Starting phenix.real_space_refine on Mon Mar 18 10:41:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8r_28934/03_2024/8f8r_28934_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8r_28934/03_2024/8f8r_28934.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8r_28934/03_2024/8f8r_28934.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8r_28934/03_2024/8f8r_28934.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8r_28934/03_2024/8f8r_28934_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8r_28934/03_2024/8f8r_28934_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 14 5.49 5 Mg 7 5.21 5 S 147 5.16 5 C 12941 2.51 5 N 3462 2.21 5 O 3955 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 237": "OE1" <-> "OE2" Residue "A ASP 244": "OD1" <-> "OD2" Residue "A GLU 270": "OE1" <-> "OE2" Residue "A ASP 311": "OD1" <-> "OD2" Residue "B ASP 51": "OD1" <-> "OD2" Residue "B GLU 117": "OE1" <-> "OE2" Residue "B GLU 241": "OE1" <-> "OE2" Residue "B ASP 244": "OD1" <-> "OD2" Residue "B GLU 276": "OE1" <-> "OE2" Residue "C ASP 51": "OD1" <-> "OD2" Residue "C GLU 107": "OE1" <-> "OE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C GLU 241": "OE1" <-> "OE2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D GLU 270": "OE1" <-> "OE2" Residue "D ASP 311": "OD1" <-> "OD2" Residue "F GLU 57": "OE1" <-> "OE2" Residue "F PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 270": "OE1" <-> "OE2" Residue "F TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 51": "OD1" <-> "OD2" Residue "G TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 270": "OE1" <-> "OE2" Residue "G ASP 311": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20526 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2897 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.31, per 1000 atoms: 0.50 Number of scatterers: 20526 At special positions: 0 Unit cell: (86.4, 108, 250.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 147 16.00 P 14 15.00 Mg 7 11.99 O 3955 8.00 N 3462 7.00 C 12941 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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=0, symmetry=0 Time building additional restraints: 7.45 Conformation dependent library (CDL) restraints added in 3.2 seconds 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4810 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 135 helices and 28 sheets defined 42.0% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.72 Creating SS restraints... Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 79 through 91 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 182 through 195 removed outlier: 3.901A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 removed outlier: 3.725A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.855A pdb=" N ARG A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 302 through 304 No H-bonds generated for 'chain 'A' and resid 302 through 304' Processing helix chain 'A' and resid 310 through 320 Processing helix chain 'A' and resid 335 through 346 removed outlier: 5.424A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 354 removed outlier: 3.963A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 351 through 354' Processing helix chain 'A' and resid 359 through 371 Proline residue: A 367 - end of helix removed outlier: 6.168A pdb=" N VAL A 370 " --> pdb=" O GLY A 366 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N HIS A 371 " --> pdb=" O PRO A 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 79 through 91 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 182 through 195 removed outlier: 3.903A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.701A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.851A pdb=" N ARG B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 261 removed outlier: 3.551A pdb=" N LEU B 261 " --> pdb=" O PRO B 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 258 through 261' Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 288 through 294 removed outlier: 4.144A pdb=" N LYS B 291 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 310 through 320 Processing helix chain 'B' and resid 335 through 346 removed outlier: 5.476A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 354 removed outlier: 4.162A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 351 through 354' Processing helix chain 'B' and resid 359 through 372 Proline residue: B 367 - end of helix removed outlier: 6.320A pdb=" N VAL B 370 " --> pdb=" O GLY B 366 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N HIS B 371 " --> pdb=" O PRO B 367 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 193 Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.901A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 252 through 256 removed outlier: 3.900A pdb=" N ARG C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 260 No H-bonds generated for 'chain 'C' and resid 258 through 260' Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 274 through 282 Processing helix chain 'C' and resid 291 through 294 No H-bonds generated for 'chain 'C' and resid 291 through 294' Processing helix chain 'C' and resid 302 through 304 No H-bonds generated for 'chain 'C' and resid 302 through 304' Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 335 through 346 removed outlier: 5.926A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 354 removed outlier: 4.128A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 351 through 354' Processing helix chain 'C' and resid 359 through 373 Proline residue: C 367 - end of helix removed