Starting phenix.real_space_refine on Tue Jul 23 22:56:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9az4_44012/07_2024/9az4_44012_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9az4_44012/07_2024/9az4_44012.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9az4_44012/07_2024/9az4_44012.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9az4_44012/07_2024/9az4_44012.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9az4_44012/07_2024/9az4_44012_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9az4_44012/07_2024/9az4_44012_neut.cif" } resolution = 3.37 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= 0.012 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 6 5.21 5 S 154 5.16 5 C 15053 2.51 5 N 4069 2.21 5 O 4571 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 80": "OD1" <-> "OD2" Residue "E GLU 364": "OE1" <-> "OE2" Residue "G TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 947": "OE1" <-> "OE2" Residue "H TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 23865 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 3140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3140 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 14, 'TRANS': 378} Chain breaks: 2 Chain: "H" Number of atoms: 3157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3157 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 15, 'TRANS': 380} Chain breaks: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 13.54, per 1000 atoms: 0.57 Number of scatterers: 23865 At special positions: 0 Unit cell: (132.84, 125.28, 230.04, 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 154 16.00 P 12 15.00 Mg 6 11.99 O 4571 8.00 N 4069 7.00 C 15053 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 - 3.50 Amino acid : False - 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.03 Conformation dependent library (CDL) restraints added in 4.0 seconds 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5662 Finding SS restraints... Secondary structure from input PDB file: 158 helices and 36 sheets defined 56.0% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.06 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.837A 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: 3.524A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 202 through 217 removed outlier: 4.060A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N CYS A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 removed outlier: 3.654A pdb=" N GLU A 226 " --> pdb=" O ASP A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.697A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 261 Processing helix chain 'A' and resid 263 through 267 removed outlier: 3.503A pdb=" N PHE A 266 " --> pdb=" O GLN A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 285 removed outlier: 3.539A pdb=" N CYS A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.510A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 4.094A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.962A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 79 through 92 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.510A pdb=" N GLU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.794A 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: 3.847A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 146 removed outlier: 3.535A pdb=" N LEU B 140 " --> pdb=" O ILE B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.695A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.811A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 216 removed outlier: 3.888A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 removed outlier: 3.546A pdb=" N GLU B 226 " --> pdb=" O ASP B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.717A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 261 Processing helix chain 'B' and resid 263 through 267 removed outlier: 3.538A pdb=" N PHE B 266 " --> pdb=" O GLN B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 289 through 295 Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.566A pdb=" N THR B 304 " --> pdb=" O GLY B 301 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 337 through 348 Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.623A pdb=" N GLN B 353 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 4.042A 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: 4.088A 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 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.559A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.755A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.523A 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: 3.776A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 4.038A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.501A 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: 3.589A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 263 removed outlier: 4.008A pdb=" N PHE C 262 " --> pdb=" O PRO C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 268 Processing helix chain 'C' and resid 273 through 285 Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 289 through 295 Processing helix chain 'C' and resid 301 through 306 removed outlier: 3.875A pdb=" N MET C 305 " --> pdb=" O GLY C 302 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 337 through 347 Processing helix chain 'C' and resid 348 through 349 No H-bonds generated for 'chain 'C' and resid 348 through 349' Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.536A pdb=" N GLN C 353 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 3.967A 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: 3.694A 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 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.520A pdb=" N GLU D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.675A 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 172 through 175 Processing helix chain 'D' and resid 181 through 194 Processing helix chain 'D' and resid 203 through 216 removed outlier: 4.201A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.519A 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 267 Processing helix chain 'D' and resid 273 through 285 Processing helix chain 'D' and resid 289 through 296 removed outlier: 3.650A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 306 removed outlier: 3.532A pdb=" N MET D 305 " --> pdb=" O GLY D 302 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 337 through 348 Processing helix chain 'D' and resid 350 through 356 removed outlier: 3.707A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TRP D 356 " --> pdb=" O GLN D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 