Starting phenix.real_space_refine on Wed Nov 20 05:05:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8r_28934/11_2024/8f8r_28934.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8r_28934/11_2024/8f8r_28934.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8r_28934/11_2024/8f8r_28934.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8r_28934/11_2024/8f8r_28934.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8r_28934/11_2024/8f8r_28934.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8r_28934/11_2024/8f8r_28934.cif" } resolution = 3.3 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= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 14 5.49 5 Mg 7 5.21 5 S 147 5.16 5 C 12941 2.51 5 N 3462 2.21 5 O 3955 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 20526 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2897 Classifications: {'peptide': 371} 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: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} 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: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 12.47, per 1000 atoms: 0.61 Number of scatterers: 20526 At special positions: 0 Unit cell: (86.4, 108, 250.56, 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 147 16.00 P 14 15.00 Mg 7 11.99 O 3955 8.00 N 3462 7.00 C 12941 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.92 Conformation dependent library (CDL) restraints added in 3.0 seconds 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4810 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 42 sheets defined 49.6% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.14 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 removed outlier: 3.656A pdb=" N MET A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.641A pdb=" N GLU A 100 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 97 through 101' Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.812A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.555A 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 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.725A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.616A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 removed outlier: 3.579A pdb=" N LEU A 261 " --> pdb=" O PRO A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 283 Processing helix chain 'A' and resid 289 through 295 Processing helix chain 'A' and resid 301 through 305 removed outlier: 3.569A pdb=" N THR A 304 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 321 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 347 Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.963A 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 367 through 372 removed outlier: 5.343A pdb=" N VAL A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS A 371 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.768A pdb=" N MET B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.683A pdb=" N GLU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.897A 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: 3.825A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.701A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 removed outlier: 3.523A pdb=" N GLU B 226 " --> pdb=" O ASP B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.616A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 removed outlier: 3.551A pdb=" N LEU B 261 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 268 removed outlier: 3.518A pdb=" N PHE B 266 " --> pdb=" O GLN B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 283 Processing helix chain 'B' and resid 289 through 295 Processing helix chain 'B' and resid 301 through 305 removed outlier: 3.664A pdb=" N THR B 304 " --> pdb=" O GLY B 301 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N MET B 305 " --> pdb=" O GLY B 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 301 through 305' Processing helix chain 'B' and resid 309 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 347 Processing helix chain 'B' and resid 350 through 355 removed outlier: 4.162A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 368 through 374 removed outlier: 3.955A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.541A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.720A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 101' Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.913A 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: 3.718A 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 194 removed outlier: 3.729A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.901A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.751A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 283 Processing helix chain 'C' and resid 290 through 295 Processing helix chain 'C' and resid 301 through 305 removed outlier: 3.691A pdb=" N THR C 304 " --> pdb=" O GLY C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.567A pdb=" N ARG C 312 " --> pdb=" O GLY C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 347 Processing helix chain 'C' and resid 350 through 355 removed outlier: 4.128A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 4.090A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 removed outlier: 3.530A pdb=" N MET D 82 " --> pdb=" O ASN D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.589A pdb=" N GLU D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 97 through 101' Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.838A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.796A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N CYS D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.659A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 263 through 268 removed outlier: 3.521A pdb=" N PHE D 266 " --> pdb=" O GLN D 263 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE D 267 " --> pdb=" O PRO D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.528A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 removed outlier: 3.525A pdb=" N THR D 304 " --> pdb=" O GLY D 301 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET D 305 " --> pdb=" O GLY D 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 301 through 305' Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.505A pdb=" N ARG D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 347 Processing helix chain 'D' and resid 351 through 355 removed outlier: 4.108A 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 368 through 374 removed outlier: 3.998A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 removed outlier: 3.548A pdb=" N MET E 82 " --> pdb=" O ASN E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.560A pdb=" N GLU E 100 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 97 through 101' Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.950A 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 172 through 175 removed outlier: 3.643A pdb=" N ILE E 175 " --> pdb=" O PRO E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 172 through 175' Processing helix chain 'E' and resid 181 through 193 Processing helix chain 'E' and resid 194 through 196 No H-bonds generated for 'chain 'E' and resid 194 through 196' Processing helix chain 'E' and resid 202 through 217 removed outlier: 3.769A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) removed outlier: 3.575A 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: 3.759A pdb=" N CYS E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 261 removed outlier: 3.575A pdb=" N LEU E 261 " --> pdb=" O PRO E 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 258 through 261' Processing helix chain 'E' and resid 263 through 268 removed outlier: 3.603A pdb=" N ILE E 267 " --> pdb=" O PRO E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 283 Processing helix chain 'E' and resid 284 through 285 No H-bonds generated for 'chain 'E' and resid 284 through 285' Processing helix chain 'E' and resid 286 through 288 No H-bonds generated for 'chain 'E' and resid 286 through 288' Processing helix chain 'E' and resid 289 through 295 Processing helix chain 'E' and resid 301 through 305 removed outlier: 3.578A pdb=" N THR E 304 " --> pdb=" O GLY E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 removed outlier: 3.520A pdb=" N ARG E 312 " --> pdb=" O GLY E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 347 Processing helix chain 'E' and resid 351 through 355 removed outlier: 4.198A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 368 through 373 removed outlier: 4.289A 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: 3.636A pdb=" N MET F 82 " --> pdb=" O ASN F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 101 removed outlier: 3.639A pdb=" N GLU F 100 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 3.832A 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: 3.821A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 146 Processing helix chain 'F' and resid 181 through 193 Processing helix chain 'F' and resid 205 through 217 removed outlier: 3.670A 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: 3.672A pdb=" N CYS F 257 " --> pdb=" O GLU F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 262 Processing helix chain 'F' and resid 263 through 268 Processing helix chain 'F' and resid 273 through 284 Processing helix chain 'F' and resid 289 through 295 removed outlier: 3.508A pdb=" N LEU F 293 " --> pdb=" O ILE F 289 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA F 295 " --> pdb=" O LYS F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 305 Processing helix chain 'F' and resid 308 through 321 removed outlier: 3.562A pdb=" N ARG F 312 " --> pdb=" O GLY F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 336 No H-bonds generated for 'chain 'F' and resid 334 through 336' Processing helix chain 'F' and resid 337 through 347 Processing helix chain 'F' and resid 359 through 366 Processing helix chain 'F' and resid 368 through 374 Processing helix chain 'G' and resid 55 through 61 Processing helix chain 'G' and resid 78 through 92 removed outlier: 3.657A pdb=" N MET G 82 " --> pdb=" O ASN G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 101 removed outlier: 3.606A pdb=" N GLU G 100 " --> pdb=" O ALA G 97 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N HIS G 101 " --> pdb=" O PRO G 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 97 through 101' Processing helix chain 'G' and resid 112 through 126 removed outlier: 3.904A pdb=" N ARG G 116 " --> pdb=" O PRO G 112 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR G 126 " --> pdb=" O ILE G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 146 Processing helix chain 'G' and resid 181 through 193 Processing helix chain 'G' and resid 202 through 217 removed outlier: 3.739A pdb=" N ILE G 208 " --> pdb=" O ALA G 204 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS G 217 " --> pdb=" O LYS G 213 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 233 Processing helix chain 'G' and resid 