Starting phenix.real_space_refine (version: dev) on Tue Dec 13 21:51:37 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5g_30085/12_2022/6m5g_30085_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5g_30085/12_2022/6m5g_30085.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5g_30085/12_2022/6m5g_30085.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5g_30085/12_2022/6m5g_30085.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5g_30085/12_2022/6m5g_30085_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m5g_30085/12_2022/6m5g_30085_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.010 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 28": "NH1" <-> "NH2" Residue "B ARG 28": "NH1" <-> "NH2" Residue "C ARG 28": "NH1" <-> "NH2" Residue "D ARG 28": "NH1" <-> "NH2" Residue "E ARG 28": "NH1" <-> "NH2" Residue "E PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 17363 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2881 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2879 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2885 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 2873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2873 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 2876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2876 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 943 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "G" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 943 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "H" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 943 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} 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} Time building chain proxies: 9.93, per 1000 atoms: 0.57 Number of scatterers: 17363 At special positions: 0 Unit cell: (129.72, 89.7, 194.58, 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 108 16.00 P 10 15.00 Mg 5 11.99 O 3311 8.00 N 2981 7.00 C 10948 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: 7.06 Conformation dependent library (CDL) restraints added in 2.5 seconds 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4074 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 106 helices and 20 sheets defined 42.9% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 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 removed outlier: 3.853A pdb=" N GLU A 83 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) 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 139 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 196 removed outlier: 3.610A pdb=" N LYS A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 removed outlier: 3.690A pdb=" N LYS A 215 " --> pdb=" O ASP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 229 Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 274 through 283 removed outlier: 3.739A pdb=" N THR A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYR A 279 " --> pdb=" O HIS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 293 removed outlier: 3.860A pdb=" N LYS A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ASP A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) 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 312 through 317 Processing helix chain 'A' and resid 335 through 348 removed outlier: 4.930A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A 347 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 367 through 373 removed outlier: 3.746A pdb=" N VAL A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N HIS A 371 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 79 through 91 removed outlier: 3.914A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.902A pdb=" N SER B 141 " --> pdb=" O GLN B 137 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 196 removed outlier: 4.133A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 removed outlier: 4.045A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 231 removed outlier: 3.717A pdb=" N ALA B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 261 Processing helix chain 'B' and resid 264 through 267 removed outlier: 3.531A pdb=" N ILE B 267 " --> pdb=" O PRO B 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 264 through 267' Processing helix chain 'B' and resid 274 through 283 removed outlier: 3.656A pdb=" N THR B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N TYR B 279 " --> pdb=" O HIS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 293 removed outlier: 3.795A pdb=" N LYS B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ASP B 292 " --> 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 312 through 