368 through 374 removed outlier: 4.041A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N CYS D 374 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.638A pdb=" N GLU E 100 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 3.671A 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: 3.822A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 removed outlier: 3.529A pdb=" N SER E 145 " --> pdb=" O SER E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 193 Processing helix chain 'E' and resid 202 through 217 removed outlier: 3.864A pdb=" N GLU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) removed outlier: 3.538A 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: 3.619A pdb=" N CYS E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 263 removed outlier: 3.915A pdb=" N PHE E 262 " --> pdb=" O PRO E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 268 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 289 through 295 removed outlier: 4.004A pdb=" N LEU E 293 " --> pdb=" O ILE E 289 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ALA E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 306 removed outlier: 3.570A pdb=" N MET E 305 " --> pdb=" O GLY E 302 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 337 through 348 Processing helix chain 'E' and resid 349 through 356 removed outlier: 3.618A pdb=" N GLN E 353 " --> pdb=" O SER E 350 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TRP E 356 " --> pdb=" O GLN E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 367 through 369 No H-bonds generated for 'chain 'E' and resid 367 through 369' Processing helix chain 'F' and resid 55 through 61 Processing helix chain 'F' and resid 79 through 92 Processing helix chain 'F' and resid 97 through 101 removed outlier: 3.760A pdb=" N GLU F 100 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 3.505A 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: 3.594A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 145 Processing helix chain 'F' and resid 181 through 194 removed outlier: 3.869A pdb=" N THR F 194 " --> pdb=" O MET F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 217 removed outlier: 3.969A pdb=" N GLU F 207 " --> pdb=" O THR F 203 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) removed outlier: 3.541A 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: 3.665A 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 267 Processing helix chain 'F' and resid 273 through 284 Processing helix chain 'F' and resid 289 through 295 removed outlier: 3.572A pdb=" N LEU F 293 " --> pdb=" O ILE F 289 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA F 295 " --> pdb=" O LYS F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 306 removed outlier: 4.314A pdb=" N TYR F 306 " --> pdb=" O THR F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 321 removed outlier: 3.613A pdb=" N ARG F 312 " --> pdb=" O GLY F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 348 removed outlier: 3.817A pdb=" N SER F 348 " --> pdb=" O SER F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 354 removed outlier: 3.648A pdb=" N GLN F 353 " --> pdb=" O SER F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 366 Processing helix chain 'F' and resid 368 through 374 removed outlier: 4.133A pdb=" N ARG F 372 " --> pdb=" O SER F 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 573 through 578 Processing helix chain 'G' and resid 584 through 589 removed outlier: 3.931A pdb=" N SER G 589 " --> pdb=" O ALA G 585 " (cutoff:3.500A) Processing helix chain 'G' and resid 598 through 606 Processing helix chain 'G' and resid 634 through 646 Processing helix chain 'G' and resid 651 through 661 Processing helix chain 'G' and resid 668 through 678 Processing helix chain 'G' and resid 681 through 691 Processing helix chain 'G' and resid 694 through 698 removed outlier: 3.880A pdb=" N LYS G 697 " --> pdb=" O GLU G 694 " (cutoff:3.500A) Processing helix chain 'G' and resid 699 through 710 Processing helix chain 'G' and resid 713 through 750 removed outlier: 3.686A pdb=" N ARG G 717 " --> pdb=" O CYS G 713 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG G 735 " --> pdb=" O LEU G 731 " (cutoff:3.500A) Proline residue: G 736 - end of helix Processing helix chain 'G' and resid 752 through 769 removed outlier: 3.807A pdb=" N ILE G 756 " --> pdb=" O ARG G 752 " (cutoff:3.500A) Processing helix chain 'G' and resid 781 through 785 removed outlier: 3.677A pdb=" N THR G 784 " --> pdb=" O LYS G 781 " (cutoff:3.500A) Processing helix chain 'G' and resid 799 through 812 removed outlier: 3.806A pdb=" N LYS G 810 " --> pdb=" O GLU G 806 " (cutoff:3.500A) Processing helix chain 'G' and resid 813 through 816 Processing helix chain 'G' and resid 817 through 822 removed outlier: 3.526A pdb=" N LEU G 822 " --> pdb=" O LEU G 818 " (cutoff:3.500A) Processing helix chain 'G' and resid 822 through 829 Processing helix chain 'G' and resid 832 through 856 removed outlier: 3.647A pdb=" N ILE G 836 " --> pdb=" O ASN G 832 " (cutoff:3.500A) Processing helix chain 'G' and resid 858 through 898 removed outlier: 5.709A pdb=" N GLU G 867 " --> pdb=" O GLU G 863 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ARG G 868 " --> pdb=" O GLN G 864 " (cutoff:3.500A) Processing helix chain 'G' and resid 905 through 947 Processing helix chain 'G' and resid 972 through 983 Processing helix chain 'H' and resid 573 through 578 Processing helix chain 'H' and resid 582 through 588 removed outlier: 3.949A pdb=" N SER H 586 " --> pdb=" O SER H 582 " (cutoff:3.500A) Processing helix chain 'H' and resid 598 through 606 Processing helix chain 'H' and resid 634 through 647 removed outlier: 3.842A pdb=" N GLN H 647 " --> pdb=" O ILE H 643 " (cutoff:3.500A) Processing helix chain 'H' and resid 651 through 662 removed outlier: 3.564A pdb=" N VAL H 655 " --> pdb=" O SER H 651 " (cutoff:3.500A) Processing helix chain 'H' and resid 668 through 678 Processing helix chain 'H' and resid 681 through 690 Processing helix chain 'H' and resid 699 through 711 Processing helix chain 'H' and resid 713 through 750 Proline residue: H 736 - end of helix removed outlier: 3.627A pdb=" N THR H 750 " --> pdb=" O GLU H 746 " (cutoff:3.500A) Processing helix chain 'H' and resid 752 through 769 removed outlier: 4.405A pdb=" N ILE H 756 " --> pdb=" O ARG H 752 " (cutoff:3.500A) Processing helix chain 'H' and resid 781 through 785 Processing helix chain 'H' and resid 786 through 790 removed outlier: 3.939A pdb=" N THR H 789 " --> pdb=" O LEU H 786 " (cutoff:3.500A) Processing helix chain 'H' and resid 799 through 811 removed outlier: 4.060A pdb=" N LYS H 810 " --> pdb=" O GLU H 806 " (cutoff:3.500A) Processing helix chain 'H' and resid 812 through 816 Processing helix chain 'H' and resid 817 through 822 removed outlier: 3.989A pdb=" N ASP H 821 " --> pdb=" O GLN H 817 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU H 822 " --> pdb=" O LEU H 818 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 817 through 822' Processing helix chain 'H' and resid 832 through 856 removed outlier: 3.844A pdb=" N ILE H 836 " --> pdb=" O ASN H 832 " (cutoff:3.500A) Processing helix chain 'H' and resid 858 through 897 removed outlier: 5.601A pdb=" N GLU H 867 " --> pdb=" O GLU H 863 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ARG H 868 " --> pdb=" O GLN H 864 " (cutoff:3.500A) Processing helix chain 'H' and resid 906 through 947 Processing helix chain 'H' and resid 972 through 983 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.137A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.484A 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: 6.086A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.344A 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: 3.964A 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: 6.343A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (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: 3.515A pdb=" N SER B 155 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 176 through 178 removed outlier: 3.910A 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: 6.279A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR C 133 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 176 through 178 removed outlier: 6.165A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.150A 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: 4.086A pdb=" N GLN E 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 4.026A pdb=" N THR D 106 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ASN D 12 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.486A 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: 6.267A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 176 through 178 removed outlier: 3.938A 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: 6.716A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR E 103 " --> pdb=" O ALA E 131 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR E 133 " --> pdb=" O THR E 103 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.252A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AD4, first strand: chain 'F' and resid 29 through 32 removed outlier: 6.447A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.568A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR F 133 " --> pdb=" O THR F 103 " (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: 6.203A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) removed outlier: 5.926A 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 1227 hydrogen bonds defined for protein. 3339 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: 8.57 Time building geometry restraints manager: 9.87 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: 7444 1.34 - 1.46: 5419 1.46 - 1.58: 11195 1.58 - 1.71: 20 1.71 - 1.83: 262 Bond restraints: 24340 Sorted by residual: bond pdb=" CA VAL G 551 " pdb=" C VAL G 551 " ideal model delta sigma weight residual 1.525 1.592 -0.067 2.10e-02 2.27e+03 1.03e+01 bond pdb=" CG MET D 325 " pdb=" SD MET D 325 " ideal model delta sigma weight residual 1.803 1.733 0.070 2.50e-02 1.60e+03 7.74e+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 7.64e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.37e+00 bond pdb=" CB MET D 325 " pdb=" CG MET D 325 " ideal model delta sigma weight residual 1.520 1.439 0.081 3.00e-02 1.11e+03 7.21e+00 ... (remaining 24335 not shown) Histogram of bond angle deviations from ideal: 87.70 - 97.38: 12 97.38 - 107.06: 916 107.06 - 116.74: 15987 116.74 - 126.41: 15711 126.41 - 136.09: 342 Bond angle restraints: 32968 Sorted by residual: angle pdb=" CB MET D 325 " pdb=" CG MET D 325 " pdb=" SD MET D 325 " ideal model delta sigma weight residual 112.70 133.49 -20.79 3.00e+00 1.11e-01 4.80e+01 angle pdb=" CG MET D 325 " pdb=" SD MET D 325 " pdb=" CE MET D 325 " ideal model delta sigma weight residual 100.90 87.70 13.20 2.20e+00 2.07e-01 3.60e+01 angle pdb=" C GLY C 46 " pdb=" N MET C 47 " pdb=" CA MET C 47 " ideal model delta sigma weight residual 121.54 132.55 -11.01 1.91e+00 2.74e-01 3.32e+01 angle pdb=" CA MET C 47 " pdb=" CB MET C 47 " pdb=" CG MET C 47 " ideal model delta sigma weight residual 114.10 125.59 -11.49 2.00e+00 2.50e-01 3.30e+01 angle pdb=" CA MET A 355 " pdb=" CB MET A 355 " pdb=" CG MET A 355 " ideal model delta sigma weight residual 114.10 125.51 -11.41 2.00e+00 2.50e-01 3.25e+01 ... (remaining 32963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 14586 35.76 - 71.52: 211 71.52 - 107.28: 12 107.28 - 143.04: 2 143.04 - 178.80: 1 Dihedral angle restraints: 14812 sinusoidal: 6041 harmonic: 8771 Sorted by residual: dihedral pdb=" O1B ADP F 401 " pdb=" O3A ADP F 401 " pdb=" PB ADP F 401 " pdb=" PA ADP F 401 " ideal model delta sinusoidal sigma weight residual -60.00 118.80 -178.80 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP B 401 " pdb=" O5' ADP B 401 " pdb=" PA ADP B 401 " pdb=" O2A ADP B 401 " ideal model delta sinusoidal sigma weight residual 300.00 157.95 142.05 1 2.00e+01 2.50e-03 4.29e+01 dihedral pdb=" O2A ADP F 401 " pdb=" O3A ADP F 401 " pdb=" PA ADP F 401 " pdb=" PB ADP F 401 " ideal model delta sinusoidal sigma weight residual 300.00 174.50 125.50 1 2.00e+01 2.50e-03 3.79e+01 ... (remaining 14809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2954 0.068 - 0.136: 628 0.136 - 0.205: 86 0.205 - 0.273: 17 0.273 - 0.341: 10 Chirality restraints: 3695 Sorted by residual: chirality pdb=" CB ILE B 151 " pdb=" CA ILE B 151 " pdb=" CG1 ILE B 151 " pdb=" CG2 ILE B 151 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CB ILE A 151 " pdb=" CA ILE A 151 " pdb=" CG1 ILE A 151 " pdb=" CG2 ILE A 151 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CB ILE B 287 " pdb=" CA ILE B 287 " pdb=" CG1 ILE B 287 " pdb=" CG2 ILE B 287 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.89e+00 ... (remaining 3692 not shown) Planarity restraints: 4230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU E 364 " -0.021 2.00e-02 2.50e+03 4.20e-02 1.77e+01 pdb=" CD GLU E 364 " 0.073 2.00e-02 2.50e+03 pdb=" OE1 GLU E 364 " -0.026 2.00e-02 2.50e+03 pdb=" OE2 GLU E 364 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 705 " -0.021 2.00e-02 2.50e+03 2.86e-02 1.64e+01 pdb=" CG TYR G 705 " 0.070 2.00e-02 2.50e+03 pdb=" CD1 TYR G 705 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR G 705 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR G 705 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR G 705 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR G 705 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR G 705 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN H 824 " -0.056 5.00e-02 4.00e+02 8.33e-02 1.11e+01 pdb=" N PRO H 825 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO H 825 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO H 825 " -0.047 5.00e-02 4.00e+02 ... (remaining 4227 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 296 2.63 - 3.20: 19868 3.20 - 3.77: 38305 3.77 - 4.33: 52733 4.33 - 4.90: 85935 Nonbonded interactions: 197137 Sorted by model distance: nonbonded pdb=" O1B ADP F 401 " pdb="MG MG F 402 " model vdw 2.069 2.170 nonbonded pdb=" O3B ADP C 401 " pdb="MG MG C 402 " model vdw 2.086 2.170 nonbonded pdb=" O1A ADP B 401 " pdb="MG MG B 402 " model vdw 2.087 2.170 nonbonded pdb=" O1A ADP A 401 " pdb="MG MG A 402 " model vdw 2.088 2.170 nonbonded pdb=" O3A ADP D 401 " pdb="MG MG D 402 " model vdw 2.095 2.170 ... (remaining 197132 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = (chain 'H' and (resid 551 through 608 or resid 626 through 983)) } 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: 0.010 Normalize map: mean=0, sd=1: 5.040 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: 0.000 Extract box with map and model: 1.240 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 61.960 Find NCS groups from input model: 1.640 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 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 : 0.007 0.092 24340 Z= 0.437 Angle : 1.057 20.786 32968 Z= 0.551 Chirality : 0.059 0.341 3695 Planarity : 0.007 0.083 4230 Dihedral : 13.816 178.803 9150 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.53 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.13), residues: 2973 helix: -1.55 (0.11), residues: 1478 sheet: -1.13 (0.24), residues: 384 loop : -1.01 (0.17), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.004 TRP A 356 HIS 0.017 0.002 HIS G 554 PHE 0.027 0.003 PHE G 920 TYR 0.070 0.003 TYR G 705 ARG 0.008 0.001 ARG C 28 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 2.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 MET cc_start: 0.9139 (mmm) cc_final: 0.8878 (mmm) REVERT: A 305 MET cc_start: 0.8452 (mmm) cc_final: 0.8219 (mmt) REVERT: A 313 MET cc_start: 0.9128 (tpp) cc_final: 0.8711 (tmm) REVERT: A 325 MET cc_start: 0.8492 (mmm) cc_final: 0.8195 (mmm) REVERT: D 82 MET cc_start: 0.8220 (tpt) cc_final: 0.7947 (tmm) REVERT: F 82 MET cc_start: 0.8866 (tpt) cc_final: 0.8294 (tpt) REVERT: F 101 HIS cc_start: 0.8569 (m-70) cc_final: 0.8270 (m90) REVERT: F 119 MET cc_start: 0.9449 (mtm) cc_final: 0.9116 (mtm) REVERT: F 305 MET cc_start: 0.8837 (mmp) cc_final: 0.8389 (mmp) REVERT: F 325 MET cc_start: 0.8541 (pmm) cc_final: 0.8278 (pmm) REVERT: G 564 MET cc_start: 0.6342 (mmp) cc_final: 0.5381 (mmp) REVERT: G 733 MET cc_start: 0.9323 (tmm) cc_final: 0.9081 (tmm) REVERT: H 705 TYR cc_start: 0.9347 (m-10) cc_final: 0.9079 (m-80) REVERT: H 721 MET cc_start: 0.9454 (mmm) cc_final: 0.8639 (mmm) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.4005 time to fit residues: 82.6324 Evaluate side-chains 120 residues out of total 2569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 2.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 20.0000 chunk 227 optimal weight: 50.0000 chunk 126 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 153 optimal weight: 4.9990 chunk 121 optimal weight: 0.0050 chunk 235 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 142 optimal weight: 9.9990 chunk 175 optimal weight: 0.9980 chunk 272 optimal weight: 10.0000 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 GLN D 162 ASN E 137 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 642 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24340 Z= 0.167 Angle : 0.568 8.286 32968 Z= 0.276 Chirality : 0.041 0.160 3695 Planarity : 0.004 0.067 4230 Dihedral : 7.254 169.736 3345 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.19 % Allowed : 2.80 % Favored : 97.00 % 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 (0.15), residues: 2973 helix: 0.20 (0.13), residues: 1529 sheet: -0.54 (0.25), residues: 402 loop : -0.53 (0.19), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 79 HIS 0.003 0.001 HIS G 554 PHE 0.013 0.001 PHE G 920 TYR 0.036 0.001 TYR G 705 ARG 0.002 0.000 ARG G 981 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 121 time to evaluate : 2.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.9052 (tpt) cc_final: 0.8833 (tpt) REVERT: A 132 MET cc_start: 0.8380 (tmm) cc_final: 0.7879 (tmm) REVERT: A 283 MET cc_start: 0.9152 (mmm) cc_final: 0.8943 (mmm) REVERT: A 355 MET cc_start: 0.8655 (tpp) cc_final: 0.8382 (tpp) REVERT: B 132 MET cc_start: 0.8435 (tmm) cc_final: 0.7930 (tmm) REVERT: B 355 MET cc_start: 0.8488 (tpp) cc_final: 0.8223 (tpp) REVERT: C 132 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7763 (tmm) REVERT: D 47 MET cc_start: 0.2959 (ptp) cc_final: 0.1057 (mmp) REVERT: D 82 MET cc_start: 0.8419 (tpt) cc_final: 0.8137 (tmm) REVERT: D 227 MET cc_start: 0.9060 (mmm) cc_final: 0.8815 (mmm) REVERT: E 299 MET cc_start: 0.8913 (mtm) cc_final: 0.8712 (mtp) REVERT: F 47 MET cc_start: 0.7314 (pmm) cc_final: 0.6952 (pmm) REVERT: F 82 MET cc_start: 0.8930 (tpt) cc_final: 0.8625 (tpt) REVERT: F 119 MET cc_start: 0.9399 (mtm) cc_final: 0.9074 (mtm) REVERT: F 132 MET cc_start: 0.9140 (ppp) cc_final: 0.8665 (ppp) REVERT: F 227 MET cc_start: 0.8215 (mmp) cc_final: 0.7829 (mmp) REVERT: F 305 MET cc_start: 0.8744 (mmp) cc_final: 0.8236 (mmp) REVERT: F 325 MET cc_start: 0.8557 (pmm) cc_final: 0.8264 (pmm) REVERT: G 564 MET cc_start: 0.6353 (mmp) cc_final: 0.5341 (mmp) REVERT: G 733 MET cc_start: 0.9357 (tmm) cc_final: 0.9142 (tmm) REVERT: H 721 MET cc_start: 0.9444 (mmm) cc_final: 0.8776 (mmm) outliers start: 5 outliers final: 2 residues processed: 123 average time/residue: 0.3275 time to fit residues: 67.5410 Evaluate side-chains 121 residues out of total 2569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 118 time to evaluate : 2.