Starting phenix.real_space_refine (version: dev) on Thu Dec 15 00:51:38 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efi_28083/12_2022/8efi_28083_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efi_28083/12_2022/8efi_28083.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efi_28083/12_2022/8efi_28083.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efi_28083/12_2022/8efi_28083.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efi_28083/12_2022/8efi_28083_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efi_28083/12_2022/8efi_28083_updated.pdb" } resolution = 3.4 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= 0.004 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 "M GLU 228": "OE1" <-> "OE2" Residue "M TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 255": "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: 23256 Number of models: 1 Model: "" Number of chains: 13 Chain: "M" Number of atoms: 5974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 5974 Classifications: {'peptide': 742} Link IDs: {'PTRANS': 28, 'TRANS': 713} Chain breaks: 3 Chain: "B" Number of atoms: 2898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "C" Number of atoms: 2898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "D" Number of atoms: 2898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "E" Number of atoms: 2898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "F" Number of atoms: 2898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "O" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1326 Classifications: {'peptide': 166} Link IDs: {'TRANS': 165} Chain: "P" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1326 Classifications: {'peptide': 166} Link IDs: {'TRANS': 165} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 13.07, per 1000 atoms: 0.56 Number of scatterers: 23256 At special positions: 0 Unit cell: (142.296, 141.218, 247.94, 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 138 16.00 P 10 15.00 Mg 5 11.99 O 4491 8.00 N 3946 7.00 C 14666 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: 9.74 Conformation dependent library (CDL) restraints added in 3.9 seconds 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5474 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 137 helices and 28 sheets defined 50.2% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.55 Creating SS restraints... Processing helix chain 'M' and resid 7 through 9 No H-bonds generated for 'chain 'M' and resid 7 through 9' Processing helix chain 'M' and resid 13 through 16 No H-bonds generated for 'chain 'M' and resid 13 through 16' Processing helix chain 'M' and resid 20 through 27 Processing helix chain 'M' and resid 73 through 75 No H-bonds generated for 'chain 'M' and resid 73 through 75' Processing helix chain 'M' and resid 82 through 84 No H-bonds generated for 'chain 'M' and resid 82 through 84' Processing helix chain 'M' and resid 90 through 92 No H-bonds generated for 'chain 'M' and resid 90 through 92' Processing helix chain 'M' and resid 98 through 110 removed outlier: 4.204A pdb=" N LEU M 102 " --> pdb=" O GLU M 98 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 134 No H-bonds generated for 'chain 'M' and resid 132 through 134' Processing helix chain 'M' and resid 136 through 142 Processing helix chain 'M' and resid 154 through 168 Processing helix chain 'M' and resid 184 through 198 Processing helix chain 'M' and resid 217 through 231 Proline residue: M 225 - end of helix Processing helix chain 'M' and resid 271 through 274 No H-bonds generated for 'chain 'M' and resid 271 through 274' Processing helix chain 'M' and resid 284 through 289 Processing helix chain 'M' and resid 295 through 301 Processing helix chain 'M' and resid 311 through 314 No H-bonds generated for 'chain 'M' and resid 311 through 314' Processing helix chain 'M' and resid 325 through 337 Processing helix chain 'M' and resid 343 through 361 removed outlier: 3.529A pdb=" N PHE M 359 " --> pdb=" O ALA M 355 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N GLY M 360 " --> pdb=" O ILE M 356 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ASN M 361 " --> pdb=" O MET M 357 " (cutoff:3.500A) Processing helix chain 'M' and resid 379 through 388 Processing helix chain 'M' and resid 392 through 400 Processing helix chain 'M' and resid 417 through 447 Processing helix chain 'M' and resid 473 through 504 Processing helix chain 'M' and resid 515 through 523 removed outlier: 4.742A pdb=" N CYS M 520 " --> pdb=" O ASP M 516 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE M 521 " --> pdb=" O LEU M 517 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU M 523 " --> pdb=" O ALA M 519 " (cutoff:3.500A) Processing