252 through 257 removed outlier: 3.646A pdb=" N CYS G 257 " --> pdb=" O GLU G 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 262 Processing helix chain 'G' and resid 263 through 268 removed outlier: 3.525A pdb=" N ILE G 267 " --> pdb=" O PRO G 264 " (cutoff:3.500A) Processing helix chain 'G' and resid 273 through 284 removed outlier: 3.506A pdb=" N LYS G 284 " --> pdb=" O ASN G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 289 through 296 removed outlier: 3.515A pdb=" N ALA G 295 " --> pdb=" O LYS G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 305 removed outlier: 3.776A pdb=" N MET G 305 " --> pdb=" O GLY G 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 321 removed outlier: 3.573A pdb=" N ARG G 312 " --> pdb=" O GLY G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 334 through 336 No H-bonds generated for 'chain 'G' and resid 334 through 336' Processing helix chain 'G' and resid 337 through 347 Processing helix chain 'G' and resid 359 through 366 Processing helix chain 'G' and resid 368 through 374 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.302A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 178 removed outlier: 6.353A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 176 through 178 removed outlier: 4.123A pdb=" N GLN C 41 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.522A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 176 through 178 removed outlier: 6.315A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 176 through 178 removed outlier: 4.257A pdb=" N GLN D 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.438A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.515A 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: 5.989A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.260A 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: 4.014A 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: 6.451A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.578A 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: 6.027A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 176 through 178 removed outlier: 4.094A 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: 6.593A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ALA E 135 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 6.392A 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 176 through 178 removed outlier: 5.976A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 176 through 178 removed outlier: 4.203A pdb=" N GLN G 41 " --> pdb=" O ALA E 170 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AD4, first strand: chain 'F' and resid 29 through 32 removed outlier: 6.510A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N THR F 103 " --> pdb=" O TYR F 133 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ALA F 135 " --> pdb=" O THR F 103 " (cutoff:3.500A) removed outlier: 6.501A 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: 6.110A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ASN F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 238 through 241 Processing sheet with id=AE1, first strand: chain 'G' and resid 29 through 32 removed outlier: 6.381A pdb=" N LEU G 8 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N THR G 106 " --> pdb=" O LEU G 8 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N CYS G 10 " --> pdb=" O THR G 106 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AE3, first strand: chain 'G' and resid 71 through 72 Processing sheet with id=AE4, first strand: chain 'G' and resid 169 through 170 removed outlier: 3.598A pdb=" N ASN G 162 " --> pdb=" O MET G 176 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N MET G 176 " --> pdb=" O ASN G 162 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 169 through 170 removed outlier: 6.162A pdb=" N ILE G 151 " --> pdb=" O VAL G 298 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N SER G 300 " --> pdb=" O ILE G 151 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N LEU G 153 " --> pdb=" O SER G 300 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ASN G 297 " --> pdb=" O ILE G 330 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 238 through 241 928 hydrogen bonds defined for protein. 2412 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.16 Time building geometry restraints manager: 5.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6618 1.34 - 1.46: 4627 1.46 - 1.58: 9447 1.58 - 1.70: 21 1.70 - 1.82: 259 Bond restraints: 20972 Sorted by residual: bond pdb=" C LEU G 242 " pdb=" N PRO G 243 " ideal model delta sigma weight residual 1.336 1.366 -0.031 1.08e-02 8.57e+03 8.02e+00 bond pdb=" CE1 HIC D 73 " pdb=" NE2 HIC D 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.95e+00 bond pdb=" CE1 HIC E 73 " pdb=" NE2 HIC E 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.90e+00 bond pdb=" CE1 HIC G 73 " pdb=" NE2 HIC G 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.80e+00 bond pdb=" CE1 HIC F 73 " pdb=" NE2 HIC F 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.67e+00 ... (remaining 20967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.19: 27987 3.19 - 6.37: 416 6.37 - 9.56: 47 9.56 - 12.75: 9 12.75 - 15.94: 4 Bond angle restraints: 28463 Sorted by residual: angle pdb=" CA MET D 47 " pdb=" CB MET D 47 " pdb=" CG MET D 47 " ideal model delta sigma weight residual 114.10 124.83 -10.73 2.00e+00 2.50e-01 2.88e+01 angle pdb=" CA MET C 47 " pdb=" CB MET C 47 " pdb=" CG MET C 47 " ideal model delta sigma weight residual 114.10 124.73 -10.63 