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain F residue 87 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 151 optimal weight: 20.0000 chunk 84 optimal weight: 3.9990 chunk 226 optimal weight: 30.0000 chunk 185 optimal weight: 20.0000 chunk 75 optimal weight: 9.9990 chunk 272 optimal weight: 5.9990 chunk 294 optimal weight: 50.0000 chunk 243 optimal weight: 7.9990 chunk 270 optimal weight: 8.9990 chunk 93 optimal weight: 10.0000 chunk 218 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 GLN C 137 GLN C 225 ASN C 297 ASN D 59 GLN ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 683 HIS ** H 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 24340 Z= 0.477 Angle : 0.736 8.140 32968 Z= 0.367 Chirality : 0.045 0.180 3695 Planarity : 0.004 0.062 4230 Dihedral : 7.294 165.885 3345 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.66 % Allowed : 5.10 % Favored : 94.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.15), residues: 2973 helix: 0.90 (0.14), residues: 1504 sheet: -0.50 (0.25), residues: 414 loop : -0.34 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 79 HIS 0.008 0.001 HIS F 87 PHE 0.022 0.002 PHE B 127 TYR 0.028 0.002 TYR G 705 ARG 0.007 0.001 ARG G 981 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 118 time to evaluate : 2.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.9150 (tpt) cc_final: 0.8947 (tpt) REVERT: A 123 MET cc_start: 0.9233 (tpp) cc_final: 0.9026 (mmm) REVERT: A 325 MET cc_start: 0.8125 (mmm) cc_final: 0.7867 (mmm) REVERT: A 355 MET cc_start: 0.8776 (tpp) cc_final: 0.8124 (tpt) REVERT: B 132 MET cc_start: 0.8452 (tmm) cc_final: 0.7953 (tmm) REVERT: B 325 MET cc_start: 0.8368 (tpp) cc_final: 0.8113 (mmt) REVERT: B 355 MET cc_start: 0.8778 (tpp) cc_final: 0.8490 (mmm) REVERT: C 132 MET cc_start: 0.8282 (ppp) cc_final: 0.7952 (tmm) REVERT: C 227 MET cc_start: 0.8867 (mmp) cc_final: 0.8562 (mmp) REVERT: C 305 MET cc_start: 0.8330 (mpp) cc_final: 0.8077 (mpp) REVERT: D 82 MET cc_start: 0.8571 (tpt) cc_final: 0.8250 (tmm) REVERT: D 176 MET cc_start: 0.8544 (ptp) cc_final: 0.8026 (pmm) REVERT: D 305 MET cc_start: 0.8977 (mmp) cc_final: 0.8698 (mmp) REVERT: E 119 MET cc_start: 0.9452 (mtm) cc_final: 0.9213 (mtm) REVERT: E 123 MET cc_start: 0.9175 (mmp) cc_final: 0.8833 (mmp) REVERT: F 47 MET cc_start: 0.8026 (pmm) cc_final: 0.7727 (pmm) REVERT: F 82 MET cc_start: 0.9103 (tpt) cc_final: 0.8734 (tpt) REVERT: F 132 MET cc_start: 0.9245 (ppp) cc_final: 0.8560 (ppp) REVERT: F 299 MET cc_start: 0.8569 (mtp) cc_final: 0.8303 (mtp) REVERT: F 305 MET cc_start: 0.8833 (mmp) cc_final: 0.8303 (mmp) REVERT: F 313 MET cc_start: 0.9391 (tpt) cc_final: 0.9149 (tpt) REVERT: F 325 MET cc_start: 0.8531 (pmm) cc_final: 0.7912 (pmm) REVERT: G 564 MET cc_start: 0.6702 (mmp) cc_final: 0.6056 (mmp) REVERT: H 721 MET cc_start: 0.9666 (mmm) cc_final: 0.9120 (mmm) outliers start: 17 outliers final: 8 residues processed: 126 average time/residue: 0.3517 time to fit residues: 74.3717 Evaluate side-chains 126 residues out of total 2569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 118 time to evaluate : 2.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain F residue 87 HIS Chi-restraints excluded: chain G residue 803 HIS Chi-restraints excluded: chain G residue 812 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 269 optimal weight: 9.9990 chunk 205 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 130 optimal weight: 7.9990 chunk 183 optimal weight: 5.9990 chunk 273 optimal weight: 10.0000 chunk 289 optimal weight: 10.0000 chunk 143 optimal weight: 0.2980 chunk 259 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 246 GLN D 246 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 642 ASN H 794 GLN ** H 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 24340 Z= 0.191 Angle : 0.568 7.687 32968 Z= 0.274 Chirality : 0.041 0.174 3695 Planarity : 0.003 0.063 4230 Dihedral : 7.070 166.313 3345 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.35 % Allowed : 6.85 % Favored : 92.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.80 (0.16), residues: 2973 helix: 1.36 (0.14), residues: 1468 sheet: -0.37 (0.25), residues: 402 loop : -0.11 (0.19), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 79 HIS 0.004 0.001 HIS G 554 PHE 0.012 0.001 PHE G 920 TYR 0.026 0.001 TYR G 705 ARG 0.003 0.000 ARG G 695 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 119 time to evaluate : 2.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.9071 (tpt) cc_final: 0.8831 (tpt) REVERT: A 132 MET cc_start: 0.8470 (tmm) cc_final: 0.7919 (tmm) REVERT: A 283 MET cc_start: 0.8860 (mmt) cc_final: 0.8640 (mmm) REVERT: A 355 MET cc_start: 0.8864 (tpp) cc_final: 0.8132 (tpt) REVERT: B 132 MET cc_start: 0.8442 (tmm) cc_final: 0.7952 (tmm) REVERT: B 325 MET cc_start: 0.8228 (tpp) cc_final: 0.8014 (mmt) REVERT: B 355 MET cc_start: 0.8799 (tpp) cc_final: 0.8567 (mmm) REVERT: C 119 MET cc_start: 0.8991 (mtt) cc_final: 0.8761 (mtm) REVERT: C 132 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7676 (tmm) REVERT: C 305 MET cc_start: 0.8180 (mpp) cc_final: 0.7921 (mpp) REVERT: D 82 MET cc_start: 0.8563 (tpt) cc_final: 0.8241 (tmm) REVERT: D 305 MET cc_start: 0.8984 (mmp) cc_final: 0.8752 (mmp) REVERT: D 325 MET cc_start: 0.5952 (OUTLIER) cc_final: 0.5629 (ppp) REVERT: E 119 MET cc_start: 0.9443 (mtm) cc_final: 0.9180 (mtm) REVERT: E 123 MET cc_start: 0.9187 (mmp) cc_final: 0.8923 (mmp) REVERT: E 305 MET cc_start: 0.8435 (mmp) cc_final: 0.8068 (mmp) REVERT: F 47 MET cc_start: 0.8094 (pmm) cc_final: 0.7758 (pmm) REVERT: F 82 MET cc_start: 0.9096 (tpt) cc_final: 0.8493 (tpt) REVERT: F 119 MET cc_start: 0.9414 (mtm) cc_final: 0.9063 (mtt) REVERT: F 132 MET cc_start: 0.9235 (ppp) cc_final: 0.8582 (ppp) REVERT: F 227 MET cc_start: 0.8348 (mmp) cc_final: 0.7879 (mmp) REVERT: F 299 MET cc_start: 0.8577 (mtp) cc_final: 0.8292 (mtp) REVERT: F 305 MET cc_start: 0.8853 (mmp) cc_final: 0.8338 (mmp) REVERT: F 313 MET cc_start: 0.9382 (tpt) cc_final: 0.9135 (tpt) REVERT: F 325 MET cc_start: 0.8657 (pmm) cc_final: 0.8178 (pmm) REVERT: G 564 MET cc_start: 0.6780 (mmp) cc_final: 0.6108 (mmp) REVERT: H 721 MET cc_start: 0.9692 (mmm) cc_final: 0.9145 (mmm) outliers start: 9 outliers final: 3 residues processed: 123 average time/residue: 0.3306 time to fit residues: 68.1554 Evaluate side-chains 124 residues out of total 2569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 119 time to evaluate : 2.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain G residue 803 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 241 optimal weight: 30.0000 chunk 164 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 215 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 chunk 247 optimal weight: 0.7980 chunk 200 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 148 optimal weight: 10.0000 chunk 260 optimal weight: 0.3980 chunk 73 optimal weight: 9.9990 overall best weight: 4.