tp) cc_final: 0.6895 (tp) REVERT: E 227 MET cc_start: 0.7468 (mmm) cc_final: 0.7119 (mmm) REVERT: F 191 LYS cc_start: 0.9267 (tttm) cc_final: 0.8899 (ttmm) REVERT: G 1000 MET cc_start: 0.9012 (ptm) cc_final: 0.8600 (ptm) REVERT: G 1019 LYS cc_start: 0.9609 (mttt) cc_final: 0.9363 (mtmm) REVERT: G 1026 HIS cc_start: 0.8831 (m90) cc_final: 0.8500 (m-70) REVERT: H 889 MET cc_start: 0.8018 (mtm) cc_final: 0.7644 (tmm) REVERT: H 1071 GLU cc_start: 0.8776 (tt0) cc_final: 0.8397 (pm20) REVERT: H 1089 MET cc_start: 0.8505 (ptt) cc_final: 0.8156 (mmp) outliers start: 19 outliers final: 12 residues processed: 197 average time/residue: 0.3175 time to fit residues: 102.7738 Evaluate side-chains 185 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 172 time to evaluate : 2.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain B residue 9 VAL 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 288 ASP Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain G residue 762 LEU Chi-restraints excluded: chain G residue 872 SER Chi-restraints excluded: chain H residue 1094 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 78 optimal weight: 0.0870 chunk 217 optimal weight: 0.2980 chunk 267 optimal weight: 8.9990 chunk 86 optimal weight: 7.9990 chunk 164 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 chunk 175 optimal weight: 0.4980 chunk 248 optimal weight: 10.0000 chunk 254 optimal weight: 9.9990 chunk 159 optimal weight: 0.8980 overall best weight: 1.1560 ------------------------------------------------------------------------------- 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** B 12 ASN E 12 ASN E 354 GLN ** G1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 928 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.077966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.056727 restraints weight = 105376.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.058408 restraints weight = 46993.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.059551 restraints weight = 27179.371| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 24323 Z= 0.120 Angle : 0.561 10.056 32908 Z= 0.270 Chirality : 0.042 0.157 3641 Planarity : 0.004 0.060 4227 Dihedral : 8.833 165.286 3313 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.09 % Allowed : 9.66 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.16), residues: 2953 helix: 1.22 (0.14), residues: 1418 sheet: -0.15 (0.28), residues: 360 loop : 0.08 (0.19), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 86 HIS 0.003 0.001 HIS E 87 PHE 0.017 0.001 PHE G1107 TYR 0.024 0.001 TYR A 143 ARG 0.008 0.000 ARG F 372 Details of bonding type rmsd hydrogen bonds : bond 0.02877 ( 1151) hydrogen bonds : angle 4.04201 ( 3210) covalent geometry : bond 0.00277 (24318) covalent geometry : angle 0.56144 (32908) Misc. bond : bond 0.00117 ( 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 207 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 179 time to evaluate : 2.799 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 82 MET cc_start: 0.8808 (tpp) cc_final: 0.8606 (tpp) REVERT: A 269 MET cc_start: 0.8487 (mtp) cc_final: 0.8220 (mtt) REVERT: B 107 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6834 (tt0) REVERT: B 283 MET cc_start: 0.7228 (mmm) cc_final: 0.6861 (tmm) REVERT: C 82 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8284 (mtp) REVERT: C 123 MET cc_start: 0.8502 (tpp) cc_final: 0.8201 (tpp) REVERT: C 299 MET cc_start: 0.8620 (mtp) cc_final: 0.8349 (mtm) REVERT: D 82 MET cc_start: 0.8469 (tpp) cc_final: 0.7582 (mmm) REVERT: D 299 MET cc_start: 0.8499 (mtm) cc_final: 0.8168 (mtm) REVERT: D 361 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8113 (mp0) REVERT: E 44 MET cc_start: 0.8534 (tpp) cc_final: 0.8155 (tpp) REVERT: E 132 MET cc_start: 0.8237 (ppp) cc_final: 0.7836 (ppp) REVERT: E 142 LEU cc_start: 0.7401 (tp) cc_final: 0.7031 (tp) REVERT: E 227 MET cc_start: 0.7582 (mmm) cc_final: 0.7201 (mmm) REVERT: F 191 LYS cc_start: 0.9234 (tttm) cc_final: 0.8891 (ttmm) REVERT: F 369 ILE cc_start: 0.7806 (OUTLIER) cc_final: 0.7492 (tt) REVERT: G 1000 MET cc_start: 0.8994 (ptm) cc_final: 0.8587 (ptm) REVERT: G 1019 LYS cc_start: 0.9627 (mttt) cc_final: 0.9380 (mtmm) REVERT: G 1026 HIS cc_start: 0.8821 (m90) cc_final: 0.8512 (m-70) REVERT: G 1094 MET cc_start: 0.8937 (ttp) cc_final: 0.8716 (mtm) REVERT: H 889 MET cc_start: 0.7978 (mtm) cc_final: 0.7612 (tmm) REVERT: H 1066 LYS cc_start: 0.6155 (OUTLIER) cc_final: 0.5758 (tmtt) REVERT: H 1071 GLU cc_start: 0.8803 (tt0) cc_final: 0.8414 (pm20) REVERT: H 1089 MET cc_start: 0.8555 (ptt) cc_final: 0.8178 (mmp) REVERT: H 1090 MET cc_start: 0.6775 (mmt) cc_final: 0.6424 (mmt) outliers start: 28 outliers final: 14 residues processed: 202 average time/residue: 0.3168 time to fit residues: 105.4682 Evaluate side-chains 190 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 172 time to evaluate : 2.546 ------------------------------------------------------------------------------- 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 B residue 107 GLU Chi-restraints excluded: chain C residue 82 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 F residue 80 ASP Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 369 ILE 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 188 optimal weight: 1.9990 chunk 148 optimal weight: 9.9990 chunk 288 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 11 optimal weight: 0.6980 chunk 196 optimal weight: 9.9990 chunk 211 optimal weight: 0.0000 chunk 253 optimal weight: 8.9990 chunk 133 optimal weight: 3.9990 chunk 154 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.1390 ------------------------------------------------------------------------------- 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** B 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 = 0.3875 r_free = 0.3875 target = 0.077928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.056925 restraints weight = 104120.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.058577 restraints weight = 47591.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.059633 restraints weight = 27689.440| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24323 Z= 0.116 Angle : 0.566 10.867 32908 Z= 0.269 Chirality : 0.042 0.167 3641 Planarity : 0.004 0.053 4227 Dihedral : 8.508 166.771 3313 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.28 % Allowed : 10.09 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.16), residues: 2953 helix: 1.34 (0.14), residues: 1424 sheet: -0.26 (0.28), residues: 366 loop : 0.27 (0.19), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 79 HIS 0.006 0.001 HIS D 40 PHE 0.021 0.001 PHE G 906 TYR 0.014 0.001 TYR G 969 ARG 0.008 0.000 ARG F 372 Details of bonding type rmsd hydrogen bonds : bond 0.02809 ( 1151) hydrogen bonds : angle 3.96728 ( 3210) covalent geometry : bond 0.00271 (24318) covalent geometry : angle 0.56582 (32908) Misc. bond : bond 0.00105 ( 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 210 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 177 time to evaluate : 2.567 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: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8838 (tpp) cc_final: 0.8568 (tpp) REVERT: A 269 MET cc_start: 0.8600 (mtp) cc_final: 0.8311 (mtt) REVERT: A 362 TYR cc_start: 0.9001 (t80) cc_final: 0.8509 (t80) REVERT: B 44 MET cc_start: 0.8231 (mmp) cc_final: 0.7344 (ptp) REVERT: B 107 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6891 (tt0) REVERT: B 283 MET