outlier: 6.006A pdb=" N VAL C 370 " --> pdb=" O GLY C 366 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N HIS C 371 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 79 through 91 Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 182 through 194 removed outlier: 4.146A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 removed outlier: 3.796A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 232 Processing helix chain 'D' and resid 252 through 256 removed outlier: 3.790A pdb=" N ARG D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 260 No H-bonds generated for 'chain 'D' and resid 258 through 260' Processing helix chain 'D' and resid 264 through 267 removed outlier: 3.543A pdb=" N ILE D 267 " --> pdb=" O PRO D 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 264 through 267' Processing helix chain 'D' and resid 274 through 283 Processing helix chain 'D' and resid 287 through 294 removed outlier: 4.882A pdb=" N LYS D 291 " --> pdb=" O ASP D 288 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR D 294 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 304 No H-bonds generated for 'chain 'D' and resid 302 through 304' Processing helix chain 'D' and resid 309 through 320 Processing helix chain 'D' and resid 335 through 346 removed outlier: 5.775A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 354 removed outlier: 4.108A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 351 through 354' Processing helix chain 'D' and resid 359 through 365 Processing helix chain 'D' and resid 369 through 373 Processing helix chain 'E' and resid 56 through 60 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 79 through 91 Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 113 through 125 Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 182 through 194 removed outlier: 3.819A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 216 removed outlier: 3.769A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 232 Processing helix chain 'E' and resid 252 through 256 removed outlier: 3.941A pdb=" N ARG E 256 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 260 No H-bonds generated for 'chain 'E' and resid 258 through 260' Processing helix chain 'E' and resid 264 through 266 No H-bonds generated for 'chain 'E' and resid 264 through 266' Processing helix chain 'E' and resid 274 through 284 Processing helix chain 'E' and resid 287 through 296 removed outlier: 4.945A pdb=" N LYS E 291 " --> pdb=" O ASP E 288 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR E 294 " --> pdb=" O LYS E 291 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN E 296 " --> pdb=" O LEU E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 304 No H-bonds generated for 'chain 'E' and resid 302 through 304' Processing helix chain 'E' and resid 309 through 320 Processing helix chain 'E' and resid 335 through 346 removed outlier: 5.351A pdb=" N VAL E 339 " --> pdb=" O LYS E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 354 removed outlier: 4.198A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 351 through 354' Processing helix chain 'E' and resid 359 through 365 Processing helix chain 'E' and resid 369 through 372 No H-bonds generated for 'chain 'E' and resid 369 through 372' Processing helix chain 'F' and resid 56 through 60 Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'F' and resid 79 through 91 Processing helix chain 'F' and resid 98 through 100 No H-bonds generated for 'chain 'F' and resid 98 through 100' Processing helix chain 'F' and resid 113 through 125 Processing helix chain 'F' and resid 137 through 145 Processing helix chain 'F' and resid 182 through 194 removed outlier: 3.965A pdb=" N THR F 194 " --> pdb=" O MET F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 216 Processing helix chain 'F' and resid 223 through 232 Processing helix chain 'F' and resid 252 through 261 removed outlier: 3.921A pdb=" N ARG F 256 " --> pdb=" O GLU F 253 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N CYS F 257 " --> pdb=" O ARG F 254 " (cutoff:3.500A) Proline residue: F 258 - end of helix Processing helix chain 'F' and resid 264 through 267 Processing helix chain 'F' and resid 274 through 283 Processing helix chain 'F' and resid 290 through 294 Processing helix chain 'F' and resid 302 through 304 No H-bonds generated for 'chain 'F' and resid 302 through 304' Processing helix chain 'F' and resid 309 through 320 Processing helix chain 'F' and resid 335 through 348 removed outlier: 5.414A pdb=" N VAL F 339 " --> pdb=" O LYS F 336 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ALA F 347 " --> pdb=" O SER F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 352 No H-bonds generated for 'chain 'F' and resid 350 through 352' Processing helix chain 'F' and resid 359 through 373 Proline residue: F 367 - end of helix removed outlier: 5.531A pdb=" N VAL F 370 " --> pdb=" O GLY F 366 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N HIS F 371 " --> pdb=" O PRO F 367 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 60 Processing helix chain 'G' and resid 62 through 64 No H-bonds generated for 'chain 'G' and resid 62 through 64' Processing helix chain 'G' and resid 79 through 91 Processing helix chain 'G' and resid 98 through 100 No H-bonds generated for 'chain 'G' and resid 98 through 100' Processing helix chain 'G' and resid 113 through 125 Processing helix chain 'G' and resid 137 through 145 Processing helix chain 'G' and resid 182 through 194 removed outlier: 3.851A pdb=" N THR G 194 " --> pdb=" O MET