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 24340 Z= 0.332 Angle : 0.616 8.225 32968 Z= 0.301 Chirality : 0.042 0.155 3695 Planarity : 0.004 0.060 4230 Dihedral : 7.027 165.861 3345 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.58 % Allowed : 7.59 % Favored : 91.83 % 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: 0.78 (0.16), residues: 2973 helix: 1.33 (0.14), residues: 1506 sheet: -0.31 (0.26), residues: 402 loop : -0.21 (0.19), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 86 HIS 0.005 0.001 HIS F 87 PHE 0.014 0.002 PHE B 127 TYR 0.022 0.001 TYR G 705 ARG 0.003 0.000 ARG G 695 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 120 time to evaluate : 2.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.9112 (tpt) cc_final: 0.8890 (tpt) REVERT: A 283 MET cc_start: 0.8857 (mmt) cc_final: 0.8421 (mmm) REVERT: A 305 MET cc_start: 0.8307 (mpp) cc_final: 0.8060 (mmp) REVERT: B 132 MET cc_start: 0.8458 (tmm) cc_final: 0.7934 (tmm) REVERT: B 325 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7987 (mmt) REVERT: B 355 MET cc_start: 0.8875 (tpp) cc_final: 0.8555 (mmm) REVERT: C 132 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7799 (tmm) REVERT: C 305 MET cc_start: 0.8182 (mpp) cc_final: 0.7881 (mpp) REVERT: D 47 MET cc_start: 0.4529 (mtt) cc_final: 0.2654 (mmt) REVERT: D 82 MET cc_start: 0.8624 (tpt) cc_final: 0.8256 (tmm) REVERT: D 176 MET cc_start: 0.8581 (ptp) cc_final: 0.8139 (pmm) REVERT: D 305 MET cc_start: 0.9035 (mmp) cc_final: 0.8810 (mmp) REVERT: D 325 MET cc_start: 0.6423 (OUTLIER) cc_final: 0.6163 (ppp) REVERT: E 305 MET cc_start: 0.8459 (mmp) cc_final: 0.8105 (mmp) REVERT: F 47 MET cc_start: 0.8294 (pmm) cc_final: 0.7891 (pmm) REVERT: F 82 MET cc_start: 0.9125 (tpt) cc_final: 0.8500 (tpt) REVERT: F 119 MET cc_start: 0.9392 (mtm) cc_final: 0.9143 (mtm) REVERT: F 132 MET cc_start: 0.9164 (ppp) cc_final: 0.8517 (ppp) REVERT: F 227 MET cc_start: 0.8527 (mmp) cc_final: 0.8097 (mmp) REVERT: F 299 MET cc_start: 0.8587 (mtp) cc_final: 0.8318 (mtp) REVERT: F 305 MET cc_start: 0.8897 (mmp) cc_final: 0.8487 (mmp) REVERT: F 313 MET cc_start: 0.9383 (tpt) cc_final: 0.9130 (tpt) REVERT: F 325 MET cc_start: 0.8643 (pmm) cc_final: 0.8055 (pmm) REVERT: G 564 MET cc_start: 0.6844 (mmp) cc_final: 0.6167 (mmp) REVERT: H 721 MET cc_start: 0.9759 (mmm) cc_final: 0.9307 (mmm) outliers start: 15 outliers final: 7 residues processed: 127 average time/residue: 0.3252 time to fit residues: 69.6083 Evaluate side-chains 129 residues out of total 2569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 119 time to evaluate : 2.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain F residue 87 HIS Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain G residue 803 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 97 optimal weight: 5.9990 chunk 261 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 170 optimal weight: 9.9990 chunk 71 optimal weight: 0.0030 chunk 290 optimal weight: 30.0000 chunk 240 optimal weight: 30.0000 chunk 134 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 152 optimal weight: 0.9980 overall best weight: 2.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24340 Z= 0.190 Angle : 0.557 11.835 32968 Z= 0.265 Chirality : 0.041 0.165 3695 Planarity : 0.003 0.061 4230 Dihedral : 6.914 166.161 3345 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.74 % Allowed : 8.14 % Favored : 91.12 % 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: 0.97 (0.16), residues: 2973 helix: 1.42 (0.14), residues: 1513 sheet: -0.21 (0.26), residues: 402 loop : -0.00 (0.20), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 79 HIS 0.003 0.001 HIS G 554 PHE 0.011 0.001 PHE G 920 TYR 0.020 0.001 TYR G 705 ARG 0.002 0.000 ARG G 695 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 119 time to evaluate : 2.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.9077 (tpt) cc_final: 0.8841 (tpt) REVERT: A 132 MET cc_start: 0.8455 (tmm) cc_final: 0.7925 (tmm) REVERT: A 283 MET cc_start: 0.8785 (mmt) cc_final: 0.8376 (mmm) REVERT: B 123 MET cc_start: 0.8737 (tpp) cc_final: 0.8537 (tpt) REVERT: B 132 MET cc_start: 0.8417 (tmm) cc_final: 0.7886 (tmm) REVERT: B 283 MET cc_start: 0.8753 (mmt) cc_final: 0.8513 (mmp) REVERT: B 355 MET cc_start: 0.8917 (tpp) cc_final: 0.8614 (mmm) REVERT: C 123 MET cc_start: 0.8884 (mmm) cc_final: 0.8474 (mmm) REVERT: C 132 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7798 (tmm) REVERT: C 305 MET cc_start: 0.8254 (mpp) cc_final: 0.7949 (mpp) REVERT: D 47 MET cc_start: 0.4661 (mtt) cc_final: 0.2642 (mmt) REVERT: D 82 MET cc_start: 0.8617 (tpt) cc_final: 0.8273 (tmm) REVERT: D 176 MET cc_start: 0.8425 (ptp) cc_final: 0.8004 (pmm) REVERT: D 305 MET cc_start: 0.9023 (mmp) cc_final: 0.8792 (mmp) REVERT: E 123 MET cc_start: 0.9087 (mmp) cc_final: 0.8866 (mmp) REVERT: E 305 MET cc_start: 0.8454 (mmp) cc_final: 0.8105 (mmp) REVERT: F 47 MET cc_start: 0.8246 (pmm) cc_final: 0.7793 (pmm) REVERT: F 82 MET cc_start: 0.9102 (tpt) cc_final: 0.8456 (tpt) REVERT: F 119 MET cc_start: 0.9410 (mtm) cc_final: 0.9018 (mtt) REVERT: F 132 MET cc_start: 0.9177 (ppp) cc_final: 0.8554 (ppp) REVERT: F 227 MET cc_start: 0.8556 (mmp) cc_final: 0.8237 (mmp) REVERT: F 299 MET cc_start: 0.8571 (mtp) cc_final: 0.8305 (mtp) REVERT: F 305 MET cc_start: 0.8886 (mmp) cc_final: 0.8481 (mmp) REVERT: F 313 MET cc_start: 0.9366 (tpt) cc_final: 0.9117 (tpt) REVERT: F 325 MET cc_start: 0.8596 (pmm) cc_final: 0.7964 (pmm) REVERT: G 564 MET cc_start: 0.6587 (mmp) cc_final: 0.5868 (mmp) REVERT: H 721 MET cc_start: 0.9761 (mmm) cc_final: 0.9305 (mmm) outliers start: 19 outliers final: 10 residues processed: 128 average time/residue: 0.3213 time to fit residues: 69.4955 Evaluate side-chains 129 residues out of total 2569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 118 time to evaluate : 2.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain F residue 87 HIS Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain G residue 803 HIS Chi-restraints excluded: chain H residue 803 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 279 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 165 optimal weight: 7.9990 chunk 211 optimal weight: 9.9990 chunk 164 optimal weight: 2.9990 chunk 244 optimal weight: 0.7980 chunk 162 optimal weight: 6.9990 chunk 289 optimal weight: 5.9990 chunk 180 optimal weight: 2.9990 chunk 176 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 246 GLN D 354 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24340 Z= 0.196 Angle : 0.548 7.400 32968 Z= 0.261 Chirality : 0.041 0.164 3695 Planarity : 0.003 0.060 4230 Dihedral : 6.820 166.044 3345 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.70 % Allowed : 8.21 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.16), residues: 2973 helix: 1.50 (0.14), residues: 1513 sheet: -0.13 (0.26), residues: 402 loop : 0.04 (0.20), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 79 HIS 0.003 0.001 HIS G 554 PHE 0.010 0.001 PHE G 920 TYR 0.019 0.001 TYR G 705 ARG 0.002 0.000 ARG G 695 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 118 time to evaluate : 2.