helix chain 'M' and resid 530 through 539 removed outlier: 3.858A pdb=" N MET M 539 " --> pdb=" O GLU M 535 " (cutoff:3.500A) Processing helix chain 'M' and resid 545 through 556 Processing helix chain 'M' and resid 593 through 597 Processing helix chain 'M' and resid 603 through 610 Processing helix chain 'M' and resid 615 through 619 Processing helix chain 'M' and resid 647 through 664 removed outlier: 3.588A pdb=" N ASN M 661 " --> pdb=" O LYS M 657 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N SER M 664 " --> pdb=" O THR M 660 " (cutoff:3.500A) Processing helix chain 'M' and resid 686 through 696 Processing helix chain 'M' and resid 698 through 707 removed outlier: 3.502A pdb=" N LYS M 707 " --> pdb=" O ARG M 703 " (cutoff:3.500A) Processing helix chain 'M' and resid 715 through 726 removed outlier: 6.356A pdb=" N ILE M 724 " --> pdb=" O GLN M 720 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N LEU M 725 " --> pdb=" O ARG M 721 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ASN M 726 " --> pdb=" O TYR M 722 " (cutoff:3.500A) Processing helix chain 'M' and resid 739 through 749 removed outlier: 3.664A pdb=" N LEU M 749 " --> pdb=" O LEU M 745 " (cutoff:3.500A) Processing helix chain 'M' and resid 753 through 755 No H-bonds generated for 'chain 'M' and resid 753 through 755' Processing helix chain 'M' and resid 767 through 780 Processing helix chain 'B' and resid 55 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 144 removed outlier: 3.749A pdb=" N SER B 141 " --> pdb=" O GLN B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 196 removed outlier: 3.891A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 removed outlier: 4.021A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 4.006A 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: 3.740A pdb=" N PHE B 255 " --> pdb=" O ASN B 252 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 252 through 256' Processing helix chain 'B' and resid 258 through 260 No H-bonds generated for 'chain 'B' and resid 258 through 260' Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 274 through 284 Processing helix chain 'B' and resid 290 through 296 Processing helix chain 'B' and resid 302 through 305 Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 338 through 348 Processing helix chain 'B' and resid 351 through 354 removed outlier: 3.833A 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 365 Processing helix chain 'B' and resid 367 through 369 No H-bonds generated for 'chain 'B' and resid 367 through 369' Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 80 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 196 removed outlier: 3.795A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.954A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 removed outlier: 3.621A pdb=" N SER C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 256 removed outlier: 3.842A pdb=" N ARG C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 261 Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 274 through 284 Processing helix chain 'C' and resid 290 through 296 Processing helix chain 'C' and resid 302 through 305 Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 338 through 347 Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 367 through 371 removed outlier: 3.552A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 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 144 Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 182 through 195 removed outlier: 3.748A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 removed outlier: 4.049A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.826A 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: 3.662A 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 Processing helix chain 'D' and resid 274 through 284 removed outlier: 3.682A pdb=" N TYR D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 295 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 338 through 348 Processing helix chain 'D' and resid 351 through 354 Processing helix chain 'D' and resid 359 through 365 Processing helix chain 'D' and resid 367 through 371 Processing helix chain 'E' and resid 55 through 57 No H-bonds generated for 'chain 'E' and resid 55 through 57' Processing helix chain 'E' and resid 59 through 61 No H-bonds generated for 'chain 'E' and resid 59 through 61' 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 144 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: 3.618A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 216 Processing helix chain 'E' and resid 224 through 232 Processing helix chain 'E' and resid 252 through 254 No H-bonds generated for 'chain 'E' and resid 252 through 