317 Processing helix chain 'B' and resid 338 through 348 removed outlier: 3.798A pdb=" N SER B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 352 No H-bonds generated for 'chain 'B' and resid 350 through 352' Processing helix chain 'B' and resid 359 through 365 Processing helix chain 'B' and resid 367 through 373 removed outlier: 3.591A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N HIS B 371 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 79 through 91 removed outlier: 3.794A pdb=" N GLU C 83 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.923A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) 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 195 removed outlier: 4.801A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.827A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS C 215 " --> pdb=" O ASP C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 231 Processing helix chain 'C' and resid 252 through 254 No H-bonds generated for 'chain 'C' and resid 252 through 254' Processing helix chain 'C' and resid 258 through 261 Processing helix chain 'C' and resid 264 through 267 removed outlier: 3.661A pdb=" N ILE C 267 " --> pdb=" O PRO C 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 264 through 267' Processing helix chain 'C' and resid 274 through 284 removed outlier: 3.562A pdb=" N THR C 278 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N TYR C 279 " --> pdb=" O HIS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 293 removed outlier: 3.972A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 305 Processing helix chain 'C' and resid 307 through 318 removed outlier: 4.495A pdb=" N ALA C 310 " --> pdb=" O PRO C 307 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP C 311 " --> pdb=" O GLY C 308 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG C 312 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N MET C 313 " --> pdb=" O ALA C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 348 Processing helix chain 'C' and resid 352 through 354 No H-bonds generated for 'chain 'C' and resid 352 through 354' Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 367 through 373 removed outlier: 3.867A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N HIS C 371 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 79 through 91 removed outlier: 3.907A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 126 Processing helix chain 'D' and resid 137 through 145 removed outlier: 4.171A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 195 removed outlier: 4.182A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 removed outlier: 4.156A pdb=" N LYS D 215 " --> pdb=" O ASP D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 231 removed outlier: 3.687A pdb=" N ALA D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 274 through 283 removed outlier: 3.517A pdb=" N THR D 278 " --> pdb=" O ILE D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 293 removed outlier: 4.085A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 305 No H-bonds generated for 'chain 'D' and resid 303 through 305' Processing helix chain 'D' and resid 307 through 318 removed outlier: 4.548A pdb=" N ALA D 310 " --> pdb=" O PRO D 307 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP D 311 " --> pdb=" O GLY D 308 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG D 312 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N MET D 313 " --> pdb=" O ALA D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 347 removed outlier: 4.691A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA D 347 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 354 removed outlier: 3.742A 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 367 through 373 Processing helix chain 'E' and resid 56 through 60 Processing helix chain 'E' and resid 79 through 91 removed outlier: 3.829A pdb=" N LYS E 84 " --> pdb=" O ASP E 80 " (cutoff:3.500A) 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 removed outlier: 4.248A pdb=" N LEU E 142 " --> pdb=" O ALA E 138 " (cutoff:3.500A) 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 195 removed outlier: 3.509A pdb=" N LYS E 191 " --> pdb=" O ASP E 187 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 216 removed outlier: 3.888A pdb=" N LYS E 215 " --> pdb=" O ASP E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 231 Processing helix chain 'E' and resid 274 through 283 removed outlier: 3.553A pdb=" N THR E 278 " --> pdb=" O ILE E 274 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N TYR E 279 " --> pdb=" O HIS E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 293 