cc_start: 0.7253 (mmm) cc_final: 0.6873 (tmm) REVERT: C 82 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8322 (mtp) REVERT: C 299 MET cc_start: 0.8639 (mtp) cc_final: 0.8366 (mtm) REVERT: D 82 MET cc_start: 0.8523 (tpp) cc_final: 0.7452 (mmm) REVERT: D 299 MET cc_start: 0.8479 (mtm) cc_final: 0.8143 (mtm) REVERT: D 361 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8163 (mp0) REVERT: E 44 MET cc_start: 0.8607 (tpp) cc_final: 0.8109 (tpp) REVERT: E 132 MET cc_start: 0.8183 (ppp) cc_final: 0.7788 (ppp) REVERT: E 142 LEU cc_start: 0.7329 (tp) cc_final: 0.6966 (tp) REVERT: E 227 MET cc_start: 0.7527 (mmm) cc_final: 0.7137 (mmm) REVERT: E 294 TYR cc_start: 0.8108 (OUTLIER) cc_final: 0.7359 (m-80) REVERT: F 44 MET cc_start: 0.9242 (mmm) cc_final: 0.8708 (mmm) REVERT: F 191 LYS cc_start: 0.9211 (tttm) cc_final: 0.8885 (ttmm) REVERT: F 369 ILE cc_start: 0.7802 (OUTLIER) cc_final: 0.7420 (tt) REVERT: G 1000 MET cc_start: 0.9022 (ptm) cc_final: 0.8601 (ptm) REVERT: G 1019 LYS cc_start: 0.9622 (mttt) cc_final: 0.9375 (mtmm) REVERT: G 1026 HIS cc_start: 0.8838 (m90) cc_final: 0.8457 (m90) REVERT: G 1094 MET cc_start: 0.8967 (ttp) cc_final: 0.8735 (mtm) REVERT: G 1119 MET cc_start: 0.9168 (mtt) cc_final: 0.8748 (mmt) REVERT: H 852 MET cc_start: 0.5897 (ttp) cc_final: 0.4917 (tmm) REVERT: H 889 MET cc_start: 0.7978 (mtm) cc_final: 0.7587 (tmm) REVERT: H 1026 HIS cc_start: 0.7503 (OUTLIER) cc_final: 0.7058 (t-90) REVERT: H 1071 GLU cc_start: 0.8809 (tt0) cc_final: 0.8368 (pm20) REVERT: H 1089 MET cc_start: 0.8387 (ptt) cc_final: 0.8026 (mmp) REVERT: H 1090 MET cc_start: 0.7018 (mmt) cc_final: 0.6778 (mmt) outliers start: 33 outliers final: 19 residues processed: 203 average time/residue: 0.3360 time to fit residues: 111.8667 Evaluate side-chains 198 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 174 time to evaluate : 2.730 ------------------------------------------------------------------------------- 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 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 82 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 294 TYR Chi-restraints excluded: chain E residue 326 LYS Chi-restraints excluded: chain F residue 80 ASP 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 H residue 1026 HIS Chi-restraints excluded: chain H residue 1066 LYS Chi-restraints excluded: chain H residue 1094 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 141 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 237 optimal weight: 2.9990 chunk 201 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 156 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 250 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 71 optimal weight: 0.0170 overall best weight: 1.1822 ------------------------------------------------------------------------------- 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** B 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 = 0.3867 r_free = 0.3867 target = 0.077611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.056648 restraints weight = 104789.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.058289 restraints weight = 47905.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.059346 restraints weight = 27888.194| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24323 Z= 0.118 Angle : 0.565 10.825 32908 Z= 0.270 Chirality : 0.042 0.181 3641 Planarity : 0.004 0.066 4227 Dihedral : 8.336 166.588 3313 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.32 % Allowed : 10.24 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.16), residues: 2953 helix: 1.43 (0.15), residues: 1424 sheet: -0.26 (0.28), residues: 366 loop : 0.34 (0.20), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 79 HIS 0.003 0.001 HIS D 40 