254' Processing helix chain 'E' and resid 258 through 261 Processing helix chain 'E' and resid 264 through 267 Processing helix chain 'E' and resid 274 through 284 removed outlier: 3.795A pdb=" N TYR E 279 " --> pdb=" O HIS E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 296 Processing helix chain 'E' and resid 302 through 305 Processing helix chain 'E' and resid 309 through 320 Processing helix chain 'E' and resid 338 through 347 Processing helix chain 'E' and resid 350 through 354 removed outlier: 3.620A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 371 Proline residue: E 367 - end of helix removed outlier: 5.438A pdb=" N VAL E 370 " --> pdb=" O GLY E 366 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N HIS E 371 " --> pdb=" O PRO E 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 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 144 Processing helix chain 'F' and resid 172 through 174 No H-bonds generated for 'chain 'F' and resid 172 through 174' Processing helix chain 'F' and resid 182 through 193 Processing helix chain 'F' and resid 203 through 216 removed outlier: 4.113A pdb=" N GLU F 207 " --> pdb=" O THR F 203 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 232 removed outlier: 3.657A pdb=" N SER F 232 " --> pdb=" O ALA F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 256 removed outlier: 3.528A pdb=" N PHE F 255 " --> pdb=" O ASN F 252 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG F 256 " --> pdb=" O GLU F 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 252 through 256' Processing helix chain 'F' and resid 258 through 262 Processing helix chain 'F' and resid 264 through 267 Processing helix chain 'F' and resid 274 through 284 removed outlier: 3.576A pdb=" N TYR F 279 " --> pdb=" O HIS F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 296 removed outlier: 3.860A pdb=" N ARG F 290 " --> pdb=" O ILE F 287 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N LYS F 291 " --> pdb=" O ASP F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 305 Processing helix chain 'F' and resid 309 through 320 Processing helix chain 'F' and resid 338 through 348 Processing helix chain 'F' and resid 351 through 354 removed outlier: 4.089A pdb=" N GLN F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 351 through 354' Processing helix chain 'F' and resid 359 through 371 Proline residue: F 367 - end of helix removed outlier: 5.313A pdb=" N VAL F 370 " --> pdb=" O GLY F 366 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N HIS F 371 " --> pdb=" O PRO F 367 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 209 removed outlier: 4.788A pdb=" N GLN O 93 " --> pdb=" O ASN O 89 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LEU O 94 " --> pdb=" O ARG O 90 " (cutoff:3.500A) Processing helix chain 'P' and resid 46 through 209 removed outlier: 3.604A pdb=" N ARG P 178 " --> pdb=" O SER P 174 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA P 209 " --> pdb=" O LYS P 205 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'M' and resid 49 through 51 Processing sheet with id= B, first strand: chain 'M' and resid 115 through 118 removed outlier: 10.258A pdb=" N CYS M 122 " --> pdb=" O PRO M 667 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N PHE M 669 " --> pdb=" O CYS M 122 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N THR M 124 " --> pdb=" O PHE M 669 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ARG M 671 " --> pdb=" O THR M 124 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN M 172 " --> pdb=" O PHE M 456 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE M 462 " --> pdb=" O ILE M 176 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N PHE M 252 " --> pdb=" O GLN M 454 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N PHE M 456 " --> pdb=" O ILE M 250 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE M 250 " --> pdb=" O PHE M 456 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLY M 458 " --> pdb=" O ILE M 248 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE M 248 " --> pdb=" O GLY M 458 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER M 260 " --> pdb=" O HIS M 251 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'M' and resid 364 through 366 Processing sheet with id= D, first strand: chain 'M' and resid 403 through 406 Processing sheet with id= E, first strand: chain 'M' and resid 577 through 581 removed outlier: 3.924A pdb=" N PHE M 577 " --> pdb=" O TYR M 588 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'M' and resid 711 through 714 removed outlier: 3.991A pdb=" N ASN M 711 " --> pdb=" O PHE M 765 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 29 through 31 removed outlier: 7.199A pdb=" N CYS B 