G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 216 removed outlier: 3.739A pdb=" N ILE G 208 " --> pdb=" O ALA G 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 232 Processing helix chain 'G' and resid 252 through 256 removed outlier: 3.928A pdb=" N ARG G 256 " --> pdb=" O GLU G 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 261 Processing helix chain 'G' and resid 264 through 266 No H-bonds generated for 'chain 'G' and resid 264 through 266' Processing helix chain 'G' and resid 274 through 283 Processing helix chain 'G' and resid 290 through 294 Processing helix chain 'G' and resid 302 through 304 No H-bonds generated for 'chain 'G' and resid 302 through 304' Processing helix chain 'G' and resid 309 through 320 Processing helix chain 'G' and resid 335 through 346 removed outlier: 5.669A pdb=" N VAL G 339 " --> pdb=" O LYS G 336 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 373 Proline residue: G 367 - end of helix removed outlier: 5.664A pdb=" N VAL G 370 " --> pdb=" O GLY G 366 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N HIS G 371 " --> pdb=" O PRO G 367 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 132 through 136 removed outlier: 6.399A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 35 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 297 through 300 removed outlier: 6.353A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 238 through 241 Processing sheet with id= E, first strand: chain 'B' and resid 132 through 136 removed outlier: 6.600A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 35 through 38 Processing sheet with id= G, first strand: chain 'B' and resid 297 through 300 removed outlier: 6.315A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= I, first strand: chain 'C' and resid 132 through 136 removed outlier: 6.479A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 35 through 38 Processing sheet with id= K, first strand: chain 'C' and resid 297 through 300 removed outlier: 5.989A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= M, first strand: chain 'D' and resid 132 through 136 removed outlier: 6.660A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 35 through 38 Processing sheet with id= O, first strand: chain 'D' and resid 297 through 300 removed outlier: 6.027A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 238 through 241 Processing sheet with id= Q, first strand: chain 'E' and resid 132 through 136 removed outlier: 6.503A pdb=" N THR E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ALA E 135 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 35 through 38 Processing sheet with id= S, first strand: chain 'E' and resid 297 through 300 removed outlier: 5.976A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 238 through 241 Processing sheet with id= U, first strand: chain 'F' and resid 132 through 136 removed outlier: 6.504A pdb=" N THR F 103 " --> pdb=" O TYR F 133 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ALA F 135 " --> pdb=" O THR F 103 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU F 105 " --> pdb=" O ALA F 135 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 35 through 38 Processing sheet with id= W, first strand: chain 'F' and resid 297 through 300 removed outlier: 6.110A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 238 through 241 Processing sheet with id= Y, first strand: chain 'G' and resid 132 through 136 removed outlier: 6.678A pdb=" N THR G 103 " --> pdb=" O TYR G 133 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ALA G 135 " --> pdb=" O THR G 103 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LEU G 105 " --> pdb=" O ALA G 135 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU G 8 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N THR G 106 " --> pdb=" O LEU G 8 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N CYS G 10 " --> pdb=" O THR G 106 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 35 through 38 Processing sheet with id= AA, first strand: chain 'G' and resid 297 through 300 removed outlier: 6.162A pdb=" N ILE G 151 " --> pdb=" O VAL G 298 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N SER G 300 " --> pdb=" O ILE G 151 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N LEU G 153 " --> pdb=" O SER G 300 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN G 162 " --> pdb=" O MET G 176 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N MET G 176 " --> pdb=" O ASN G 162 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 238 through 241 719 hydrogen bonds defined for protein. 1794 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: 6.24 Time building geometry restraints manager: 8.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6618 1.34 - 1.46: 4627 1.46 - 1.58: 9447 1.58 - 1.70: 21 1.70 - 1.82: 259 Bond restraints: 20972 Sorted by residual: bond pdb=" C LEU G 242 " pdb=" N PRO G 243 " ideal model delta sigma weight residual 1.336 1.366 -0.031 1.08e-02 8.57e+03 8.02e+00 bond pdb=" CE1 HIC D 73 " pdb=" NE2 HIC D 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.95e+00 bond pdb=" CE1 HIC E 73 " pdb=" NE2 HIC E 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.90e+00 bond pdb=" CE1 HIC G 73 " pdb=" NE2 HIC G 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.80e+00 bond pdb=" CE1 HIC F 73 " pdb=" NE2 HIC F 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.67e+00 ... (remaining 20967 not shown) Histogram of bond angle deviations from ideal: 93.18 - 101.82: 98 101.82 - 110.46: 5586 110.46 - 119.09: 11831 119.09 - 127.73: 10755 127.73 - 136.37: 193 Bond