removed outlier: 4.250A pdb=" N LYS E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N ASP E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 305 Processing helix chain 'E' and resid 309 through 318 removed outlier: 3.884A pdb=" N GLN E 314 " --> pdb=" O ALA E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 348 Processing helix chain 'E' and resid 352 through 354 No H-bonds generated for 'chain 'E' and resid 352 through 354' Processing helix chain 'E' and resid 359 through 365 Processing helix chain 'E' and resid 367 through 373 removed outlier: 3.589A pdb=" N VAL E 370 " --> pdb=" O PRO E 367 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N HIS E 371 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 47 removed outlier: 3.862A pdb=" N LYS F 35 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER F 46 " --> pdb=" O ALA F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 74 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 112 through 116 removed outlier: 3.532A pdb=" N VAL F 116 " --> pdb=" O GLY F 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 112 through 116' Processing helix chain 'F' and resid 120 through 123 No H-bonds generated for 'chain 'F' and resid 120 through 123' Processing helix chain 'F' and resid 126 through 134 Processing helix chain 'G' and resid 21 through 47 removed outlier: 4.212A pdb=" N GLU G 28 " --> pdb=" O ARG G 25 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS G 35 " --> pdb=" O VAL G 32 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER G 46 " --> pdb=" O ALA G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 74 removed outlier: 3.517A pdb=" N GLU G 71 " --> pdb=" O LEU G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 103 removed outlier: 4.165A pdb=" N ASN G 103 " --> pdb=" O VAL G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'G' and resid 120 through 123 No H-bonds generated for 'chain 'G' and resid 120 through 123' Processing helix chain 'G' and resid 125 through 134 Processing helix chain 'H' and resid 21 through 47 removed outlier: 3.984A pdb=" N LYS H 35 " --> pdb=" O VAL H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 74 removed outlier: 3.982A pdb=" N LEU H 69 " --> pdb=" O LYS H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 102 Processing helix chain 'H' and resid 113 through 116 No H-bonds generated for 'chain 'H' and resid 113 through 116' Processing helix chain 'H' and resid 120 through 123 No H-bonds generated for 'chain 'H' and resid 120 through 123' Processing helix chain 'H' and resid 126 through 134 removed outlier: 3.647A pdb=" N TRP H 134 " --> pdb=" O ILE H 130 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 8 through 12 removed outlier: 3.572A pdb=" N ALA A 19 " --> pdb=" O ALA A 29 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 103 through 107 Processing sheet with id= C, first strand: chain 'A' and resid 163 through 165 removed outlier: 3.558A pdb=" N VAL A 298 " --> pdb=" O ILE A 151 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 160 through 162 Processing sheet with id= E, first strand: chain 'B' and resid 8 through 10 removed outlier: 4.215A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 16 through 19 removed outlier: 3.674A pdb=" N ALA B 29 " --> pdb=" O ALA B 19 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 34 through 38 removed outlier: 3.740A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 150 through 152 removed outlier: 3.710A pdb=" N VAL B 152 " --> pdb=" O VAL B 163 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 7 through 10 removed outlier: 7.553A pdb=" N CYS C 10 " --> pdb=" O PRO C 102 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU C 104 " --> pdb=" O CYS C 10 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 16 through 19 removed outlier: 3.665A pdb=" N ALA C 19 " --> pdb=" O ALA C 29 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA C 29 " --> pdb=" O ALA C 19 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 35 through 37 Processing sheet with id= L, first strand: chain 'C' and resid 150 through 155 removed outlier: 3.754A pdb=" N VAL C 152 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN C 162 " --> pdb=" O MET C 176 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 239 through 241 Processing sheet with id= N, first strand: chain 'D' and resid 16 through 19 removed outlier: 3.602A pdb=" N PHE D 31 " --> pdb=" O VAL D 17 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 35 through 37 Processing sheet with id= P, first strand: chain 'D' and resid 103 through 107 Processing sheet with id= Q, first strand: chain 'D' and resid 