PHE 0.016 0.001 PHE G1107 TYR 0.013 0.001 TYR G 969 ARG 0.006 0.000 ARG F 372 Details of bonding type rmsd hydrogen bonds : bond 0.02780 ( 1151) hydrogen bonds : angle 3.94618 ( 3210) covalent geometry : bond 0.00272 (24318) covalent geometry : angle 0.56462 (32908) Misc. bond : bond 0.00116 ( 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 214 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 180 time to evaluate : 3.280 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8883 (tpp) cc_final: 0.8651 (tpp) REVERT: A 123 MET cc_start: 0.8647 (tpp) cc_final: 0.7877 (tpp) REVERT: A 362 TYR cc_start: 0.9000 (t80) cc_final: 0.8422 (t80) REVERT: B 44 MET cc_start: 0.8166 (mmp) cc_final: 0.7352 (ptt) REVERT: B 283 MET cc_start: 0.7229 (mmm) cc_final: 0.6848 (tmm) REVERT: C 82 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8325 (mtp) REVERT: C 123 MET cc_start: 0.8488 (tpp) cc_final: 0.8166 (tpp) REVERT: C 299 MET cc_start: 0.8643 (mtp) cc_final: 0.8408 (mtm) REVERT: D 82 MET cc_start: 0.8527 (tpp) cc_final: 0.7879 (mmm) REVERT: D 299 MET cc_start: 0.8473 (mtm) cc_final: 0.7920 (mtt) REVERT: D 361 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8147 (mp0) REVERT: E 44 MET cc_start: 0.8587 (tpp) cc_final: 0.8095 (tpp) REVERT: E 132 MET cc_start: 0.8206 (ppp) cc_final: 0.7760 (ppp) REVERT: E 142 LEU cc_start: 0.7390 (tp) cc_final: 0.7009 (tp) REVERT: E 227 MET cc_start: 0.7534 (mmm) cc_final: 0.7140 (mmm) REVERT: E 294 TYR cc_start: 0.8075 (OUTLIER) cc_final: 0.7377 (m-80) REVERT: F 44 MET cc_start: 0.9242 (mmm) cc_final: 0.8769 (mmm) REVERT: F 132 MET cc_start: 0.7950 (tmm) cc_final: 0.7617 (tmm) REVERT: F 191 LYS cc_start: 0.9204 (tttm) cc_final: 0.8890 (ttmm) REVERT: G 1000 MET cc_start: 0.9020 (ptm) cc_final: 0.8599 (ptm) REVERT: G 1019 LYS cc_start: 0.9624 (mttt) cc_final: 0.9378 (mtmm) REVERT: G 1026 HIS cc_start: 0.8875 (m90) cc_final: 0.8490 (m90) REVERT: G 1089 MET cc_start: 0.9157 (ppp) cc_final: 0.8889 (ppp) REVERT: G 1090 MET cc_start: 0.8650 (mmm) cc_final: 0.8245 (mtt) REVERT: G 1119 MET cc_start: 0.9170 (mtt) cc_final: 0.8714 (mmt) REVERT: H 852 MET cc_start: 0.6120 (ttp) cc_final: 0.5179 (tmm) REVERT: H 889 MET cc_start: 0.8154 (mtm) cc_final: 0.7734 (tmm) REVERT: H 1071 GLU cc_start: 0.8746 (tt0) cc_final: 0.8331 (pm20) REVERT: H 1089 MET cc_start: 0.8344 (ptt) cc_final: 0.7934 (mmp) REVERT: H 1119 MET cc_start: 0.7096 (ptt) cc_final: 0.6771 (mmm) outliers start: 34 outliers final: 22 residues processed: 207 average time/residue: 0.4060 time to fit residues: 140.8894 Evaluate side-chains 199 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 175 time to evaluate : 2.608 ------------------------------------------------------------------------------- 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 267 ILE Chi-restraints excluded: chain C residue 82 MET 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 288 ASP Chi-restraints excluded: chain E residue 294 TYR 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 G residue 762 LEU Chi-restraints excluded: chain G residue 859 ASN Chi-restraints excluded: chain G residue 872 SER Chi-restraints excluded: chain H residue 1066 LYS Chi-restraints excluded: chain H residue 1094 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 17 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 159 optimal weight: 7.9990 chunk 281 optimal weight: 40.0000 chunk 99 optimal weight: 0.4980 chunk 291 optimal weight: 10.0000 chunk 195 optimal weight: 0.2980 chunk 37 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 202 optimal weight: 7.9990 chunk 215 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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** B 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 = 0.3849 r_free = 0.3849 target = 0.076804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.055842 restraints weight = 105322.