10 " --> pdb=" O PRO B 102 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N LEU B 104 " --> pdb=" O CYS B 10 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 35 through 38 Processing sheet with id= I, first strand: chain 'B' and resid 298 through 300 removed outlier: 3.501A pdb=" N VAL B 152 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS B 161 " --> pdb=" O ASP B 154 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 238 through 240 Processing sheet with id= K, first strand: chain 'C' and resid 8 through 11 Processing sheet with id= L, first strand: chain 'C' and resid 52 through 54 removed outlier: 3.514A pdb=" N VAL C 35 " --> pdb=" O LYS C 68 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 103 through 107 Processing sheet with id= N, first strand: chain 'C' and resid 298 through 300 removed outlier: 3.537A pdb=" N ILE C 165 " --> pdb=" O GLY C 150 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL C 152 " --> pdb=" O VAL C 163 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 238 through 240 Processing sheet with id= P, first strand: chain 'D' and resid 132 through 136 removed outlier: 6.650A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 34 through 38 Processing sheet with id= R, first strand: chain 'D' and resid 298 through 300 removed outlier: 3.617A pdb=" N SER D 155 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS D 161 " --> pdb=" O ASP D 154 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 238 through 240 Processing sheet with id= T, first strand: chain 'E' and resid 8 through 11 Processing sheet with id= U, first strand: chain 'E' and resid 35 through 38 removed outlier: 3.574A pdb=" N ARG E 37 " --> pdb=" O THR E 66 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 103 through 107 Processing sheet with id= W, first strand: chain 'E' and resid 297 through 300 removed outlier: 6.194A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL E 152 " --> pdb=" O VAL E 163 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N HIS E 161 " --> pdb=" O ASP E 154 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 238 through 240 Processing sheet with id= Y, first strand: chain 'F' and resid 132 through 136 removed outlier: 6.734A pdb=" N THR F 103 " --> pdb=" O TYR F 133 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N ALA F 135 " --> pdb=" O THR F 103 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU F 105 " --> pdb=" O ALA F 135 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 35 through 38 removed outlier: 3.694A pdb=" N ARG F 37 " --> pdb=" O THR F 66 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 298 through 300 Processing sheet with id= AB, first strand: chain 'F' and resid 238 through 240 1087 hydrogen bonds defined for protein. 3006 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.16 Time building geometry restraints manager: 10.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5937 1.33 - 1.45: 4217 1.45 - 1.57: 13297 1.57 - 1.69: 15 1.69 - 1.81: 241 Bond restraints: 23707 Sorted by residual: bond pdb=" C ALA M 13 " pdb=" N PRO M 14 " ideal model delta sigma weight residual 1.335 1.362 -0.027 1.38e-02 5.25e+03 3.83e+00 bond pdb=" CG GLN P 103 " pdb=" CD GLN P 103 " ideal model delta sigma weight residual 1.516 1.483 0.033 2.50e-02 1.60e+03 1.76e+00 bond pdb=" C4 ADP F 401 " pdb=" C5 ADP F 401 " ideal model delta sigma weight residual 1.490 1.467 0.023 2.00e-02 2.50e+03 1.27e+00 bond pdb=" CG1 ILE B 212 " pdb=" CD1 ILE B 212 " ideal model delta sigma weight residual 1.513 1.470 0.043 3.90e-02 6.57e+02 1.19e+00 bond pdb=" C4 ADP C 401 " pdb=" C5 ADP C 401 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.17e+00 ... (remaining 23702 not shown) Histogram of bond angle deviations from ideal: 99.02 - 106.47: 695 106.47 - 113.93: 13443 113.93 - 121.38: 12321 121.38 - 128.83: 5456 128.83 - 136.28: 132 Bond angle restraints: 32047 Sorted by residual: angle pdb=" C GLU O 104 " pdb=" N ARG O 105 " pdb=" CA ARG O 105 " ideal model delta sigma weight residual 121.58 113.14 8.44 1.95e+00 2.63e-01 1.87e+01 angle pdb=" C ASP P 100 " pdb=" N ARG P 101 " pdb=" CA ARG P 101 " ideal model delta sigma weight residual 121.58 113.56 8.02 1.95e+00 2.63e-01 1.69e+01 angle pdb=" N GLN P 111 " pdb=" CA GLN P 111 " pdb=" CB GLN P 111 " ideal model delta sigma weight residual 110.28 116.16 -5.88 1.55e+00 4.16e-01 1.44e+01 angle pdb=" C GLU P 124 " pdb=" N ARG P 125 " pdb=" CA ARG P 125 " ideal model delta sigma weight residual 120.68 114.43 6.25 1.70e+00 3.46e-01 1.35e+01 angle pdb=" CA ARG O 105 " pdb=" CB ARG O 105 " pdb=" CG ARG O 105 " ideal model delta sigma weight residual 114.10 121.30 -7.20 2.00e+00 2.50e-01 1.30e+01 ... (remaining 32042 