150 through 154 removed outlier: 3.561A pdb=" N VAL D 152 " --> pdb=" O VAL D 163 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 132 through 136 removed outlier: 6.618A pdb=" N THR E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ALA E 135 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL E 9 " --> pdb=" O GLY E 20 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 150 through 154 removed outlier: 3.727A pdb=" N VAL E 152 " --> pdb=" O VAL E 163 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP E 154 " --> pdb=" O HIS E 161 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 238 through 241 removed outlier: 3.724A pdb=" N LYS E 238 " --> pdb=" O ILE E 250 " (cutoff:3.500A) 548 hydrogen bonds defined for protein. 1260 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: 4.96 Time building geometry restraints manager: 7.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5672 1.33 - 1.45: 2332 1.45 - 1.57: 9519 1.57 - 1.68: 15 1.68 - 1.80: 191 Bond restraints: 17729 Sorted by residual: bond pdb=" CA ARG E 335 " pdb=" C ARG E 335 " ideal model delta sigma weight residual 1.523 1.441 0.083 1.80e-02 3.09e+03 2.10e+01 bond pdb=" CA ALA C 310 " pdb=" C ALA C 310 " ideal model delta sigma weight residual 1.522 1.469 0.053 1.72e-02 3.38e+03 9.48e+00 bond pdb=" C GLN C 263 " pdb=" N PRO C 264 " ideal model delta sigma weight residual 1.334 1.310 0.023 8.40e-03 1.42e+04 7.70e+00 bond pdb=" C LEU D 171 " pdb=" N PRO D 172 " ideal model delta sigma weight residual 1.337 1.312 0.025 9.80e-03 1.04e+04 6.42e+00 bond pdb=" C TYR B 69 " pdb=" N PRO B 70 " ideal model delta sigma weight residual 1.336 1.310 0.026 1.20e-02 6.94e+03 4.73e+00 ... (remaining 17724 not shown) Histogram of bond angle deviations from ideal: 98.54 - 106.03: 488 106.03 - 113.52: 10266 113.52 - 121.01: 8557 121.01 - 128.51: 4573 128.51 - 136.00: 160 Bond angle restraints: 24044 Sorted by residual: angle pdb=" C GLY B 308 " pdb=" N ILE B 309 " pdb=" CA ILE B 309 " ideal model delta sigma weight residual 121.97 129.35 -7.38 1.80e+00 3.09e-01 1.68e+01 angle pdb=" C GLY A 308 " pdb=" N ILE A 309 " pdb=" CA ILE A 309 " ideal model delta sigma weight residual 121.97 129.19 -7.22 1.80e+00 3.09e-01 1.61e+01 angle pdb=" N GLY E 268 " pdb=" CA GLY E 268 " pdb=" C GLY E 268 " ideal model delta sigma weight residual 114.95 110.30 4.65 1.41e+00 5.03e-01 1.09e+01 angle pdb=" N ARG B 335 " pdb=" CA ARG B 335 " pdb=" C ARG B 335 " ideal model delta sigma weight residual 113.21 109.78 3.43 1.15e+00 7.56e-01 8.92e+00 angle pdb=" C HIS A 161 " pdb=" CA HIS A 161 " pdb=" CB HIS A 161 " ideal model delta sigma weight residual 112.99 106.93 6.06 2.10e+00 2.27e-01 8.34e+00 ... (remaining 24039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.51: 10150 25.51 - 51.02: 468 51.02 - 76.54: 40 76.54 - 102.05: 5 102.05 - 127.56: 2 Dihedral angle restraints: 10665 sinusoidal: 4315 harmonic: 6350 Sorted by residual: dihedral pdb=" C5' ADP C 402 " pdb=" O5' ADP C 402 " pdb=" PA ADP C 402 " pdb=" O2A ADP C 402 " ideal model delta sinusoidal sigma weight residual -60.00 67.56 -127.56 1 2.00e+01 2.50e-03 3.86e+01 dihedral pdb=" C5' ADP B 402 " pdb=" O5' ADP B 402 " pdb=" PA ADP B 402 " pdb=" O2A ADP B 402 " ideal model delta sinusoidal sigma weight residual -60.00 54.81 -114.80 1 2.00e+01 2.50e-03 3.41e+01 dihedral pdb=" CA GLY A 308 " pdb=" C GLY A 308 " pdb=" N ILE A 309 " pdb=" CA ILE A 309 " ideal model delta harmonic sigma weight residual -180.00 -153.72 -26.28 0 5.00e+00 4.00e-02 2.76e+01 ... (remaining 10662 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1484 0.039 - 0.077: 874 0.077 - 0.116: 283 0.116 - 0.154: 39 0.154 - 0.192: 11 Chirality restraints: 2691 Sorted by residual: chirality pdb=" C2' ADP B 402 " pdb=" C1' ADP B 402 " pdb=" C3' ADP B 402 " pdb=" O2' ADP B 402 " both_signs ideal model delta sigma weight residual False -2.51 -2.70 0.19 2.00e-01 2.50e+01 9.26e-01 chirality pdb=" CB ILE C 151 " pdb=" CA ILE C 151 " pdb=" CG1 ILE C 151 " pdb=" CG2 ILE C 151 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.15e-01 chirality pdb=" CB ILE D 151 " pdb=" CA ILE D 151 " pdb=" CG1 ILE D 151 " pdb=" CG2 ILE D 151 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.63e-01 ... (remaining 2688 not shown) Planarity restraints: 3070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 306 " 0.035 5.00e-02 4.00e+02 5.31e-02 4.52e+00 pdb=" N PRO C 307 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO C 307 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 307 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 181 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.57e+00 