angle restraints: 28463 Sorted by residual: angle pdb=" CA MET D 47 " pdb=" CB MET D 47 " pdb=" CG MET D 47 " ideal model delta sigma weight residual 114.10 124.83 -10.73 2.00e+00 2.50e-01 2.88e+01 angle pdb=" CA MET C 47 " pdb=" CB MET C 47 " pdb=" CG MET C 47 " ideal model delta sigma weight residual 114.10 124.73 -10.63 2.00e+00 2.50e-01 2.83e+01 angle pdb=" CB MET F 44 " pdb=" CG MET F 44 " pdb=" SD MET F 44 " ideal model delta sigma weight residual 112.70 128.64 -15.94 3.00e+00 1.11e-01 2.82e+01 angle pdb=" C ILE E 282 " pdb=" N MET E 283 " pdb=" CA MET E 283 " ideal model delta sigma weight residual 122.66 114.52 8.14 1.63e+00 3.76e-01 2.49e+01 angle pdb=" C GLY D 46 " pdb=" N MET D 47 " pdb=" CA MET D 47 " ideal model delta sigma weight residual 121.54 130.53 -8.99 1.91e+00 2.74e-01 2.21e+01 ... (remaining 28458 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.69: 12362 33.69 - 67.38: 204 67.38 - 101.08: 37 101.08 - 134.77: 7 134.77 - 168.46: 7 Dihedral angle restraints: 12617 sinusoidal: 5101 harmonic: 7516 Sorted by residual: dihedral pdb=" C5' ADP F 401 " pdb=" O5' ADP F 401 " pdb=" PA ADP F 401 " pdb=" O2A ADP F 401 " ideal model delta sinusoidal sigma weight residual -60.00 108.46 -168.46 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C5' ADP D 401 " pdb=" O5' ADP D 401 " pdb=" PA ADP D 401 " pdb=" O2A ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 104.91 -164.91 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 103.58 -163.57 1 2.00e+01 2.50e-03 4.70e+01 ... (remaining 12614 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2347 0.057 - 0.113: 655 0.113 - 0.170: 134 0.170 - 0.227: 20 0.227 - 0.283: 5 Chirality restraints: 3161 Sorted by residual: chirality pdb=" CB ILE F 151 " pdb=" CA ILE F 151 " pdb=" CG1 ILE F 151 " pdb=" CG2 ILE F 151 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA MET D 47 " pdb=" N MET D 47 " pdb=" C MET D 47 " pdb=" CB MET D 47 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA MET F 47 " pdb=" N MET F 47 " pdb=" C MET F 47 " pdb=" CB MET F 47 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 3158 not shown) Planarity restraints: 3639 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG F 37 " -0.056 5.00e-02 4.00e+02 8.60e-02 1.18e+01 pdb=" N PRO F 38 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO F 38 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO F 38 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 37 " -0.056 5.00e-02 4.00e+02 8.56e-02 1.17e+01 pdb=" N PRO B 38 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO B 38 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 38 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 37 " 0.056 5.00e-02 4.00e+02 8.53e-02 1.17e+01 pdb=" N PRO A 38 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO A 38 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 38 " 0.046 5.00e-02 4.00e+02 ... (remaining 3636 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 180 2.61 - 3.19: 16299 3.19 - 3.76: 31421 3.76 - 4.33: 44916 4.33 - 4.90: 73799 Nonbonded interactions: 166615 Sorted by model distance: nonbonded pdb=" O1B ADP G 401 " pdb="MG MG G 402 " model vdw 2.042 2.170 nonbonded pdb=" O1B ADP B 401 " pdb="MG MG B 402 " model vdw 2.085 2.170 nonbonded pdb=" O1B ADP C 401 " pdb="MG MG C 402 " model vdw 2.114 2.170 nonbonded pdb=" O1B ADP A 401 " pdb="MG MG A 402 " model vdw 2.138 2.170 nonbonded pdb=" O1B ADP D 401 " pdb="MG MG D 402 " model vdw 2.172 2.170 ... (remaining 166610 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' and (resid 5 through 374 or resid 401 through 402)) selection = (chain 'B' and (resid 5 through 374 or resid 401 through 402)) selection = (chain 'C' and (resid 5 through 374 or resid 401 through 402)) selection = (chain 'D' and (resid 5 through 374 or resid 401 through 402)) selection = (chain 'E' and (resid 5 through 374 or resid 401 through 402)) selection = (chain 'F' and (resid 5 through 374 or resid 401 through 402)) selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 13.910 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 50.860 Find NCS groups from input model: 1.740 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 20972 Z= 0.319 Angle : 0.962 15.935 28463 Z= 0.512 Chirality : 0.055 0.283 3161 Planarity : 0.010 0.089 3639 Dihedral : 15.053 168.459 7807 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.15), residues: 2566 helix: -2.16 (0.12), residues: 1083 sheet: -0.23 (0.24), residues: 456 loop : -0.41 (0.19), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 356 HIS 0.018 0.001 HIS F 371 PHE 0.039 0.002 PHE F 127 TYR 0.031 0.002 TYR E 279 ARG 0.019 0.001 ARG F 210 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 2.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.9423 (tpp) cc_final: 0.9201 (tpt) REVERT: B 361 GLU cc_start: 0.9330 (mt-10) cc_final: 0.8986 (mp0) REVERT: B 372 ARG cc_start: 0.8548 (ptp90) cc_final: 0.8273 (ptp90) REVERT: C 132 MET cc_start: 0.9115 (tmm) cc_final: 0.8447 (tmm) REVERT: E 305 MET cc_start: 0.9126 (mmm) cc_final: 0.8836 (mmm) REVERT: F 180 LEU cc_start: 0.9325 (tp) cc_final: 0.9113 (tp) REVERT: G 283 MET cc_start: 0.8989 (ppp) cc_final: 0.8786 (ppp) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.3081 time to fit residues: 82.5584 Evaluate side-chains 138 residues out of total 2195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 2.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 218 optimal weight: 5.9990 chunk 196 optimal weight: 5.9990 chunk 108 optimal weight: 0.2980 chunk 67 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 123 optimal weight: 3.9990 chunk 151 optimal weight: 6.9990 chunk 235 optimal weight: 8.