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.04: 13569 23.04 - 46.08: 727 46.08 - 69.11: 93 69.11 - 92.15: 38 92.15 - 115.19: 2 Dihedral angle restraints: 14429 sinusoidal: 5922 harmonic: 8507 Sorted by residual: dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 55.19 -115.19 1 2.00e+01 2.50e-03 3.42e+01 dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 -172.06 112.05 1 2.00e+01 2.50e-03 3.30e+01 dihedral pdb=" C5' ADP E 401 " pdb=" O5' ADP E 401 " pdb=" PA ADP E 401 " pdb=" O2A ADP E 401 " ideal model delta sinusoidal sigma weight residual -60.00 20.96 -80.96 1 2.00e+01 2.50e-03 2.02e+01 ... (remaining 14426 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2663 0.043 - 0.086: 640 0.086 - 0.129: 230 0.129 - 0.172: 10 0.172 - 0.215: 1 Chirality restraints: 3544 Sorted by residual: chirality pdb=" CA ARG O 105 " pdb=" N ARG O 105 " pdb=" C ARG O 105 " pdb=" CB ARG O 105 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB ILE O 92 " pdb=" CA ILE O 92 " pdb=" CG1 ILE O 92 " pdb=" CG2 ILE O 92 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.39e-01 chirality pdb=" CG LEU P 176 " pdb=" CB LEU P 176 " pdb=" CD1 LEU P 176 " pdb=" CD2 LEU P 176 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.51e-01 ... (remaining 3541 not shown) Planarity restraints: 4130 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN D 111 " 0.034 5.00e-02 4.00e+02 5.16e-02 4.26e+00 pdb=" N PRO D 112 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO D 112 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 112 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL M 39 " 0.028 5.00e-02 4.00e+02 4.29e-02 2.94e+00 pdb=" N PRO M 40 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO M 40 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO M 40 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN P 68 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.56e+00 pdb=" C GLN P 68 " -0.028 2.00e-02 2.50e+03 pdb=" O GLN P 68 " 0.010 2.00e-02 2.50e+03 pdb=" N GLU P 69 " 0.009 2.00e-02 2.50e+03 ... (remaining 4127 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 218 2.63 - 3.20: 21072 3.20 - 3.77: 35592 3.77 - 4.33: 47584 4.33 - 4.90: 79847 Nonbonded interactions: 184313 Sorted by model distance: nonbonded pdb=" O1B ADP F 401 " pdb="MG MG F 402 " model vdw 2.065 2.170 nonbonded pdb=" O LYS P 140 " pdb=" NE2 GLN P 144 " model vdw 2.188 2.520 nonbonded pdb=" O LYS O 149 " pdb=" ND1 HIS O 153 " model vdw 2.234 2.520 nonbonded pdb=" O LEU O 64 " pdb=" NE2 GLN O 68 " model vdw 2.245 2.520 nonbonded pdb=" O THR E 304 " pdb=" NH1 ARG E 335 " model vdw 2.270 2.520 ... (remaining 184308 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'O' selection = chain 'P' } 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 138 5.16 5 C 14666 2.51 5 N 3946 2.21 5 O 4491 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 19.880 Check model and map are aligned: 0.330 Convert atoms to be neutral: 0.210 Process input model: 61.040 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.170 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: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 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 : 0.003 0.043 23707 Z= 0.193 Angle : 0.575 8.703 32047 Z= 0.303 Chirality : 0.042 0.215 3544 Planarity : 0.004 0.052 4130 Dihedral : 14.289 115.189 8955 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 0.04 % 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: 1.40 (0.16), residues: 2907 helix: 1.71 (0.15), residues: 1350 sheet: 0.44 (0.28), residues: 390 loop : 0.32 (0.20), residues: 1167 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 154 time to evaluate : 2.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 154 average time/residue: 0.3718 time to fit residues: 88.9567 Evaluate side-chains 134 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 2.965 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 245 optimal weight: 1.9990 chunk 220 optimal weight: 0.2980 chunk 122 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 chunk 117 optimal weight: 6.9990 chunk 228 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 169 optimal weight: 7.9990 chunk 264 optimal weight: 0.9980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 161 HIS F 225 ASN ** O 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.0727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 23707 Z= 0.248 Angle : 0.559 8.305 32047 Z= 0.282 Chirality : 0.043 0.154 3544 Planarity : 0.004 0.044 4130 Dihedral : 5.252 102.316 3236 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer Outliers : 0.36 % 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: 1.37 (0.16), residues: 2907 helix: 1.77 (0.15), residues: 1363 sheet: 0.25 (0.27), residues: 407 loop : 0.22 (0.20), residues: 1137 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 145 time to evaluate : 2.