2.00e+00 2.50e-01 2.83e+01 angle pdb=" CB MET F 44 " pdb=" CG MET F 44 " pdb=" SD MET F 44 " ideal model delta sigma weight residual 112.70 128.64 -15.94 3.00e+00 1.11e-01 2.82e+01 angle pdb=" C ILE E 282 " pdb=" N MET E 283 " pdb=" CA MET E 283 " ideal model delta sigma weight residual 122.66 114.52 8.14 1.63e+00 3.76e-01 2.49e+01 angle pdb=" C GLY D 46 " pdb=" N MET D 47 " pdb=" CA MET D 47 " ideal model delta sigma weight residual 121.54 130.53 -8.99 1.91e+00 2.74e-01 2.21e+01 ... (remaining 28458 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.69: 12362 33.69 - 67.38: 204 67.38 - 101.08: 37 101.08 - 134.77: 7 134.77 - 168.46: 7 Dihedral angle restraints: 12617 sinusoidal: 5101 harmonic: 7516 Sorted by residual: 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 -60.00 108.46 -168.46 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C5' ADP D 401 " pdb=" O5' ADP D 401 " pdb=" PA ADP D 401 " pdb=" O2A ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 104.91 -164.91 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 103.58 -163.57 1 2.00e+01 2.50e-03 4.70e+01 ... (remaining 12614 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2347 0.057 - 0.113: 655 0.113 - 0.170: 134 0.170 - 0.227: 20 0.227 - 0.283: 5 Chirality restraints: 3161 Sorted by residual: chirality pdb=" CB ILE F 151 " pdb=" CA ILE F 151 " pdb=" CG1 ILE F 151 " pdb=" CG2 ILE F 151 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA MET D 47 " pdb=" N MET D 47 " pdb=" C MET D 47 " pdb=" CB MET D 47 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA MET F 47 " pdb=" N MET F 47 " pdb=" C MET F 47 " pdb=" CB MET F 47 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 3158 not shown) Planarity restraints: 3639 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG F 37 " -0.056 5.00e-02 4.00e+02 8.60e-02 1.18e+01 pdb=" N PRO F 38 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO F 38 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO F 38 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 37 " -0.056 5.00e-02 4.00e+02 8.56e-02 1.17e+01 pdb=" N PRO B 38 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO B 38 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 38 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 37 " 0.056 5.00e-02 4.00e+02 8.53e-02 1.17e+01 pdb=" N PRO A 38 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO A 38 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 38 " 0.046 5.00e-02 4.00e+02 ... (remaining 3636 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 177 2.61 - 3.19: 16189 3.19 - 3.76: 31283 3.76 - 4.33: 44493 4.33 - 4.90: 73733 Nonbonded interactions: 165875 Sorted by model distance: nonbonded pdb=" O1B ADP G 401 " pdb="MG MG G 402 " model vdw 2.042 2.170 nonbonded pdb=" O1B ADP B 401 " pdb="MG MG B 402 " model vdw 2.085 2.170 nonbonded pdb=" O1B ADP C 401 " pdb="MG MG C 402 " model vdw 2.114 2.170 nonbonded pdb=" O1B ADP A 401 " pdb="MG MG A 402 " model vdw 2.138 2.170 nonbonded pdb=" O1B ADP D 401 " pdb="MG MG D 402 " model vdw 2.172 2.170 ... (remaining 165870 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 374 or resid 401 through 402)) selection = (chain 'B' and (resid 5 through 374 or resid 401 through 402)) selection = (chain 'C' and (resid 5 through 374 or resid 401 through 402)) selection = (chain 'D' and (resid 5 through 374 or resid 401 through 402)) selection = (chain 'E' and (resid 5 through 374 or resid 401 through 402)) selection = (chain 'F' and (resid 5 through 374 or resid 401 through 402)) selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.640 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: 0.740 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 47.060 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 20972 Z= 0.322 Angle : 0.962 15.935 28463 Z= 0.512 Chirality : 0.055 0.283 3161 Planarity : 0.010 0.089 3639 Dihedral : 15.053 168.459 7807 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: -1.91 (0.15), residues: 2566 helix: -2.16 (0.12), residues: 1083 sheet: -0.23 (0.24), residues: 456 loop : -0.41 (0.19), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 356 HIS 0.018 0.001 HIS F 371 PHE 0.039 0.002 PHE F 127 TYR 0.031 0.002 TYR E 279 ARG 0.019 0.001 ARG F 210 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 2.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.9423 (tpp) cc_final: 0.9201 (tpt) REVERT: B 361 GLU cc_start: 0.9330 (mt-10) cc_final: 0.8986 (mp0) REVERT: B 372 ARG cc_start: 0.8548 (ptp90) cc_final: 0.8273 (ptp90) REVERT: C 132 MET cc_start: 0.9115 (tmm) cc_final: 0.8447 (tmm) REVERT: E 305 MET cc_start: 0.9126 (mmm) cc_final: 0.8836 (mmm) REVERT: F 180 LEU cc_start: 0.9325 (tp) cc_final: 0.9113 (tp) REVERT: G 283 MET cc_start: 0.8989 (ppp) cc_final: 0.8786 (ppp) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.3190 time to fit residues: 85.4872 Evaluate side-chains 138 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 2.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 218 optimal weight: 2.9990 chunk 196 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 67 optimal weight: 0.6980 chunk 132 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 chunk 203 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 123 optimal weight: 0.9980 chunk 151 optimal weight: 5.9990 chunk 235 optimal weight: 10.