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 111 ASN D 115 ASN F 162 ASN ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 20972 Z= 0.333 Angle : 0.649 8.968 28463 Z= 0.314 Chirality : 0.046 0.171 3161 Planarity : 0.006 0.058 3639 Dihedral : 9.904 171.078 2921 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.46 % Allowed : 4.69 % Favored : 94.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.16), residues: 2566 helix: -0.54 (0.15), residues: 1067 sheet: 0.08 (0.24), residues: 463 loop : -0.16 (0.20), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 340 HIS 0.006 0.001 HIS B 371 PHE 0.019 0.002 PHE G 124 TYR 0.026 0.001 TYR E 279 ARG 0.005 0.001 ARG F 147 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 136 time to evaluate : 2.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 361 GLU cc_start: 0.9327 (mt-10) cc_final: 0.9068 (mp0) REVERT: B 372 ARG cc_start: 0.8613 (ptp90) cc_final: 0.8230 (ptp90) REVERT: C 132 MET cc_start: 0.9196 (tmm) cc_final: 0.8608 (tmm) REVERT: D 123 MET cc_start: 0.9131 (tpp) cc_final: 0.8879 (mmm) REVERT: E 132 MET cc_start: 0.9095 (ptt) cc_final: 0.8895 (ptt) REVERT: E 305 MET cc_start: 0.9180 (mmm) cc_final: 0.8752 (mmm) REVERT: F 82 MET cc_start: 0.8880 (mmm) cc_final: 0.8122 (tmm) outliers start: 10 outliers final: 8 residues processed: 141 average time/residue: 0.3019 time to fit residues: 68.9270 Evaluate side-chains 142 residues out of total 2195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 134 time to evaluate : 2.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain D residue 111 ASN Chi-restraints excluded: chain E residue 106 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 130 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 195 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 235 optimal weight: 5.9990 chunk 254 optimal weight: 9.9990 chunk 209 optimal weight: 2.9990 chunk 233 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 189 optimal weight: 6.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 111 ASN E 137 GLN ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 20972 Z= 0.308 Angle : 0.611 7.855 28463 Z= 0.293 Chirality : 0.045 0.181 3161 Planarity : 0.005 0.047 3639 Dihedral : 8.319 144.792 2921 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.55 % Allowed : 6.65 % 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: -0.07 (0.17), residues: 2566 helix: 0.03 (0.16), residues: 1067 sheet: 0.20 (0.24), residues: 463 loop : -0.00 (0.20), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 340 HIS 0.004 0.001 HIS F 161 PHE 0.012 0.001 PHE G 223 TYR 0.021 0.001 TYR E 279 ARG 0.004 0.000 ARG F 254 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 132 time to evaluate : 2.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 132 MET cc_start: 0.9066 (tmm) cc_final: 0.8635 (tmm) REVERT: B 372 ARG cc_start: 0.8645 (ptp90) cc_final: 0.8247 (ptp90) REVERT: C 132 MET cc_start: 0.9178 (tmm) cc_final: 0.8632 (tmm) REVERT: D 123 MET cc_start: 0.9134 (tpp) cc_final: 0.8831 (mmm) REVERT: D 372 ARG cc_start: 0.9293 (mtp-110) cc_final: 0.8914 (mtm-85) REVERT: E 305 MET cc_start: 0.9176 (mmm) cc_final: 0.8788 (mmm) REVERT: F 82 MET cc_start: 0.9011 (mmm) cc_final: 0.8256 (tmm) REVERT: F 276 GLU cc_start: 0.8002 (pm20) cc_final: 0.7527 (pm20) REVERT: F 355 MET cc_start: 0.8958 (mmm) cc_final: 0.8663 (mmm) outliers start: 12 outliers final: 7 residues processed: 139 average time/residue: 0.2995 time to fit residues: 67.1792 Evaluate side-chains 137 residues out of total 2195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 130 time to evaluate : 3.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain E residue 106 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 232 optimal weight: 9.9990 chunk 177 optimal weight: 4.9990 chunk 122 optimal weight: 0.6980 chunk 26 optimal weight: 0.3980 chunk 112 optimal weight: 0.9990 chunk 158 optimal weight: 0.4980 chunk 236 optimal weight: 7.9990 chunk 250 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 224 optimal weight: 0.0000 chunk 67 optimal weight: 2.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 173 HIS E 137 GLN E 173 HIS ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 371 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20972 Z= 0.125 Angle : 0.522 8.044 28463 Z= 0.244 Chirality : 0.043 0.161 3161 Planarity : 0.004 0.047 3639 Dihedral : 6.754 143.798 2921 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.41 % Allowed : 7.74 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.17), residues: 2566 helix: 0.39 (0.17), residues: 1068 sheet: 0.27 (0.24), residues: 471 loop : 0.16 (0.21), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 340 HIS 0.002 0.000 HIS F 161 PHE 0.010 0.001 PHE G 223 TYR 0.022 0.001 TYR E 279 ARG 0.003 0.000 ARG G 147 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 139 time to evaluate : 2.699 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.9149 (tmm) cc_final: 0.8305 (tmm) REVERT: A 283 MET cc_start: 0.9233 (mmm) cc_final: 0.8789 (mpp) REVERT: B 372 ARG cc_start: 0.8620 (ptp90) cc_final: 0.8226 (ptp90) REVERT: C 132 MET cc_start: 0.9087 (tmm) cc_final: 0.8709 (tmm) REVERT: C 355 MET cc_start: 0.9532 (mtp) cc_final: 0.9307 (mtm) REVERT: D 372 ARG cc_start: 0.9314 (mtp-110) cc_final: 0.8929 (mtm-85) REVERT: E 305 MET cc_start: 0.9129 (mmm) cc_final: 0.8899 (mmm) REVERT: F 82 MET cc_start: 0.8914 (mmm) cc_final: 0.8208 (tmm) REVERT: F 123 MET cc_start: 0.9301 (mmm) cc_final: 0.8471 (mmm) REVERT: F 276 GLU cc_start: 0.8059 (pm20) cc_final: 0.7612 (pm20) REVERT: F 355 MET cc_start: 0.8987 (mmm) cc_final: 0.8697 (mmm) REVERT: G 44 MET cc_start: 0.9351 (mmm) cc_final: 0.9086 (mmm) outliers start: 9 outliers final: 5 residues processed: 144 average time/residue: 0.2854 time to fit residues: 67.1487 Evaluate side-chains 139 residues out of total 2195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 134 time to evaluate : 1.