pdb=" C ALA E 181 " 0.033 2.00e-02 2.50e+03 pdb=" O ALA E 181 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY E 182 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR B 306 " -0.031 5.00e-02 4.00e+02 4.60e-02 3.39e+00 pdb=" N PRO B 307 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 307 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 307 " -0.025 5.00e-02 4.00e+02 ... (remaining 3067 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 186 2.54 - 3.13: 14816 3.13 - 3.72: 25643 3.72 - 4.31: 37786 4.31 - 4.90: 64204 Nonbonded interactions: 142635 Sorted by model distance: nonbonded pdb="MG MG E 401 " pdb=" O1B ADP E 402 " model vdw 1.951 2.170 nonbonded pdb="MG MG A 401 " pdb=" O1B ADP A 402 " model vdw 1.987 2.170 nonbonded pdb=" N ASP B 56 " pdb=" OD1 ASP B 56 " model vdw 2.127 2.520 nonbonded pdb=" N ASP A 56 " pdb=" OD1 ASP A 56 " model vdw 2.194 2.520 nonbonded pdb=" OG SER D 350 " pdb=" OE2 GLU F 81 " model vdw 2.199 2.440 ... (remaining 142630 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 148 or (resid 149 and (name N or name CA or name \ C or name O or name CB )) or resid 150 through 204 or (resid 205 and (name N or \ name CA or name C or name O or name CB )) or resid 206 through 212 or (resid 21 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 214 through \ 233 or (resid 234 and (name N or name CA or name C or name O or name CB )) or re \ sid 235 through 245 or (resid 246 and (name N or name CA or name C or name O or \ name CB )) or resid 247 through 374 or resid 401 through 402)) selection = (chain 'B' and (resid 5 through 204 or (resid 205 and (name N or name CA or name \ C or name O or name CB )) or resid 206 through 212 or (resid 213 and (name N or \ name CA or name C or name O or name CB )) or resid 214 through 233 or (resid 23 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 235 through \ 258 or (resid 259 and (name N or name CA or name C or name O or name CB )) or re \ sid 260 through 374 or resid 401 through 402)) selection = (chain 'C' and (resid 5 through 148 or (resid 149 and (name N or name CA or name \ C or name O or name CB )) or resid 150 through 204 or (resid 205 and (name N or \ name CA or name C or name O or name CB )) or resid 206 through 212 or (resid 21 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 214 through \ 233 or (resid 234 and (name N or name CA or name C or name O or name CB )) or re \ sid 235 through 245 or (resid 246 and (name N or name CA or name C or name O or \ name CB )) or resid 247 through 258 or (resid 259 and (name N or name CA or name \ C or name O or name CB )) or resid 260 through 374 or resid 401 through 402)) selection = (chain 'D' and (resid 5 through 148 or (resid 149 and (name N or name CA or name \ C or name O or name CB )) or resid 150 through 233 or (resid 234 and (name N or \ name CA or name C or name O or name CB )) or resid 235 through 245 or (resid 24 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 247 through \ 374 or resid 401 through 402)) selection = (chain 'E' and (resid 5 through 148 or (resid 149 and (name N or name CA or name \ C or name O or name CB )) or resid 150 through 245 or (resid 246 and (name N or \ name CA or name C or name O or name CB )) or resid 247 through 258 or (resid 25 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 260 through \ 374 or resid 401 through 402)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 108 5.16 5 C 10948 2.51 5 N 2981 2.21 5 O 3311 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.950 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: 0.010 Extract box with map and model: 5.180 Check model and map are aligned: 0.270 Convert atoms to be neutral: 0.160 Process input model: 46.140 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 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 : 0.010 0.083 17729 Z= 0.678 Angle : 0.820 7.377 24044 Z= 0.430 Chirality : 0.050 0.192 2691 Planarity : 0.004 0.053 3070 Dihedral : 13.870 127.561 6591 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.41 % Favored : 90.40 % Rotamer Outliers : 9.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.64 (0.15), residues: 2188 helix: -1.80 (0.15), residues: 923 sheet: -2.41 (0.30), residues: 265 loop : -3.00 (0.17), residues: 1000 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 244 time to evaluate : 2.161 Fit side-chains revert: symmetry clash outliers start: 174 outliers final: 117 residues processed: 407 average time/residue: 0.2934 time to fit residues: 177.1437 Evaluate side-chains 342 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 225 time to evaluate : 2.106 Switching outliers to nearest non-outliers outliers start: 117 outliers final: 0 residues processed: 117 average time/residue: 0.1753 time to fit residues: 39.1685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 184 optimal weight: 0.4980 chunk 165 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 170 optimal weight: 1.9990 chunk 66 optimal weight: 0.0770 chunk 103 optimal weight: 0.9980 chunk 127 optimal weight: 0.9990 chunk 197 optimal weight: 5.