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.057461 restraints weight = 48454.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.058505 restraints weight = 28254.794| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24323 Z= 0.153 Angle : 0.603 11.124 32908 Z= 0.290 Chirality : 0.043 0.225 3641 Planarity : 0.004 0.050 4227 Dihedral : 8.359 165.118 3313 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.32 % Allowed : 10.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.16), residues: 2953 helix: 1.38 (0.14), residues: 1432 sheet: -0.34 (0.28), residues: 366 loop : 0.32 (0.20), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 767 HIS 0.003 0.001 HIS D 40 PHE 0.016 0.001 PHE G1107 TYR 0.029 0.001 TYR A 143 ARG 0.004 0.000 ARG B 372 Details of bonding type rmsd hydrogen bonds : bond 0.02946 ( 1151) hydrogen bonds : angle 4.07962 ( 3210) covalent geometry : bond 0.00352 (24318) covalent geometry : angle 0.60331 (32908) Misc. bond : bond 0.00143 ( 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 212 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 178 time to evaluate : 2.627 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 8 LEU cc_start: 0.8633 (mm) cc_final: 0.8428 (pp) REVERT: A 82 MET cc_start: 0.8890 (tpp) cc_final: 0.8679 (tpp) REVERT: A 123 MET cc_start: 0.8646 (tpp) cc_final: 0.7853 (tpp) REVERT: A 269 MET cc_start: 0.8636 (mtp) cc_final: 0.8411 (ttm) REVERT: A 362 TYR cc_start: 0.9035 (t80) cc_final: 0.8425 (t80) REVERT: B 283 MET cc_start: 0.7246 (mmm) cc_final: 0.6860 (tmm) REVERT: C 82 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8324 (mtp) REVERT: C 299 MET cc_start: 0.8670 (mtp) cc_final: 0.8396 (mtm) REVERT: C 305 MET cc_start: 0.9143 (mmm) cc_final: 0.8880 (tpp) REVERT: D 82 MET cc_start: 0.8564 (tpp) cc_final: 0.7933 (mmm) REVERT: D 299 MET cc_start: 0.8459 (mtm) cc_final: 0.7911 (mtt) REVERT: E 44 MET cc_start: 0.8608 (tpp) cc_final: 0.8114 (tpp) REVERT: E 132 MET cc_start: 0.8239 (ppp) cc_final: 0.7773 (ppp) REVERT: E 142 LEU cc_start: 0.7360 (tp) cc_final: 0.7065 (tp) REVERT: E 294 TYR cc_start: 0.8325 (OUTLIER) cc_final: 0.7644 (m-80) REVERT: F 44 MET cc_start: 0.9233 (mmm) cc_final: 0.8690 (mmm) REVERT: F 132 MET cc_start: 0.8011 (tmm) cc_final: 0.7665 (tmm) REVERT: F 191 LYS cc_start: 0.9203 (tttm) cc_final: 0.8998 (ttmt) REVERT: F 270 GLU cc_start: 0.8378 (pm20) cc_final: 0.8170 (pm20) REVERT: G 1000 MET cc_start: 0.9103 (ptm) cc_final: 0.8608 (ptm) REVERT: G 1019 LYS cc_start: 0.9630 (mttt) cc_final: 0.9386 (mtmm) REVERT: G 1026 HIS cc_start: 0.8867 (m90) cc_final: 0.8485 (m90) REVERT: G 1089 MET cc_start: 0.9193 (ppp) cc_final: 0.8917 (ppp) REVERT: G 1090 MET cc_start: 0.8692 (mmm) cc_final: 0.8299 (mtt) REVERT: G 1119 MET cc_start: 0.9163 (mtt) cc_final: 0.8906 (mtm) REVERT: H 756 TYR cc_start: 0.5309 (m-80) cc_final: 0.3908 (m-10) REVERT: H 852 MET cc_start: 0.6260 (ttp) cc_final: 0.5270 (tmm) REVERT: H 889 MET cc_start: 0.8289 (mtm) cc_final: 0.7921 (tmm) REVERT: H 1026 HIS cc_start: 0.7501 (OUTLIER) cc_final: 0.7034 (t-90) REVERT: H 1066 LYS cc_start: 0.6151 (OUTLIER) cc_final: 0.5827 (tmtt) REVERT: H 1071 GLU cc_start: 0.8690 (tt0) cc_final: 0.8262 (pm20) REVERT: H 1089 MET cc_start: 0.8318 (ptt) cc_final: 0.7853 (mmp) REVERT: H 1090 MET cc_start: 0.6730 (mmt) cc_final: 0.6245 (mmt) outliers start: 34 outliers final: 24 residues processed: 203 average time/residue: 0.3373 time to fit residues: 112.4175 Evaluate side-chains 201 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 173 time to evaluate : 2.788 ------------------------------------------------------------------------------- 