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 162 ASN ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20972 Z= 0.223 Angle : 0.610 9.707 28463 Z= 0.294 Chirality : 0.045 0.158 3161 Planarity : 0.005 0.055 3639 Dihedral : 9.736 170.598 2921 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.36 % Allowed : 3.96 % Favored : 95.67 % 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: -0.22 (0.17), residues: 2566 helix: -0.26 (0.16), residues: 1051 sheet: -0.01 (0.25), residues: 429 loop : 0.17 (0.20), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 86 HIS 0.005 0.001 HIS B 371 PHE 0.021 0.001 PHE G 223 TYR 0.026 0.001 TYR E 279 ARG 0.005 0.000 ARG F 147 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 139 time to evaluate : 2.488 Fit side-chains revert: symmetry clash REVERT: A 123 MET cc_start: 0.9260 (tpp) cc_final: 0.8872 (tpt) REVERT: B 361 GLU cc_start: 0.9340 (mt-10) cc_final: 0.9117 (mp0) REVERT: B 372 ARG cc_start: 0.8594 (ptp90) cc_final: 0.8198 (ptp90) REVERT: C 132 MET cc_start: 0.8472 (tmm) cc_final: 0.8043 (tmm) REVERT: C 355 MET cc_start: 0.9564 (mtp) cc_final: 0.9282 (mtm) REVERT: D 123 MET cc_start: 0.9085 (tpp) cc_final: 0.8823 (mmm) REVERT: E 305 MET cc_start: 0.9169 (mmm) cc_final: 0.8790 (mmm) REVERT: F 123 MET cc_start: 0.9306 (mmm) cc_final: 0.8549 (mmm) outliers start: 8 outliers final: 6 residues processed: 143 average time/residue: 0.3112 time to fit residues: 71.7815 Evaluate side-chains 142 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 136 time to evaluate : 2.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain E residue 106 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 130 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 195 optimal weight: 0.9980 chunk 160 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 235 optimal weight: 0.3980 chunk 254 optimal weight: 6.9990 chunk 209 optimal weight: 5.9990 chunk 233 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 189 optimal weight: 0.2980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 173 HIS F 12 ASN ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 20972 Z= 0.265 Angle : 0.601 8.250 28463 Z= 0.290 Chirality : 0.045 0.167 3161 Planarity : 0.004 0.044 3639 Dihedral : 8.037 143.555 2921 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.59 % Allowed : 5.33 % Favored : 94.08 % 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: 0.36 (0.17), residues: 2566 helix: 0.41 (0.16), residues: 1070 sheet: 0.19 (0.25), residues: 438 loop : 0.32 (0.20), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 340 HIS 0.004 0.001 HIS B 371 PHE 0.022 0.001 PHE G 124 TYR 0.022 0.001 TYR E 279 ARG 0.004 0.000 ARG G 147 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 2.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 MET cc_start: 0.8920 (OUTLIER) cc_final: 0.8666 (mmm) REVERT: B 372 ARG cc_start: 0.8559 (ptp90) cc_final: 0.8279 (ptp90) REVERT: C 132 MET cc_start: 0.8741 (tmm) cc_final: 0.8429 (tmm) REVERT: C 355 MET cc_start: 0.9572 (mtp) cc_final: 0.9300 (mtm) REVERT: D 123 MET cc_start: 0.9093 (tpp) cc_final: 0.8821 (mmm) REVERT: E 47 MET cc_start: 0.7597 (pmm) cc_final: 0.7066 (pmm) REVERT: E 305 MET cc_start: 0.9220 (mmm) cc_final: 0.8781 (mmm) REVERT: F 82 MET cc_start: 0.8942 (mmm) cc_final: 0.8234 (tmm) REVERT: F 123 MET cc_start: 0.9429 (mmm) cc_final: 0.8585 (mmm) REVERT: F 276 GLU cc_start: 0.8183 (pm20) cc_final: 0.7783 (pm20) REVERT: F 355 MET cc_start: 0.8969 (mmm) cc_final: 0.8640 (mmm) REVERT: G 44 MET cc_start: 0.9418 (mmm) cc_final: 0.9132 (mmm) outliers start: 13 outliers final: 9 residues processed: 147 average time/residue: 0.3221 time to fit residues: 75.8695 Evaluate side-chains 146 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 2.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain G residue 10 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 232 optimal weight: 2.9990 chunk 177 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 chunk 236 optimal weight: 1.9990 chunk 250 optimal weight: 3.9990 chunk 123 optimal weight: 0.6980 chunk 224 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20972 Z= 0.209 Angle : 0.562 7.706 28463 Z= 0.268 Chirality : 0.044 0.167 3161 Planarity : 0.004 0.040 3639 Dihedral : 6.506 140.138 2921 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.59 % Allowed : 6.38 % Favored : 93.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.17), residues: 2566 helix: 0.93 (0.17), residues: 1043 sheet: 0.25 (0.25), residues: 437 loop : 0.28 (0.20), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 340 HIS 0.004 0.001 HIS F 161 PHE 0.011 0.001 PHE G 223 TYR 0.019 0.001 TYR E 279 ARG 0.004 0.000 ARG D 372 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 2.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8561 (tmm) cc_final: 0.8053 (tmm) REVERT: A 283 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8416 (mtm) REVERT: B 372 ARG cc_start: 0.8565 (ptp90) cc_final: 0.8119 (ptp90) REVERT: C 132 MET cc_start: 0.8592 (tmm) cc_final: 0.8316 (tmm) REVERT: D 47 MET cc_start: 0.8873 (pmm) cc_final: 0.8649 (pmm) REVERT: D 123 MET cc_start: 0.9145 (tpp) cc_final: 0.8842 (mmm) REVERT: E 305 MET cc_start: 0.9162 (mmm) cc_final: 0.8829 (mmm) REVERT: F 82 MET cc_start: 0.8935 (mmm) cc_final: 0.8181 (tmm) REVERT: F 123 MET cc_start: 0.9382 (mmm) cc_final: 0.8541 (mmm) REVERT: F 276 GLU cc_start: 0.8090 (pm20) cc_final: 0.7690 (pm20) REVERT: F 355 MET cc_start: 0.9000 (mmm) cc_final: 0.8725 (mmm) REVERT: G 44 MET cc_start: 0.9409 (mmm) cc_final: 0.8989 (mmm) REVERT: G 323 SER cc_start: 0.8861 (p) cc_final: 0.8661 (t) outliers start: 13 outliers final: 5 residues processed: 148 average time/residue: 0.3492 time to fit residues: 82.4933 Evaluate side-chains 141 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 135 time to evaluate : 2.