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 364 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 208 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 186 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 213 optimal weight: 1.9990 chunk 173 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 127 optimal weight: 1.9990 chunk 224 optimal weight: 0.2980 chunk 63 optimal weight: 0.0980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN D 115 ASN ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 371 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20972 Z= 0.227 Angle : 0.555 8.851 28463 Z= 0.262 Chirality : 0.044 0.172 3161 Planarity : 0.004 0.045 3639 Dihedral : 6.244 143.162 2921 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.68 % Allowed : 8.43 % Favored : 90.89 % 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: 0.44 (0.17), residues: 2566 helix: 0.54 (0.17), residues: 1073 sheet: 0.32 (0.24), residues: 473 loop : 0.24 (0.21), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 340 HIS 0.003 0.001 HIS B 371 PHE 0.011 0.001 PHE G 124 TYR 0.026 0.001 TYR E 279 ARG 0.003 0.000 ARG F 254 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 135 time to evaluate : 1.812 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.9217 (tmm) cc_final: 0.8361 (tmm) REVERT: A 283 MET cc_start: 0.9151 (mmm) cc_final: 0.8923 (mmt) REVERT: A 325 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.8038 (mtp) REVERT: B 372 ARG cc_start: 0.8619 (ptp90) cc_final: 0.8221 (ptp90) REVERT: C 132 MET cc_start: 0.9149 (tmm) cc_final: 0.8704 (tmm) REVERT: C 355 MET cc_start: 0.9556 (mtp) cc_final: 0.9329 (mtm) REVERT: D 372 ARG cc_start: 0.9308 (mtp-110) cc_final: 0.8941 (mtm-85) REVERT: E 305 MET cc_start: 0.9164 (mmm) cc_final: 0.8791 (mmm) REVERT: F 82 MET cc_start: 0.8966 (mmm) cc_final: 0.8153 (tmm) REVERT: F 123 MET cc_start: 0.9314 (mmm) cc_final: 0.8425 (mmm) REVERT: F 276 GLU cc_start: 0.8002 (pm20) cc_final: 0.7364 (pm20) REVERT: F 355 MET cc_start: 0.9004 (mmm) cc_final: 0.8728 (mmm) REVERT: G 44 MET cc_start: 0.9342 (mmm) cc_final: 0.8919 (mmm) REVERT: G 323 SER cc_start: 0.8841 (p) cc_final: 0.8613 (t) outliers start: 15 outliers final: 11 residues processed: 142 average time/residue: 0.2704 time to fit residues: 62.2005 Evaluate side-chains 146 residues out of total 2195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 134 time to evaluate : 2.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 364 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 84 optimal weight: 0.0970 chunk 225 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 250 optimal weight: 5.9990 chunk 208 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 131 optimal weight: 0.6980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN E 137 GLN ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 161 HIS G 371 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20972 Z= 0.287 Angle : 0.585 9.132 28463 Z= 0.279 Chirality : 0.045 0.180 3161 Planarity : 0.004 0.043 3639 Dihedral : 6.147 140.328 2921 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.05 % Allowed : 8.84 % Favored : 90.11 % 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: 0.49 (0.18), residues: 2566 helix: 0.58 (0.17), residues: 1075 sheet: 0.28 (0.24), residues: 473 loop : 0.30 (0.21), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 86 HIS 0.004 0.001 HIS E 101 PHE 0.011 0.001 PHE B 255 TYR 0.026 0.001 TYR E 279 ARG 0.003 0.000 ARG F 254 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 134 time to evaluate : 2.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.9288 (tmm) cc_final: 0.8704 (tmm) REVERT: A 283 MET cc_start: 0.9144 (mmm) cc_final: 0.8919 (mmt) REVERT: A 325 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.7921 (mtp) REVERT: B 372 ARG cc_start: 0.8628 (ptp90) cc_final: 0.8218 (ptp90) REVERT: C 132 MET cc_start: 0.9119 (tmm) cc_final: 0.8669 (tmm) REVERT: C 355 MET cc_start: 0.9570 (mtp) cc_final: 0.9324 (mtm) REVERT: D 372 ARG cc_start: 0.9294 (mtp-110) cc_final: 0.8943 (mtm-85) REVERT: E 305 MET cc_start: 0.9214 (mmm) cc_final: 0.8793 (mmm) REVERT: F 82 MET cc_start: 0.9024 (mmm) cc_final: 0.8286 (tmm) REVERT: F 355 MET cc_start: 0.9036 (mmm) cc_final: 0.8768 (mmm) REVERT: G 44 MET cc_start: 0.9392 (mmm) cc_final: 0.8706 (mmm) REVERT: G 123 MET cc_start: 0.8801 (tpp) cc_final: 0.8485 (tpt) REVERT: G 124 PHE cc_start: 0.8479 (OUTLIER) cc_final: 0.8013 (t80) outliers start: 23 outliers final: 15 residues processed: 148 average time/residue: 0.2940 time to fit residues: 71.3944 Evaluate side-chains 148 residues out of total 2195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 131 time to evaluate : 2.