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 A residue 349 LEU Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain C residue 82 MET 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 288 ASP 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 762 LEU Chi-restraints excluded: chain G residue 859 ASN Chi-restraints excluded: chain G residue 872 SER Chi-restraints excluded: chain H residue 1026 HIS 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 211 optimal weight: 10.0000 chunk 163 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 131 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 284 optimal weight: 20.0000 chunk 197 optimal weight: 10.0000 chunk 227 optimal weight: 0.9990 chunk 128 optimal weight: 0.6980 chunk 203 optimal weight: 1.9990 chunk 69 optimal weight: 0.0010 overall best weight: 0.8790 ------------------------------------------------------------------------------- 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** B 12 ASN ** 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 = 0.3869 r_free = 0.3869 target = 0.077618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.056650 restraints weight = 104455.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.058261 restraints weight = 47699.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.059344 restraints weight = 27940.151| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24323 Z= 0.109 Angle : 0.593 13.826 32908 Z= 0.281 Chirality : 0.042 0.212 3641 Planarity : 0.004 0.071 4227 Dihedral : 8.218 163.980 3313 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.97 % Allowed : 11.13 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.16), residues: 2953 helix: 1.45 (0.15), residues: 1433 sheet: -0.00 (0.27), residues: 402 loop : 0.35 (0.20), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 79 HIS 0.003 0.001 HIS D 40 PHE 0.016 0.001 PHE G1107 TYR 0.033 0.001 TYR A 143 ARG 0.011 0.000 ARG F 372 Details of bonding type rmsd hydrogen bonds : bond 0.02768 ( 1151) hydrogen bonds : angle 4.00008 ( 3210) covalent geometry : bond 0.00251 (24318) covalent geometry : angle 0.59345 (32908) Misc. bond : bond 0.00112 ( 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 206 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 181 time to evaluate : 3.745 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: symmetry clash REVERT: A 82 MET cc_start: 0.8893 (tpp) cc_final: 0.8616 (tpp) REVERT: A 123 MET cc_start: 0.8613 (tpp) cc_final: 0.7822 (tpp) REVERT: A 269 MET cc_start: 0.8573 (mtp) cc_final: 0.8355 (ttm) REVERT: B 44 MET cc_start: 0.8141 (mmp) cc_final: 0.7177 (ptt) REVERT: B 283 MET cc_start: 0.7207 (mmm) cc_final: 0.6829 (tmm) REVERT: C 82 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8318 (mtp) REVERT: C 299 MET cc_start: 0.8641 (mtp) cc_final: 0.8403 (mtm) REVERT: C 305 MET cc_start: 0.9120 (mmm) cc_final: 0.8850 (tpp) REVERT: D 82 MET cc_start: 0.8512 (tpp) cc_final: 0.7866 (mmm) REVERT: D 299 MET cc_start: 0.8462 (mtm) cc_final: 0.8126 (mtm) REVERT: D 361 GLU cc_start: 0.8952 (mt-10) cc_final: 0.8334 (mp0) REVERT: E 44 MET cc_start: 0.8569 (tpp) cc_final: 0.8126 (tpp) REVERT: E 132 MET cc_start: 0.8195 (ppp) cc_final: 0.7748 (ppp) REVERT: E 142 LEU cc_start: 0.7341 (tp) cc_final: 0.7047 (tp) REVERT: E 294 TYR cc_start: 0.8310 (OUTLIER) cc_final: 0.7718 (m-80) REVERT: F 132 MET cc_start: 0.7965 (tmm) cc_final: 0.7622 (tmm) REVERT: F 191 LYS cc_start: 0.9189 (tttm) cc_final: 0.8977 (ttmt) REVERT: G 1000 MET cc_start: 0.9167 (ptm) cc_final: 0.8870 (ptm) REVERT: G 1019 LYS cc_start: 0.9617 (mttt) cc_final: 0.9356 (mtmm) REVERT: G 1026 HIS cc_start: 0.8898 (m90) cc_final: 0.8542 (m90) REVERT: G 1089 MET cc_start: 0.9228 (ppp) cc_final: 0.8963 (ppp) REVERT: G 1090 MET cc_start: 0.8643 (mmm) cc_final: 0.8252 (mtt) REVERT: G 1119 MET cc_start: 0.9176 (mtt) cc_final: 0.8925 (mtm) REVERT: H 756 TYR cc_start: 0.5338 (m-80) cc_final: 0.3983 (m-10) REVERT: H 852 MET cc_start: 0.6294 (ttp) cc_final: 0.5663 (tmm) REVERT: H 889 MET cc_start: 0.8293 (mtm) cc_final: 0.7954 (tmm) REVERT: H 1071 GLU cc_start: 0.8684 (tt0) cc_final: 0.8282 (pm20) REVERT: H 1089 MET cc_start: 0.8342 (ptt) cc_final: 0.7896 (mmp) REVERT: H 1090 MET cc_start: 0.6797 (mmt) cc_final: 0.6392 (mmt) outliers start: 25 outliers final: 17 residues processed: 202 average time/residue: 0.3624 time to fit residues: 120.9677 Evaluate side-chains 193 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 3.315 ------------------------------------------------------------------------------- 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 B residue 267 ILE Chi-restraints excluded: chain C residue 82 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 294 TYR 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 G residue 762 LEU Chi-restraints excluded: chain G residue 859 ASN Chi-restraints excluded: chain G residue 872 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 94 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 chunk 282 optimal weight: 4.9990 chunk 195 optimal weight: 4.9990 chunk 174 optimal weight: 7.9990 chunk 275 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 2 optimal weight: 0.0000 chunk 18 optimal weight: 3.9990 chunk 256 optimal weight: 8.9990 chunk 265 optimal weight: 4.9990 overall best weight: 2.2790 ------------------------------------------------------------------------------- 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 B 12 ASN C 297 ASN D 354 GLN ** G1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.076101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.055216 restraints weight = 106063.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.056801 restraints weight = 48830.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.057834 restraints weight = 28766.278| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 24323 Z= 0.191 Angle : 0.664 17.206 32908 Z= 0.319 Chirality : 0.044 0.202 3641 Planarity : 0.004 0.074 4227 Dihedral : 8.418 162.020 3313 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.97 % Allowed : 11.29 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.16), residues: 2953 helix: 1.36 (0.14), residues: 1422 sheet: -0.44 (0.27), residues: 378 loop : 0.26 (0.20), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 767 HIS 0.005 0.001 HIS E 87 PHE 0.018 0.001 PHE G1107 TYR 0.036 0.002 TYR A 143 ARG 0.008 0.000 ARG F 372 Details of bonding type rmsd hydrogen bonds : bond 0.03159 ( 1151) hydrogen bonds : angle 4.22791 ( 3210) covalent geometry : bond 0.00438 (24318) covalent geometry : angle 0.66428 (32908) Misc. bond : bond 0.00179 ( 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 203 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 178 time to evaluate : 6.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8910 (tpp) cc_final: 0.8631 (tpp) REVERT: A 123 MET cc_start: 0.8671 (tpp) cc_final: 0.8271 (tmm) REVERT: A 269 MET cc_start: 0.8650 (mtp) cc_final: 0.8404 (ttm) REVERT: B 44 MET cc_start: 0.8117 (mmp) cc_final: 0.7152 (mtm) REVERT: B 82 MET cc_start: 0.9027 (mmm) cc_final: 0.8578 (mmm) REVERT: B 283 MET cc_start: 0.7262 (mmm) cc_final: 0.6859 (tmm) REVERT: B 355 MET cc_start: 0.8175 (tpt) cc_final: 0.7953 (tpt) REVERT: C 82 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8356 (mtp) REVERT: C 299 MET cc_start: 0.8720 (mtp) cc_final: 0.8456 (mtm) REVERT: C 305 MET cc_start: 0.9159 (mmm) cc_final: 0.8916 (tpp) REVERT: D 82 MET cc_start: 0.8614 (tpp) cc_final: 0.7906 (mmm) REVERT: D 299 MET cc_start: 0.8481 (mtm) cc_final: 