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 101 HIS ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 HIS A 353 GLN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 HIS B 92 ASN B 162 ASN C 12 ASN C 88 HIS C 111 ASN C 161 HIS C 162 ASN C 275 HIS D 40 HIS D 296 ASN E 88 HIS ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN E 162 ASN E 275 HIS F 88 HIS F 120 HIS F 135 GLN G 120 HIS H 88 HIS H 102 GLN H 120 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 17729 Z= 0.154 Angle : 0.612 10.028 24044 Z= 0.303 Chirality : 0.043 0.182 2691 Planarity : 0.004 0.040 3070 Dihedral : 6.714 113.444 2439 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.20 % Favored : 95.70 % Rotamer Outliers : 2.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.17), residues: 2188 helix: -0.67 (0.17), residues: 894 sheet: -1.96 (0.31), residues: 260 loop : -2.15 (0.18), residues: 1034 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 261 time to evaluate : 2.095 Fit side-chains revert: symmetry clash outliers start: 39 outliers final: 10 residues processed: 295 average time/residue: 0.3232 time to fit residues: 140.9683 Evaluate side-chains 245 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 235 time to evaluate : 2.111 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1783 time to fit residues: 5.9472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 110 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 198 optimal weight: 0.0870 chunk 214 optimal weight: 7.9990 chunk 176 optimal weight: 0.0270 chunk 196 optimal weight: 0.0570 chunk 67 optimal weight: 0.8980 chunk 159 optimal weight: 7.9990 overall best weight: 0.6136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 HIS C 12 ASN C 162 ASN D 88 HIS D 161 HIS ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 GLN G 42 ASN G 120 HIS H 98 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 17729 Z= 0.138 Angle : 0.564 8.201 24044 Z= 0.275 Chirality : 0.042 0.297 2691 Planarity : 0.004 0.035 3070 Dihedral : 6.140 96.460 2439 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.30 % Favored : 95.61 % Rotamer Outliers : 2.46 % 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: -1.68 (0.18), residues: 2188 helix: -0.36 (0.17), residues: 892 sheet: -1.71 (0.31), residues: 260 loop : -1.57 (0.19), residues: 1036 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 257 time to evaluate : 2.068 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 23 residues processed: 286 average time/residue: 0.3024 time to fit residues: 129.0811 Evaluate side-chains 261 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 238 time to evaluate : 2.068 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1517 time to fit residues: 9.3731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 195 optimal weight: 20.0000 chunk 149 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 199 optimal weight: 6.9990 chunk 210 optimal weight: 20.0000 chunk 103 optimal weight: 5.9990 chunk 188 optimal weight: 20.0000 chunk 56 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 GLN D 137 GLN ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 29 HIS G 42 ASN G 88 HIS ** G 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 HIS H 29 HIS H 94 ASN H 98 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.056 17729 Z= 0.582 Angle : 0.761 12.673 24044 Z= 0.375 Chirality : 0.050 0.410 2691 Planarity : 0.005 0.042 3070 Dihedral : 6.901 112.661 2439 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.95 % Favored : 93.01 % Rotamer Outliers : 2.83 % 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: -2.03 (0.17), residues: 2188 helix: -0.69 (0.17), residues: 911 sheet: -1.71 (0.34), residues: 230 loop : -1.82 (0.18), residues: 1047 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 238 time to evaluate : 2.114 Fit side-chains revert: symmetry clash outliers start: 53 outliers final: 33 residues processed: 277 average time/residue: 0.3148 time to fit residues: 128.8438 Evaluate side-chains 266 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 233 time to evaluate : 1.961 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.1861 time to fit residues: 