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 150 average time/residue: 0.3849 time to fit residues: 90.3191 Evaluate side-chains 140 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 136 time to evaluate : 2.754 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2379 time to fit residues: 5.9860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 146 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 219 optimal weight: 0.5980 chunk 179 optimal weight: 0.9980 chunk 72 optimal weight: 30.0000 chunk 264 optimal weight: 8.9990 chunk 285 optimal weight: 5.9990 chunk 235 optimal weight: 0.9980 chunk 262 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 623 ASN ** M 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 HIS ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 275 HIS ** O 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 23707 Z= 0.210 Angle : 0.538 8.952 32047 Z= 0.270 Chirality : 0.042 0.169 3544 Planarity : 0.003 0.039 4130 Dihedral : 5.090 96.471 3236 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer Outliers : 0.52 % 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: 1.39 (0.16), residues: 2907 helix: 1.79 (0.15), residues: 1362 sheet: 0.32 (0.27), residues: 407 loop : 0.19 (0.19), residues: 1138 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 145 time to evaluate : 3.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 154 average time/residue: 0.3771 time to fit residues: 91.1890 Evaluate side-chains 141 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 134 time to evaluate : 3.161 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2441 time to fit residues: 7.3499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 261 optimal weight: 5.9990 chunk 199 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 29 optimal weight: 9.9990 chunk 126 optimal weight: 2.9990 chunk 177 optimal weight: 7.9990 chunk 265 optimal weight: 20.0000 chunk 281 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 chunk 251 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN ** O 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 135 GLN ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 68 GLN ** P 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 23707 Z= 0.234 Angle : 0.551 9.297 32047 Z= 0.276 Chirality : 0.042 0.176 3544 Planarity : 0.004 0.044 4130 Dihedral : 4.980 87.891 3236 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer Outliers : 0.56 % 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: 1.34 (0.16), residues: 2907 helix: 1.77 (0.15), residues: 1364 sheet: 0.28 (0.27), residues: 408 loop : 0.16 (0.19), residues: 1135 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 142 time to evaluate : 3.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 153 average time/residue: 0.3860 time to fit residues: 91.6262 Evaluate side-chains 144 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 136 time to evaluate : 2.952 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2234 time to fit residues: 7.0767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 234 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 chunk 4 optimal weight: 40.0000 chunk 209 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 chunk 240 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 chunk 0 optimal weight: 40.0000 chunk 143 optimal weight: 0.0770 chunk 252 optimal weight: 0.9980 chunk 70 optimal weight: 30.0000 overall best weight: 2.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 353 GLN ** O 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 23707 Z= 0.254 Angle : 0.565 10.279 32047 Z= 0.283 Chirality : 0.043 0.194 3544 Planarity : 0.004 0.046 4130 Dihedral : 4.880 72.844 3236 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer Outliers : 0.56 % 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: 1.29 (0.16), residues: 2907 helix: 1.75 (0.15), residues: 1376 sheet: 0.24 (0.27), residues: 410 loop : 0.09 (0.20), residues: 1121 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 141 time to evaluate : 3.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 153 average time/residue: 0.3867 time to fit residues: 93.1278 Evaluate side-chains 142 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 134 time to evaluate : 3.198 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2164 time to fit residues: 7.2546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 94 optimal weight: 3.9990 chunk 253 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 165 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 chunk 281 optimal weight: 5.9990 chunk 233 optimal weight: 0.6980 chunk 130 optimal weight: 6.9990 chunk 23 optimal weight: 20.0000 chunk 93 optimal weight: 5.9990 chunk 147 optimal weight: 0.0870 overall best weight: 2.