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 106 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 208 optimal weight: 6.9990 chunk 142 optimal weight: 2.9990 chunk 3 optimal weight: 0.0270 chunk 186 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 213 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 127 optimal weight: 0.9980 chunk 224 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 overall best weight: 1.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN D 12 ASN ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 161 HIS ** G 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20972 Z= 0.275 Angle : 0.588 8.659 28463 Z= 0.283 Chirality : 0.045 0.173 3161 Planarity : 0.004 0.037 3639 Dihedral : 6.178 134.758 2921 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.87 % Allowed : 6.88 % Favored : 92.26 % 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: 0.85 (0.17), residues: 2566 helix: 1.12 (0.17), residues: 1049 sheet: 0.29 (0.24), residues: 462 loop : 0.30 (0.20), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 340 HIS 0.004 0.001 HIS F 161 PHE 0.011 0.001 PHE G 223 TYR 0.017 0.001 TYR E 279 ARG 0.006 0.000 ARG D 372 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 2.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 355 MET cc_start: 0.8973 (mtm) cc_final: 0.8345 (pmm) REVERT: B 372 ARG cc_start: 0.8575 (ptp90) cc_final: 0.8116 (ptp90) REVERT: C 82 MET cc_start: 0.8854 (tpt) cc_final: 0.8545 (tpt) REVERT: C 132 MET cc_start: 0.8622 (tmm) cc_final: 0.8380 (tmm) REVERT: D 123 MET cc_start: 0.9203 (tpp) cc_final: 0.8862 (mmm) REVERT: E 305 MET cc_start: 0.9199 (mmm) cc_final: 0.8912 (mmm) REVERT: F 82 MET cc_start: 0.8974 (mmm) cc_final: 0.8262 (tmm) REVERT: F 123 MET cc_start: 0.9400 (mmm) cc_final: 0.8493 (mmm) REVERT: F 276 GLU cc_start: 0.8068 (pm20) cc_final: 0.7669 (pm20) REVERT: F 355 MET cc_start: 0.8998 (mmm) cc_final: 0.8776 (mmm) REVERT: G 44 MET cc_start: 0.9403 (mmm) cc_final: 0.8920 (mmm) REVERT: G 123 MET cc_start: 0.8803 (tpt) cc_final: 0.8298 (tpp) REVERT: G 323 SER cc_start: 0.8876 (p) cc_final: 0.8671 (t) outliers start: 19 outliers final: 9 residues processed: 148 average time/residue: 0.3094 time to fit residues: 73.9068 Evaluate side-chains 145 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 136 time to evaluate : 2.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain G residue 10 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 84 optimal weight: 0.9990 chunk 225 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 146 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 250 optimal weight: 3.9990 chunk 208 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN C 173 HIS D 12 ASN ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 371 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20972 Z= 0.172 Angle : 0.550 9.605 28463 Z= 0.261 Chirality : 0.044 0.167 3161 Planarity : 0.003 0.036 3639 Dihedral : 5.962 130.304 2921 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.64 % Allowed : 7.52 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.17), residues: 2566 helix: 1.26 (0.17), residues: 1049 sheet: 0.40 (0.25), residues: 437 loop : 0.34 (0.20), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 340 HIS 0.003 0.000 HIS B 371 PHE 0.009 0.001 PHE G 223 TYR 0.030 0.001 TYR A 279 ARG 0.004 0.000 ARG D 372 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 2.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.7940 (mtp) REVERT: B 132 MET cc_start: 0.9076 (tmm) cc_final: 0.8559 (tmm) REVERT: B 355 MET cc_start: 0.9002 (mtm) cc_final: 0.8613 (ptp) REVERT: B 372 ARG cc_start: 0.8581 (ptp90) cc_final: 0.8284 (ptp90) REVERT: C 82 MET cc_start: 0.8815 (tpt) cc_final: 0.8471 (tpt) REVERT: C 132 MET cc_start: 0.8567 (tmm) cc_final: 0.8352 (tmm) REVERT: D 123 MET cc_start: 0.9204 (tpp) cc_final: 0.8867 (mmm) REVERT: D 372 ARG cc_start: 0.9245 (mtp-110) cc_final: 0.8789 (mtm-85) REVERT: E 305 MET cc_start: 0.9195 (mmm) cc_final: 0.8959 (mmm) REVERT: F 82 MET cc_start: 0.8931 (mmm) cc_final: 0.8268 (tmm) REVERT: F 123 MET cc_start: 0.9406 (mmm) cc_final: 0.8512 (mmm) REVERT: F 276 GLU cc_start: 0.8070 (pm20) cc_final: 0.7687 (pm20) REVERT: F 355 MET cc_start: 0.8987 (mmm) cc_final: 0.8752 (mmm) REVERT: G 44 MET cc_start: 0.9408 (mmm) cc_final: 0.8915 (mmm) REVERT: G 123 MET cc_start: 0.8685 (tpt) cc_final: 0.8354 (tpp) REVERT: G 127 PHE cc_start: 0.8399 (m-10) cc_final: 0.8114 (m-10) REVERT: G 323 SER cc_start: 0.8876 (p) cc_final: 0.8666 (t) outliers start: 14 outliers final: 9 residues processed: 146 average time/residue: 0.3097 time to fit residues: 73.0916 Evaluate side-chains 145 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 2.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain G residue 124 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 241 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 142 optimal weight: 0.3980 chunk 182 optimal weight: 6.9990 chunk 141 optimal weight: 0.7980 chunk 210 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 249 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 152 optimal weight: 0.4980 chunk 115 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN D 12 ASN ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 371 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20972 Z= 0.214 Angle : 0.564 10.147 28463 Z= 0.268 Chirality : 0.044 0.178 3161 Planarity : 0.003 0.037 3639 Dihedral : 5.871 128.272 2921 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.59 % Allowed : 7.70 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.17), residues: 2566 helix: 1.32 (0.17), residues: 1049 sheet: 0.36 (0.24), residues: 462 loop : 0.40 (0.20), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 340 HIS 0.003 0.001 HIS F 161 PHE 0.008 0.001 PHE C 127 TYR 0.039 0.001 TYR A 279 ARG 0.003 0.000 ARG D 372 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 2.