0.7937 (mtt) REVERT: D 361 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8420 (mp0) REVERT: E 44 MET cc_start: 0.8655 (tpp) cc_final: 0.8154 (tpp) REVERT: E 132 MET cc_start: 0.8259 (ppp) cc_final: 0.7790 (ppp) REVERT: E 142 LEU cc_start: 0.7358 (tp) cc_final: 0.7099 (tp) REVERT: E 294 TYR cc_start: 0.8429 (OUTLIER) cc_final: 0.7875 (m-80) REVERT: F 132 MET cc_start: 0.8026 (tmm) cc_final: 0.7701 (tmm) REVERT: F 191 LYS cc_start: 0.9219 (tttm) cc_final: 0.8994 (ttmt) REVERT: G 852 MET cc_start: 0.5406 (tmm) cc_final: 0.5178 (ppp) REVERT: G 1000 MET cc_start: 0.9234 (ptm) cc_final: 0.8925 (ptm) REVERT: G 1019 LYS cc_start: 0.9640 (mttt) cc_final: 0.9373 (mtmm) REVERT: G 1026 HIS cc_start: 0.8951 (m90) cc_final: 0.8566 (m90) REVERT: G 1089 MET cc_start: 0.9239 (ppp) cc_final: 0.8994 (ppp) REVERT: G 1090 MET cc_start: 0.8760 (mmm) cc_final: 0.8301 (mtt) REVERT: G 1119 MET cc_start: 0.9181 (mtt) cc_final: 0.8938 (mtm) REVERT: H 756 TYR cc_start: 0.5484 (m-80) cc_final: 0.4019 (m-10) REVERT: H 889 MET cc_start: 0.8323 (mtm) cc_final: 0.7921 (tmm) REVERT: H 1071 GLU cc_start: 0.8603 (tt0) cc_final: 0.8333 (pm20) REVERT: H 1089 MET cc_start: 0.8328 (ptt) cc_final: 0.7876 (mmp) REVERT: H 1090 MET cc_start: 0.6854 (mmt) cc_final: 0.6459 (mmt) outliers start: 25 outliers final: 19 residues processed: 198 average time/residue: 0.5256 time to fit residues: 179.4803 Evaluate side-chains 190 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 169 time to evaluate : 7.122 ------------------------------------------------------------------------------- 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 267 ILE Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain C residue 82 MET 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 106 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 294 TYR 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 G residue 859 ASN Chi-restraints excluded: chain G residue 872 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 13 optimal weight: 0.6980 chunk 142 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 44 optimal weight: 0.2980 chunk 251 optimal weight: 0.0470 chunk 128 optimal weight: 5.9990 chunk 277 optimal weight: 10.0000 chunk 181 optimal weight: 5.9990 chunk 168 optimal weight: 0.9980 chunk 288 optimal weight: 20.0000 chunk 183 optimal weight: 8.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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** B 12 ASN ** 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 = 0.3875 r_free = 0.3875 target = 0.077876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.057006 restraints weight = 104027.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.058665 restraints weight = 47559.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.059749 restraints weight = 27665.907| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24323 Z= 0.101 Angle : 0.599 14.314 32908 Z= 0.283 Chirality : 0.042 0.191 3641 Planarity : 0.004 0.071 4227 Dihedral : 8.132 161.206 3313 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.62 % Allowed : 11.68 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.16), residues: 2953 helix: 1.52 (0.15), residues: 1432 sheet: -0.00 (0.27), residues: 402 loop : 0.35 (0.20), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 356 HIS 0.003 0.001 HIS D 40 PHE 0.015 0.001 PHE G1117 TYR 0.014 0.001 TYR A 143 ARG 0.006 0.000 ARG F 372 Details of bonding type rmsd hydrogen bonds : bond 0.02694 ( 1151) hydrogen bonds : angle 4.00177 ( 3210) covalent geometry : bond 0.00233 (24318) covalent geometry : angle 0.59918 (32908) Misc. bond : bond 0.00126 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8617.02 seconds wall clock time: 155 minutes 11.79 seconds (9311.79 seconds total)