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.9080 (tpt) cc_final: 0.8858 (tpt) REVERT: A 132 MET cc_start: 0.8461 (tmm) cc_final: 0.7983 (tmm) REVERT: A 283 MET cc_start: 0.8797 (mmt) cc_final: 0.8405 (mmm) REVERT: B 132 MET cc_start: 0.8431 (tmm) cc_final: 0.7877 (tmm) REVERT: B 283 MET cc_start: 0.8743 (mmt) cc_final: 0.8500 (mmp) REVERT: B 355 MET cc_start: 0.8956 (tpp) cc_final: 0.8669 (mmm) REVERT: C 123 MET cc_start: 0.8887 (mmm) cc_final: 0.8388 (mmm) REVERT: C 132 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7780 (tmm) REVERT: C 305 MET cc_start: 0.8251 (mpp) cc_final: 0.7916 (mpp) REVERT: D 47 MET cc_start: 0.4901 (mtt) cc_final: 0.3175 (mmt) REVERT: D 82 MET cc_start: 0.8631 (tpt) cc_final: 0.8287 (tmm) REVERT: D 123 MET cc_start: 0.8405 (mmm) cc_final: 0.8067 (tmm) REVERT: D 162 ASN cc_start: 0.8525 (OUTLIER) cc_final: 0.8314 (m-40) REVERT: E 123 MET cc_start: 0.9104 (mmp) cc_final: 0.8875 (mmp) REVERT: E 305 MET cc_start: 0.8482 (mmp) cc_final: 0.8115 (mmp) REVERT: F 47 MET cc_start: 0.8318 (pmm) cc_final: 0.7888 (pmm) REVERT: F 82 MET cc_start: 0.9098 (tpt) cc_final: 0.8448 (tpt) REVERT: F 119 MET cc_start: 0.9403 (mtm) cc_final: 0.9194 (mtm) REVERT: F 132 MET cc_start: 0.9176 (ppp) cc_final: 0.8635 (ppp) REVERT: F 227 MET cc_start: 0.8580 (mmp) cc_final: 0.8287 (mmp) REVERT: F 299 MET cc_start: 0.8561 (mtp) cc_final: 0.8293 (mtp) REVERT: F 305 MET cc_start: 0.8883 (mmp) cc_final: 0.8480 (mmp) REVERT: F 325 MET cc_start: 0.8628 (pmm) cc_final: 0.7974 (pmm) REVERT: G 564 MET cc_start: 0.6637 (mmp) cc_final: 0.5905 (mmp) REVERT: H 721 MET cc_start: 0.9757 (mmm) cc_final: 0.9301 (mmm) outliers start: 18 outliers final: 12 residues processed: 129 average time/residue: 0.3235 time to fit residues: 70.4189 Evaluate side-chains 132 residues out of total 2569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 118 time to evaluate : 2.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 87 HIS Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain G residue 803 HIS Chi-restraints excluded: chain H residue 655 VAL Chi-restraints excluded: chain H residue 803 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 178 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 chunk 172 optimal weight: 10.0000 chunk 87 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 chunk 196 optimal weight: 10.0000 chunk 142 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 227 optimal weight: 50.0000 chunk 263 optimal weight: 5.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 275 HIS D 246 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 642 ASN ** G 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 24340 Z= 0.305 Angle : 0.605 10.642 32968 Z= 0.292 Chirality : 0.042 0.168 3695 Planarity : 0.003 0.059 4230 Dihedral : 6.816 165.107 3345 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.62 % Allowed : 8.64 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.16), residues: 2973 helix: 1.48 (0.14), residues: 1512 sheet: 0.06 (0.27), residues: 372 loop : -0.06 (0.19), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 79 HIS 0.005 0.001 HIS F 87 PHE 0.015 0.001 PHE B 127 TYR 0.018 0.001 TYR G 705 ARG 0.004 0.000 ARG A 335 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 118 time to evaluate : 2.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 MET cc_start: 0.8823 (mmt) cc_final: 0.8440 (mmm) REVERT: B 132 MET cc_start: 0.8381 (tmm) cc_final: 0.7826 (tmm) REVERT: B 283 MET cc_start: 0.8701 (mmt) cc_final: 0.8452 (mmp) REVERT: B 355 MET cc_start: 0.8969 (tpp) cc_final: 0.8602 (mmm) REVERT: C 123 MET cc_start: 0.8895 (mmm) cc_final: 0.8540 (mmm) REVERT: C 132 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7744 (tmm) REVERT: C 305 MET cc_start: 0.8302 (mpp) cc_final: 0.7968 (mpp) REVERT: D 47 MET cc_start: 0.5032 (mtt) cc_final: 0.3549 (mmt) REVERT: D 82 MET cc_start: 0.8647 (tpt) cc_final: 0.8248 (tmm) REVERT: D 162 ASN cc_start: 0.8539 (OUTLIER) cc_final: 0.8202 (m-40) REVERT: D 176 MET cc_start: 0.8600 (ptp) cc_final: 0.8114 (pmm) REVERT: D 305 MET cc_start: 0.9033 (mmm) cc_final: 0.8718 (mmp) REVERT: D 355 MET cc_start: 0.8992 (pmm) cc_final: 0.8778 (pmm) REVERT: E 305 MET cc_start: 0.8510 (mmp) cc_final: 0.8201 (mmp) REVERT: F 47 MET cc_start: 0.8510 (pmm) cc_final: 0.8177 (pmm) REVERT: F 82 MET cc_start: 0.9138 (tpt) cc_final: 0.8508 (tpt) REVERT: F 119 MET cc_start: 0.9401 (mtm) cc_final: 0.9185 (mtm) REVERT: F 132 MET cc_start: 0.9141 (ppp) cc_final: 0.8561 (ppp) REVERT: F 227 MET cc_start: 0.8537 (mmp) cc_final: 0.8205 (mmp) REVERT: F 305 MET cc_start: 0.8906 (mmp) cc_final: 0.8509 (mmp) REVERT: F 325 MET cc_start: 0.8665 (pmm) cc_final: 0.7929 (pmm) REVERT: G 564 MET cc_start: 0.6826 (mmp) cc_final: 0.6147 (mmp) REVERT: H 658 MET cc_start: 0.8122 (ttt) cc_final: 0.7848 (ttt) REVERT: H 721 MET cc_start: 0.9788 (mmm) cc_final: 0.9405 (mmm) outliers start: 16 outliers final: 11 residues processed: 129 average time/residue: 0.3199 time to fit residues: 69.8272 Evaluate side-chains 131 residues out of total 2569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 118 time to evaluate : 2.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain F residue 87 HIS Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain G residue 803 HIS Chi-restraints excluded: chain H residue 655 VAL Chi-restraints excluded: chain H residue 803 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 277 optimal weight: 8.9990 chunk 252 optimal weight: 5.9990 chunk 269 optimal weight: 0.3980 chunk 276 optimal weight: 9.9990 chunk 162 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 chunk 211 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 243 optimal weight: 20.0000 chunk 254 optimal weight: 20.0000 chunk 268 optimal weight: 9.9990 overall best weight: 4.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 246 GLN D 297 ASN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 ASN ** F 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 864 GLN ** H 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 24340 Z= 0.308 Angle : 0.620 11.981 32968 Z= 0.298 Chirality : 0.042 0.162 3695 Planarity : 0.003 0.059 4230 Dihedral : 6.805 165.611 3345 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.78 % Allowed : 8.76 % Favored : 90.46 % 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: 1.01 (0.16), residues: 2973 helix: 1.47 (0.14), residues: 1510 sheet: -0.26 (0.26), residues: 407 loop : 0.04 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 79 HIS 0.004 0.001 HIS F 87 PHE 0.017 0.001 PHE D 124 TYR 0.017 0.001 TYR G 705 ARG 0.003 0.000 ARG D 116 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 118 time to evaluate : 2.