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8735 (tmm) cc_final: 0.8222 (tmm) REVERT: A 325 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.7865 (mtp) REVERT: B 132 MET cc_start: 0.9082 (tmm) cc_final: 0.8558 (tmm) REVERT: B 355 MET cc_start: 0.9005 (mtm) cc_final: 0.8575 (ptp) REVERT: B 372 ARG cc_start: 0.8592 (ptp90) cc_final: 0.8291 (ptp90) REVERT: C 82 MET cc_start: 0.8847 (tpt) cc_final: 0.8493 (tpt) REVERT: D 123 MET cc_start: 0.9216 (tpp) cc_final: 0.8859 (mmm) REVERT: D 372 ARG cc_start: 0.9284 (mtp-110) cc_final: 0.8797 (mtm-85) REVERT: E 305 MET cc_start: 0.9202 (mmm) cc_final: 0.8946 (mmm) REVERT: F 82 MET cc_start: 0.8950 (mmm) cc_final: 0.8267 (tmm) REVERT: F 123 MET cc_start: 0.9424 (mmm) cc_final: 0.8507 (mmm) REVERT: F 276 GLU cc_start: 0.8090 (pm20) cc_final: 0.7698 (pm20) REVERT: F 355 MET cc_start: 0.8997 (mmm) cc_final: 0.8770 (mmm) REVERT: G 44 MET cc_start: 0.9372 (mmm) cc_final: 0.8708 (mmm) REVERT: G 123 MET cc_start: 0.8824 (tpt) cc_final: 0.8548 (tpp) REVERT: G 127 PHE cc_start: 0.8490 (m-10) cc_final: 0.8188 (m-10) outliers start: 13 outliers final: 9 residues processed: 144 average time/residue: 0.3119 time to fit residues: 72.1433 Evaluate side-chains 144 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 2.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain G residue 124 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 154 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 158 optimal weight: 0.7980 chunk 170 optimal weight: 1.9990 chunk 123 optimal weight: 0.0670 chunk 23 optimal weight: 3.9990 chunk 196 optimal weight: 4.9990 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 371 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20972 Z= 0.172 Angle : 0.551 10.557 28463 Z= 0.260 Chirality : 0.044 0.179 3161 Planarity : 0.003 0.037 3639 Dihedral : 5.734 123.543 2921 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.46 % Allowed : 7.88 % Favored : 91.66 % 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: 1.13 (0.17), residues: 2566 helix: 1.38 (0.17), residues: 1049 sheet: 0.38 (0.25), residues: 462 loop : 0.46 (0.20), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 340 HIS 0.002 0.000 HIS F 161 PHE 0.007 0.001 PHE G 124 TYR 0.038 0.001 TYR A 279 ARG 0.003 0.000 ARG D 372 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 140 time to evaluate : 2.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8732 (tmm) cc_final: 0.8224 (tmm) REVERT: A 325 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7909 (mtp) REVERT: B 132 MET cc_start: 0.9039 (tmm) cc_final: 0.8573 (tmm) REVERT: B 355 MET cc_start: 0.8992 (mtm) cc_final: 0.8758 (ptp) REVERT: B 372 ARG cc_start: 0.8588 (ptp90) cc_final: 0.8284 (ptp90) REVERT: C 82 MET cc_start: 0.8893 (tpt) cc_final: 0.8549 (tpt) REVERT: D 47 MET cc_start: 0.8872 (pmm) cc_final: 0.8610 (pmm) REVERT: D 123 MET cc_start: 0.9210 (tpp) cc_final: 0.8852 (mmm) REVERT: D 372 ARG cc_start: 0.9278 (mtp-110) cc_final: 0.8799 (mtm-85) REVERT: E 305 MET cc_start: 0.9192 (mmm) cc_final: 0.8951 (mmm) REVERT: F 82 MET cc_start: 0.8938 (mmm) cc_final: 0.8281 (tmm) REVERT: F 123 MET cc_start: 0.9415 (mmm) cc_final: 0.8505 (mmm) REVERT: F 276 GLU cc_start: 0.8082 (pm20) cc_final: 0.7695 (pm20) REVERT: F 355 MET cc_start: 0.8991 (mmm) cc_final: 0.8760 (mmm) REVERT: G 44 MET cc_start: 0.9361 (mmm) cc_final: 0.8836 (mmm) REVERT: G 123 MET cc_start: 0.8874 (tpt) cc_final: 0.8529 (tpp) REVERT: G 127 PHE cc_start: 0.8514 (m-10) cc_final: 0.8188 (m-10) outliers start: 10 outliers final: 8 residues processed: 146 average time/residue: 0.3193 time to fit residues: 74.6925 Evaluate side-chains 145 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 136 time to evaluate : 2.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain G residue 124 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 227 optimal weight: 5.9990 chunk 239 optimal weight: 2.9990 chunk 218 optimal weight: 0.3980 chunk 232 optimal weight: 10.0000 chunk 140 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 182 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 210 optimal weight: 0.5980 chunk 220 optimal weight: 7.9990 chunk 231 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 371 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20972 Z= 0.274 Angle : 0.596 11.256 28463 Z= 0.283 Chirality : 0.045 0.192 3161 Planarity : 0.003 0.035 3639 Dihedral : 5.780 122.440 2921 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.59 % Allowed : 8.06 % Favored : 91.34 % 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 (0.17), residues: 2566 helix: 1.35 (0.17), residues: 1050 sheet: 0.33 (0.24), residues: 462 loop : 0.45 (0.20), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 86 HIS 0.003 0.001 HIS B 371 PHE 0.010 0.001 PHE C 127 TYR 0.045 0.001 TYR A 279 ARG 0.003 0.000 ARG F 254 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 2.