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain G residue 124 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 241 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 142 optimal weight: 4.9990 chunk 182 optimal weight: 4.9990 chunk 141 optimal weight: 0.7980 chunk 210 optimal weight: 0.8980 chunk 139 optimal weight: 0.4980 chunk 249 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 115 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN B 12 ASN D 12 ASN E 137 GLN ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 371 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 20972 Z= 0.138 Angle : 0.532 9.815 28463 Z= 0.250 Chirality : 0.043 0.165 3161 Planarity : 0.003 0.049 3639 Dihedral : 5.832 133.735 2921 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.82 % Allowed : 9.16 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.68 (0.18), residues: 2566 helix: 0.73 (0.17), residues: 1064 sheet: 0.39 (0.25), residues: 473 loop : 0.41 (0.21), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 340 HIS 0.003 0.000 HIS B 371 PHE 0.009 0.001 PHE G 255 TYR 0.027 0.001 TYR E 279 ARG 0.002 0.000 ARG E 210 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 134 time to evaluate : 2.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.9306 (tmm) cc_final: 0.8470 (tmm) REVERT: A 283 MET cc_start: 0.9151 (mmm) cc_final: 0.8944 (mmt) REVERT: A 325 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7848 (mtp) REVERT: B 132 MET cc_start: 0.9326 (tmm) cc_final: 0.8913 (tmm) REVERT: B 355 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.8152 (mtm) REVERT: B 372 ARG cc_start: 0.8617 (ptp90) cc_final: 0.8225 (ptp90) REVERT: C 132 MET cc_start: 0.9024 (tmm) cc_final: 0.8702 (tmm) REVERT: C 355 MET cc_start: 0.9562 (mtp) cc_final: 0.9301 (mtm) REVERT: D 372 ARG cc_start: 0.9312 (mtp-110) cc_final: 0.8966 (mtm-85) REVERT: E 305 MET cc_start: 0.9165 (mmm) cc_final: 0.8943 (mmm) REVERT: F 82 MET cc_start: 0.8952 (mmm) cc_final: 0.8291 (tmm) REVERT: F 355 MET cc_start: 0.8998 (mmm) cc_final: 0.8740 (mmm) REVERT: G 44 MET cc_start: 0.9311 (mmm) cc_final: 0.8623 (mmm) REVERT: G 123 MET cc_start: 0.8735 (tpp) cc_final: 0.8282 (tpp) REVERT: G 127 PHE cc_start: 0.8429 (m-10) cc_final: 0.7992 (m-10) REVERT: G 325 MET cc_start: 0.6472 (ptp) cc_final: 0.5132 (pmm) outliers start: 18 outliers final: 9 residues processed: 145 average time/residue: 0.2892 time to fit residues: 68.3854 Evaluate side-chains 142 residues out of total 2195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 131 time to evaluate : 2.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 287 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 154 optimal weight: 3.9990 chunk 99 optimal weight: 0.1980 chunk 149 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 158 optimal weight: 0.0050 chunk 170 optimal weight: 2.9990 chunk 123 optimal weight: 0.0470 chunk 23 optimal weight: 4.9990 chunk 196 optimal weight: 1.9990 overall best weight: 0.3692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN E 115 ASN ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 371 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20972 Z= 0.123 Angle : 0.525 10.172 28463 Z= 0.245 Chirality : 0.043 0.168 3161 Planarity : 0.003 0.050 3639 Dihedral : 5.614 127.290 2921 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.68 % Allowed : 9.29 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.18), residues: 2566 helix: 0.77 (0.17), residues: 1074 sheet: 0.47 (0.25), residues: 473 loop : 0.50 (0.21), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 340 HIS 0.002 0.000 HIS B 371 PHE 0.016 0.001 PHE G 124 TYR 0.025 0.001 TYR E 279 ARG 0.002 0.000 ARG E 210 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 137 time to evaluate : 2.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.9289 (tmm) cc_final: 0.8470 (tmm) REVERT: A 283 MET cc_start: 0.9145 (mmm) cc_final: 0.8921 (mmt) REVERT: A 325 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7803 (mtp) REVERT: B 132 MET cc_start: 0.9316 (tmm) cc_final: 0.8948 (tmm) REVERT: B 355 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.8087 (mtm) REVERT: B 372 ARG cc_start: 0.8598 (ptp90) cc_final: 0.8188 (ptp90) REVERT: C 132 MET cc_start: 0.9028 (tmm) cc_final: 0.8769 (ppp) REVERT: C 355 MET cc_start: 0.9553 (mtp) cc_final: 0.9304 (mtm) REVERT: D 372 ARG cc_start: 0.9309 (mtp-110) cc_final: 0.8969 (mtm-85) REVERT: E 305 MET cc_start: 0.9151 (mmm) cc_final: 0.8819 (mmm) REVERT: F 82 MET cc_start: 0.8937 (mmm) cc_final: 0.8278 (tmm) REVERT: F 123 MET cc_start: 0.9392 (mmm) cc_final: 0.8591 (mmm) REVERT: G 44 MET cc_start: 0.9318 (mmm) cc_final: 0.8556 (mmm) REVERT: G 123 MET cc_start: 0.8684 (tpp) cc_final: 0.8359 (tpp) REVERT: G 176 MET cc_start: 0.7945 (ptp) cc_final: 0.7587 (pmm) REVERT: G 325 MET cc_start: 0.6559 (ptp) cc_final: 0.5237 (pmm) outliers start: 15 outliers final: 12 residues processed: 147 average time/residue: 0.3067 time to fit residues: 72.5913 Evaluate side-chains 147 residues out of total 2195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 133 time to evaluate : 2.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain G residue 124 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 227 optimal weight: 7.9990 chunk 239 optimal weight: 10.0000 chunk 218 optimal weight: 0.8980 chunk 232 optimal weight: 7.9990 chunk 140 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 182 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 210 optimal weight: 0.6980 chunk 220 optimal weight: 3.9990 chunk 231 optimal weight: 0.0980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN E 115 ASN ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 371 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20972 Z= 0.263 Angle : 0.575 10.918 28463 Z= 0.271 Chirality : 0.045 0.179 3161 Planarity : 0.003 0.046 3639 Dihedral : 5.671 125.229 2921 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.77 % Allowed : 9.48 % Favored : 89.75 % 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: 0.75 (0.18), residues: 2566 helix: 0.76 (0.17), residues: 1071 sheet: 0.40 (0.25), residues: 473 loop : 0.48 (0.22), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 86 HIS 0.003 0.001 HIS B 371 PHE 0.014 0.001 PHE G 124 TYR 0.022 0.001 TYR E 279 ARG 0.003 0.000 ARG F 254 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 132 time to evaluate : 2.