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 MET cc_start: 0.8801 (mmt) cc_final: 0.8431 (mmm) REVERT: B 132 MET cc_start: 0.8412 (tmm) cc_final: 0.7902 (tmm) REVERT: B 283 MET cc_start: 0.8676 (mmt) cc_final: 0.8413 (mmp) REVERT: B 355 MET cc_start: 0.8974 (tpp) cc_final: 0.8574 (mmm) REVERT: C 123 MET cc_start: 0.8912 (mmm) cc_final: 0.8535 (mmm) REVERT: C 132 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7721 (tmm) REVERT: C 305 MET cc_start: 0.8338 (mpp) cc_final: 0.8123 (mpp) REVERT: D 47 MET cc_start: 0.5138 (mtt) cc_final: 0.4020 (mmt) REVERT: D 82 MET cc_start: 0.8663 (tpt) cc_final: 0.8267 (tmm) REVERT: D 162 ASN cc_start: 0.8536 (OUTLIER) cc_final: 0.8125 (m-40) REVERT: D 176 MET cc_start: 0.8541 (ptp) cc_final: 0.8047 (pmm) REVERT: D 305 MET cc_start: 0.9030 (mmm) cc_final: 0.8726 (mmp) REVERT: E 176 MET cc_start: 0.8315 (mtp) cc_final: 0.8092 (mtt) REVERT: E 299 MET cc_start: 0.8850 (mtp) cc_final: 0.8593 (mtm) REVERT: E 305 MET cc_start: 0.8524 (mmp) cc_final: 0.8200 (mmp) REVERT: F 47 MET cc_start: 0.8604 (pmm) cc_final: 0.8299 (pmm) REVERT: F 82 MET cc_start: 0.9142 (tpt) cc_final: 0.8512 (tpt) REVERT: F 132 MET cc_start: 0.9186 (ppp) cc_final: 0.8607 (ppp) REVERT: F 162 ASN cc_start: 0.8717 (OUTLIER) cc_final: 0.8406 (m-40) REVERT: F 227 MET cc_start: 0.8662 (mmp) cc_final: 0.8355 (mmp) REVERT: F 305 MET cc_start: 0.8919 (mmp) cc_final: 0.8523 (mmp) REVERT: G 564 MET cc_start: 0.6403 (mmp) cc_final: 0.5797 (mmp) REVERT: H 658 MET cc_start: 0.8165 (ttt) cc_final: 0.7878 (ttt) REVERT: H 721 MET cc_start: 0.9794 (mmm) cc_final: 0.9434 (mmm) outliers start: 20 outliers final: 12 residues processed: 130 average time/residue: 0.3216 time to fit residues: 70.6961 Evaluate side-chains 133 residues out of total 2569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 118 time to evaluate : 2.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain G residue 803 HIS Chi-restraints excluded: chain H residue 655 VAL Chi-restraints excluded: chain H residue 803 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 176 optimal weight: 3.9990 chunk 284 optimal weight: 20.0000 chunk 173 optimal weight: 3.9990 chunk 135 optimal weight: 10.0000 chunk 198 optimal weight: 4.9990 chunk 298 optimal weight: 8.9990 chunk 275 optimal weight: 6.9990 chunk 237 optimal weight: 30.0000 chunk 24 optimal weight: 0.4980 chunk 183 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.141 24340 Z= 0.321 Angle : 0.756 59.059 32968 Z= 0.401 Chirality : 0.042 0.189 3695 Planarity : 0.003 0.058 4230 Dihedral : 6.805 165.590 3345 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.54 % Allowed : 8.91 % Favored : 90.54 % Cbeta Deviations : 0.04 % 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: 1.02 (0.16), residues: 2973 helix: 1.47 (0.14), residues: 1510 sheet: -0.19 (0.26), residues: 402 loop : 0.02 (0.20), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 79 HIS 0.006 0.001 HIS F 161 PHE 0.016 0.001 PHE D 124 TYR 0.016 0.001 TYR G 705 ARG 0.002 0.000 ARG D 116 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 118 time to evaluate : 3.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8479 (tmm) cc_final: 0.7939 (tmm) REVERT: A 283 MET cc_start: 0.8818 (mmt) cc_final: 0.8428 (mmm) REVERT: B 132 MET cc_start: 0.8427 (tmm) cc_final: 0.7898 (tmm) REVERT: B 283 MET cc_start: 0.8673 (mmt) cc_final: 0.8416 (mmp) REVERT: B 355 MET cc_start: 0.8974 (tpp) cc_final: 0.8576 (mmm) REVERT: C 123 MET cc_start: 0.8912 (mmm) cc_final: 0.8524 (mmm) REVERT: C 132 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.7721 (tmm) REVERT: C 305 MET cc_start: 0.8337 (mpp) cc_final: 0.8124 (mpp) REVERT: D 47 MET cc_start: 0.5137 (mtt) cc_final: 0.4019 (mmt) REVERT: D 82 MET cc_start: 0.8664 (tpt) cc_final: 0.8265 (tmm) REVERT: D 162 ASN cc_start: 0.8534 (OUTLIER) cc_final: 0.8123 (m-40) REVERT: D 176 MET cc_start: 0.8538 (ptp) cc_final: 0.8043 (pmm) REVERT: D 305 MET cc_start: 0.9066 (mmm) cc_final: 0.8786 (mmp) REVERT: E 176 MET cc_start: 0.8333 (mtp) cc_final: 0.8126 (mtt) REVERT: E 299 MET cc_start: 0.8893 (mtp) cc_final: 0.8593 (mtm) REVERT: E 305 MET cc_start: 0.8535 (mmp) cc_final: 0.8202 (mmp) REVERT: F 47 MET cc_start: 0.8595 (pmm) cc_final: 0.8291 (pmm) REVERT: F 82 MET cc_start: 0.9142 (tpt) cc_final: 0.8509 (tpt) REVERT: F 119 MET cc_start: 0.9138 (mtm) cc_final: 0.8891 (mtt) REVERT: F 132 MET cc_start: 0.9183 (ppp) cc_final: 0.8606 (ppp) REVERT: F 227 MET cc_start: 0.8662 (mmp) cc_final: 0.8356 (mmp) REVERT: F 305 MET cc_start: 0.8918 (mmp) cc_final: 0.8523 (mmp) REVERT: G 564 MET cc_start: 0.6403 (mmp) cc_final: 0.5796 (mmp) REVERT: H 721 MET cc_start: 0.9794 (mmm) cc_final: 0.9429 (mmm) outliers start: 14 outliers final: 12 residues processed: 126 average time/residue: 0.3405 time to fit residues: 72.9795 Evaluate side-chains 132 residues out of total 2569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 118 time to evaluate : 2.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain G residue 803 HIS Chi-restraints excluded: chain H residue 655 VAL Chi-restraints excluded: chain H residue 803 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 189 optimal weight: 9.9990 chunk 253 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 219 optimal weight: 20.0000 chunk 35 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 238 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 244 optimal weight: 20.0000 chunk 30 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.042826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.033645 restraints weight = 292817.505| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 4.96 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 24340 Z= 0.243 Angle : 0.751 59.199 32968 Z= 0.387 Chirality : 0.041 0.224 3695 Planarity : 0.003 0.058 4230 Dihedral : 6.817 165.405 3345 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.51 % Allowed : 8.95 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.16), residues: 2973 helix: 1.47 (0.14), residues: 1510 sheet: -0.18 (0.26), residues: 402 loop : 0.03 (0.20), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 79 HIS 0.004 0.001 HIS F 87 PHE 0.014 0.001 PHE D 124 TYR 0.016 0.001 TYR G 705 ARG 0.002 0.000 ARG G 981 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3630.17 seconds wall clock time: 67 minutes 13.71 seconds (4033.71 seconds total)