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8871 (tmm) cc_final: 0.8355 (tmm) REVERT: A 325 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7983 (mtp) REVERT: B 132 MET cc_start: 0.9089 (tmm) cc_final: 0.8542 (tmm) REVERT: B 355 MET cc_start: 0.9030 (mtm) cc_final: 0.8796 (ptp) REVERT: B 372 ARG cc_start: 0.8630 (ptp90) cc_final: 0.8314 (ptp90) REVERT: C 82 MET cc_start: 0.8915 (tpt) cc_final: 0.8635 (tpt) REVERT: D 123 MET cc_start: 0.9264 (tpp) cc_final: 0.8935 (mmm) REVERT: D 184 ASP cc_start: 0.9222 (m-30) cc_final: 0.8952 (m-30) REVERT: D 372 ARG cc_start: 0.9276 (mtp-110) cc_final: 0.8846 (mtm-85) REVERT: E 305 MET cc_start: 0.9252 (mmm) cc_final: 0.8943 (mmm) REVERT: F 82 MET cc_start: 0.9009 (mmm) cc_final: 0.8330 (tmm) REVERT: F 123 MET cc_start: 0.9441 (mmm) cc_final: 0.8533 (mmm) REVERT: F 276 GLU cc_start: 0.8081 (pm20) cc_final: 0.7740 (pm20) REVERT: F 355 MET cc_start: 0.9019 (mmm) cc_final: 0.8721 (mmm) REVERT: G 44 MET cc_start: 0.9332 (mmm) cc_final: 0.8785 (mmm) REVERT: G 123 MET cc_start: 0.8911 (tpt) cc_final: 0.8545 (tpp) REVERT: G 127 PHE cc_start: 0.8582 (m-10) cc_final: 0.8232 (m-10) outliers start: 13 outliers final: 9 residues processed: 143 average time/residue: 0.3211 time to fit residues: 74.6276 Evaluate side-chains 144 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 2.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain G residue 124 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 152 optimal weight: 0.3980 chunk 245 optimal weight: 0.7980 chunk 150 optimal weight: 0.0050 chunk 116 optimal weight: 0.7980 chunk 171 optimal weight: 6.9990 chunk 258 optimal weight: 4.9990 chunk 237 optimal weight: 5.9990 chunk 205 optimal weight: 0.9990 chunk 21 optimal weight: 0.3980 chunk 158 optimal weight: 1.9990 chunk 125 optimal weight: 0.1980 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN D 161 HIS E 115 ASN ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 371 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20972 Z= 0.125 Angle : 0.547 11.724 28463 Z= 0.256 Chirality : 0.043 0.179 3161 Planarity : 0.003 0.038 3639 Dihedral : 5.505 108.926 2921 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.46 % Allowed : 8.20 % Favored : 91.34 % 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: 1.27 (0.17), residues: 2566 helix: 1.49 (0.17), residues: 1041 sheet: 0.48 (0.25), residues: 437 loop : 0.54 (0.20), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 340 HIS 0.002 0.000 HIS F 161 PHE 0.008 0.001 PHE C 223 TYR 0.035 0.001 TYR A 279 ARG 0.003 0.000 ARG D 372 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 140 time to evaluate : 2.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8823 (tmm) cc_final: 0.8356 (tmm) REVERT: A 325 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.7852 (mtp) REVERT: B 132 MET cc_start: 0.8959 (tmm) cc_final: 0.8572 (tmm) REVERT: B 372 ARG cc_start: 0.8645 (ptp90) cc_final: 0.8339 (ptp90) REVERT: C 82 MET cc_start: 0.8884 (tpt) cc_final: 0.8602 (tpt) REVERT: D 47 MET cc_start: 0.8897 (pmm) cc_final: 0.8590 (pmm) REVERT: D 123 MET cc_start: 0.9176 (tpp) cc_final: 0.8785 (mmm) REVERT: D 184 ASP cc_start: 0.9164 (m-30) cc_final: 0.8884 (m-30) REVERT: D 372 ARG cc_start: 0.9303 (mtp-110) cc_final: 0.8787 (mtm-85) REVERT: E 305 MET cc_start: 0.9193 (mmm) cc_final: 0.8963 (mmm) REVERT: F 82 MET cc_start: 0.8893 (mmm) cc_final: 0.8297 (tmm) REVERT: F 123 MET cc_start: 0.9400 (mmm) cc_final: 0.8532 (mmm) REVERT: F 276 GLU cc_start: 0.8062 (pm20) cc_final: 0.7747 (pm20) REVERT: F 355 MET cc_start: 0.8987 (mmm) cc_final: 0.8761 (mmm) REVERT: G 44 MET cc_start: 0.9328 (mmm) cc_final: 0.8850 (mmm) REVERT: G 123 MET cc_start: 0.8908 (tpt) cc_final: 0.8525 (tpp) REVERT: G 127 PHE cc_start: 0.8566 (m-10) cc_final: 0.8215 (m-10) REVERT: G 176 MET cc_start: 0.8053 (ptp) cc_final: 0.7696 (pmm) REVERT: G 325 MET cc_start: 0.6721 (ptp) cc_final: 0.5705 (pmm) outliers start: 10 outliers final: 8 residues processed: 146 average time/residue: 0.3208 time to fit residues: 75.0193 Evaluate side-chains 146 residues out of total 2195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 137 time to evaluate : 2.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain G residue 124 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 163 optimal weight: 5.9990 chunk 218 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 189 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 205 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 211 optimal weight: 3.9990 chunk 26 optimal weight: 0.4980 chunk 37 optimal weight: 8.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN G 371 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.055428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.042766 restraints weight = 74703.002| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 3.37 r_work: 0.2653 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20972 Z= 0.155 Angle : 0.547 11.580 28463 Z= 0.255 Chirality : 0.044 0.170 3161 Planarity : 0.003 0.038 3639 Dihedral : 5.402 97.365 2921 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.50 % Allowed : 8.29 % Favored : 91.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.17), residues: 2566 helix: 1.53 (0.17), residues: 1042 sheet: 0.50 (0.25), residues: 437 loop : 0.56 (0.20), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 356 HIS 0.002 0.000 HIS F 161 PHE 0.007 0.001 PHE G 124 TYR 0.021 0.001 TYR E 279 ARG 0.003 0.000 ARG A 372 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3384.19 seconds wall clock time: 63 minutes 42.73 seconds (3822.73 seconds total)