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.9319 (tmm) cc_final: 0.8484 (tmm) REVERT: A 325 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.7858 (mtp) REVERT: B 132 MET cc_start: 0.9378 (tmm) cc_final: 0.8922 (tmm) REVERT: B 355 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8138 (mtm) REVERT: B 372 ARG cc_start: 0.8633 (ptp90) cc_final: 0.8221 (ptp90) REVERT: C 132 MET cc_start: 0.9112 (tmm) cc_final: 0.8713 (tmm) REVERT: D 372 ARG cc_start: 0.9306 (mtp-110) cc_final: 0.8965 (mtm-85) REVERT: E 305 MET cc_start: 0.9215 (mmm) cc_final: 0.8790 (mmm) REVERT: F 82 MET cc_start: 0.9012 (mmm) cc_final: 0.8261 (tmm) REVERT: F 123 MET cc_start: 0.9428 (mmm) cc_final: 0.8634 (mmm) REVERT: G 44 MET cc_start: 0.9324 (mmm) cc_final: 0.8482 (mmm) REVERT: G 123 MET cc_start: 0.8741 (tpp) cc_final: 0.8384 (tpp) outliers start: 17 outliers final: 15 residues processed: 143 average time/residue: 0.2935 time to fit residues: 68.7671 Evaluate side-chains 148 residues out of total 2195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 131 time to evaluate : 2.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain G residue 124 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 152 optimal weight: 0.0370 chunk 245 optimal weight: 0.9980 chunk 150 optimal weight: 0.0050 chunk 116 optimal weight: 1.9990 chunk 171 optimal weight: 7.9990 chunk 258 optimal weight: 8.9990 chunk 237 optimal weight: 9.9990 chunk 205 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 125 optimal weight: 0.0000 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 371 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20972 Z= 0.136 Angle : 0.537 11.156 28463 Z= 0.250 Chirality : 0.043 0.172 3161 Planarity : 0.003 0.053 3639 Dihedral : 5.518 117.683 2921 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.77 % Allowed : 9.43 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.18), residues: 2566 helix: 0.82 (0.17), residues: 1069 sheet: 0.46 (0.25), residues: 473 loop : 0.51 (0.22), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 340 HIS 0.003 0.000 HIS B 371 PHE 0.014 0.001 PHE G 124 TYR 0.023 0.001 TYR E 279 ARG 0.002 0.000 ARG E 210 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5132 Ramachandran restraints generated. 2566 Oldfield, 0 Emsley, 2566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 133 time to evaluate : 2.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.9315 (tmm) cc_final: 0.8484 (tmm) REVERT: A 325 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7815 (mtp) REVERT: B 132 MET cc_start: 0.9330 (tmm) cc_final: 0.8995 (tmm) REVERT: B 355 MET cc_start: 0.8369 (OUTLIER) cc_final: 0.8106 (mtm) REVERT: B 372 ARG cc_start: 0.8652 (ptp90) cc_final: 0.8246 (ptp90) REVERT: C 132 MET cc_start: 0.9038 (tmm) cc_final: 0.8746 (tmm) REVERT: C 355 MET cc_start: 0.9486 (mtp) cc_final: 0.9271 (mtm) REVERT: D 372 ARG cc_start: 0.9308 (mtp-110) cc_final: 0.8966 (mtm-85) REVERT: E 305 MET cc_start: 0.9174 (mmm) cc_final: 0.8796 (mmm) REVERT: E 325 MET cc_start: 0.8159 (ptp) cc_final: 0.7644 (ptp) REVERT: F 82 MET cc_start: 0.8940 (mmm) cc_final: 0.8264 (tmm) REVERT: G 44 MET cc_start: 0.9307 (mmm) cc_final: 0.8455 (mmm) REVERT: G 123 MET cc_start: 0.8767 (tpp) cc_final: 0.8397 (tpp) REVERT: G 325 MET cc_start: 0.6976 (ptp) cc_final: 0.5525 (pmm) outliers start: 17 outliers final: 15 residues processed: 144 average time/residue: 0.3026 time to fit residues: 71.3187 Evaluate side-chains 149 residues out of total 2195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 132 time to evaluate : 2.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain G residue 124 PHE Chi-restraints excluded: chain G residue 370 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 163 optimal weight: 5.9990 chunk 218 optimal weight: 4.9990 chunk 62 optimal weight: 0.0050 chunk 189 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 205 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 211 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 overall best weight: 2.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 371 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.054866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.041954 restraints weight = 75155.931| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 3.43 r_work: 0.2631 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 20972 Z= 0.253 Angle : 0.695 59.174 28463 Z= 0.372 Chirality : 0.046 0.383 3161 Planarity : 0.004 0.089 3639 Dihedral : 5.531 117.664 2921 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.84 % Favored : 97.12 % Rotamer: Outliers : 0.82 % Allowed : 9.43 % Favored : 89.75 % 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 (0.18), residues: 2566 helix: 0.78 (0.17), residues: 1069 sheet: 0.44 (0.25), residues: 473 loop : 0.50 (0.21), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 356 HIS 0.003 0.001 HIS F 161 PHE 0.014 0.001 PHE G 124 TYR 0.023 0.001 TYR E 279 ARG 0.002 0.000 ARG C 210 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3360.80 seconds wall clock time: 62 minutes 40.71 seconds (3760.71 seconds total)