13.6152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 175 optimal weight: 0.9990 chunk 119 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 156 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 189 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 GLN ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 HIS H 98 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 17729 Z= 0.173 Angle : 0.584 8.551 24044 Z= 0.283 Chirality : 0.043 0.340 2691 Planarity : 0.004 0.038 3070 Dihedral : 6.356 99.500 2439 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.57 % Favored : 95.38 % Rotamer Outliers : 1.55 % 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: -1.62 (0.18), residues: 2188 helix: -0.36 (0.18), residues: 911 sheet: -1.64 (0.33), residues: 240 loop : -1.52 (0.19), residues: 1037 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 245 time to evaluate : 2.170 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 15 residues processed: 268 average time/residue: 0.3132 time to fit residues: 124.3109 Evaluate side-chains 249 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 234 time to evaluate : 1.982 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1602 time to fit residues: 7.4322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 70 optimal weight: 5.9990 chunk 189 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 210 optimal weight: 10.0000 chunk 175 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 HIS ** H 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 17729 Z= 0.257 Angle : 0.601 7.596 24044 Z= 0.293 Chirality : 0.044 0.321 2691 Planarity : 0.004 0.041 3070 Dihedral : 6.306 96.741 2439 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.16 % Favored : 94.79 % Rotamer Outliers : 1.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.18), residues: 2188 helix: -0.32 (0.18), residues: 917 sheet: -1.57 (0.33), residues: 240 loop : -1.44 (0.19), residues: 1031 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 242 time to evaluate : 2.100 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 14 residues processed: 260 average time/residue: 0.3079 time to fit residues: 119.0660 Evaluate side-chains 254 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 240 time to evaluate : 2.061 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1786 time to fit residues: 7.2015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 203 optimal weight: 9.9990 chunk 23 optimal weight: 0.0470 chunk 120 optimal weight: 0.0870 chunk 154 optimal weight: 0.3980 chunk 119 optimal weight: 3.9990 chunk 177 optimal weight: 5.9990 chunk 117 optimal weight: 0.0170 chunk 210 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 overall best weight: 0.7096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 HIS B 59 GLN ** E 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 GLN F 98 GLN ** F 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 HIS ** H 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.049 17729 Z= 0.137 Angle : 0.556 6.837 24044 Z= 0.270 Chirality : 0.042 0.264 2691 Planarity : 0.004 0.053 3070 Dihedral : 5.876 85.826 2439 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.25 % Favored : 95.70 % Rotamer Outliers : 0.64 % 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: -1.24 (0.18), residues: 2188 helix: -0.10 (0.18), residues: 906 sheet: -1.44 (0.33), residues: 240 loop : -1.26 (0.19), residues: 1042 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 241 time to evaluate : 2.216 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 4 residues processed: 248 average time/residue: 0.3168 time to fit residues: 116.1358 Evaluate side-chains 240 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 236 time to evaluate : 1.900 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1661 time to fit residues: 4.0608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 129 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 chunk 63 optimal weight: 0.0980 chunk 41 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 133 optimal weight: 0.8980 chunk 143 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 165 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 111 ASN F 92 ASN F 98 GLN ** F 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 HIS H 109 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 17729 Z= 0.136 Angle : 0.553 7.919 24044 Z= 0.268 Chirality : 0.042 0.240 2691 Planarity : 0.003 0.038 3070 Dihedral : 5.628 80.179 2439 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.20 % Favored : 95.75 % Rotamer Outliers : 0.43 % 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: -1.08 (0.18), residues: 2188 helix: 0.00 (0.18), residues: 912 sheet: -1.32 (0.33), residues: 240 loop : -1.16 (0.19), residues: 1036 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 250 time to evaluate : 2.229 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 255 average time/residue: 0.3175 time to fit residues: 120.4375 Evaluate side-chains 238 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 235 time to evaluate : 1.975 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1557 time to fit residues: 3.4820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 191 optimal weight: 10.0000 chunk 201 optimal weight: 3.9990 chunk 183 optimal weight: 0.4980 chunk 195 optimal weight: 8.9990 chunk 117 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 153 optimal weight: 8.9990 chunk 60 optimal weight: 0.9990 chunk 176 optimal weight: 0.5980 chunk 185 optimal weight: 4.9990 chunk 128 optimal weight: 0.8980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 92 ASN F 98 GLN ** F 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 GLN G 120 HIS H 109 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.064 17729 Z= 0.141 Angle : 0.546 8.013 24044 Z= 0.266 Chirality : 0.042 0.238 2691 Planarity : 0.003 0.038 3070 Dihedral : 5.444 76.472 2439 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.98 % Favored : 95.98 % Rotamer Outliers : 0.43 % 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 (0.18), residues: 2188 helix: 0.09 (0.18), residues: 906 sheet: -1.27 (0.33), residues: 240 loop : -1.07 (0.19), residues: 1042 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 242 time to evaluate : 2.147 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 244 average time/residue: 0.3136 time to fit residues: 114.2825 Evaluate side-chains 242 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 237 time to evaluate : 2.127 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1828 time to fit residues: 4.6777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 207 optimal weight: 4.9990 chunk 126 optimal weight: 7.9990 chunk 98 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 217 optimal weight: 10.0000 chunk 199 optimal weight: 0.4980 chunk 172 optimal weight: 0.8980 chunk 17 optimal weight: 8.9990 chunk 133 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 137 optimal weight: 6.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 92 ASN F 103 ASN ** F 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 133 HIS G 120 HIS H 109 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 17729 Z= 0.145 Angle : 0.550 8.204 24044 Z= 0.269 Chirality : 0.042 0.237 2691 Planarity : 0.003 0.040 3070 Dihedral : 5.317 72.911 2439 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer Outliers : 0.16 % 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: -0.87 (0.18), residues: 2188 helix: 0.17 (0.18), residues: 906 sheet: -1.21 (0.34), residues: 240 loop : -1.01 (0.20), residues: 1042 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 246 time to evaluate : 2.241 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 247 average time/residue: 0.3086 time to fit residues: 113.5994 Evaluate side-chains 239 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 238 time to evaluate : 2.126 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1553 time to fit residues: 3.1886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 184 optimal weight: 0.7980 chunk 52 optimal weight: 9.9990 chunk 159 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 173 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 177 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 92 ASN F 98 GLN ** F 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.071279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.056436 restraints weight = 45280.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.058047 restraints weight = 22378.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.058521 restraints weight = 15195.281| |-----------------------------------------------------------------------------| r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 17729 Z= 0.254 Angle : 0.593 8.007 24044 Z= 0.291 Chirality : 0.044 0.254 2691 Planarity : 0.004 0.040 3070 Dihedral : 5.514 76.333 2439 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.18), residues: 2188 helix: 0.01 (0.18), residues: 936 sheet: -1.27 (0.34), residues: 240 loop : -1.05 (0.20), residues: 1012 =============================================================================== Job complete usr+sys time: 3147.34 seconds wall clock time: 58 minutes 29.92 seconds (3509.92 seconds total)