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 GLN ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 23707 Z= 0.250 Angle : 0.560 10.345 32047 Z= 0.281 Chirality : 0.042 0.184 3544 Planarity : 0.004 0.068 4130 Dihedral : 4.782 57.909 3236 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.16), residues: 2907 helix: 1.76 (0.15), residues: 1371 sheet: 0.26 (0.27), residues: 410 loop : 0.12 (0.20), residues: 1126 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 138 time to evaluate : 3.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 5 residues processed: 153 average time/residue: 0.4030 time to fit residues: 95.4774 Evaluate side-chains 138 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 133 time to evaluate : 2.773 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2382 time to fit residues: 5.7555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 271 optimal weight: 8.9990 chunk 31 optimal weight: 20.0000 chunk 160 optimal weight: 4.9990 chunk 205 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 237 optimal weight: 7.9990 chunk 157 optimal weight: 0.0370 chunk 280 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 overall best weight: 1.3662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 GLN ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 23707 Z= 0.182 Angle : 0.548 11.615 32047 Z= 0.275 Chirality : 0.042 0.197 3544 Planarity : 0.004 0.055 4130 Dihedral : 4.655 58.478 3236 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer Outliers : 0.28 % 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: 1.40 (0.16), residues: 2907 helix: 1.82 (0.15), residues: 1371 sheet: 0.29 (0.27), residues: 410 loop : 0.17 (0.20), residues: 1126 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 137 time to evaluate : 2.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 143 average time/residue: 0.3916 time to fit residues: 87.0297 Evaluate side-chains 137 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 133 time to evaluate : 2.883 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.4619 time to fit residues: 6.5661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 173 optimal weight: 0.0060 chunk 112 optimal weight: 0.0870 chunk 167 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 chunk 178 optimal weight: 0.9990 chunk 191 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 220 optimal weight: 6.9990 overall best weight: 1.2180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 23707 Z= 0.169 Angle : 0.539 11.390 32047 Z= 0.270 Chirality : 0.041 0.197 3544 Planarity : 0.004 0.070 4130 Dihedral : 4.575 55.817 3236 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % 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: 1.42 (0.16), residues: 2907 helix: 1.83 (0.15), residues: 1371 sheet: 0.31 (0.27), residues: 410 loop : 0.18 (0.20), residues: 1126 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 136 time to evaluate : 3.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 139 average time/residue: 0.3922 time to fit residues: 84.6989 Evaluate side-chains 137 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 135 time to evaluate : 2.800 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1982 time to fit residues: 4.3841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 255 optimal weight: 5.9990 chunk 268 optimal weight: 7.9990 chunk 245 optimal weight: 1.9990 chunk 261 optimal weight: 8.9990 chunk 157 optimal weight: 5.9990 chunk 113 optimal weight: 0.8980 chunk 205 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 236 optimal weight: 3.9990 chunk 247 optimal weight: 2.9990 chunk 260 optimal weight: 6.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 23707 Z= 0.199 Angle : 0.562 11.787 32047 Z= 0.281 Chirality : 0.042 0.240 3544 Planarity : 0.004 0.089 4130 Dihedral : 4.574 51.131 3236 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.16), residues: 2907 helix: 1.79 (0.15), residues: 1369 sheet: 0.31 (0.27), residues: 410 loop : 0.18 (0.20), residues: 1128 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 140 time to evaluate : 2.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 143 average time/residue: 0.3919 time to fit residues: 86.8693 Evaluate side-chains 136 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 134 time to evaluate : 2.766 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2263 time to fit residues: 4.5594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 171 optimal weight: 0.9990 chunk 276 optimal weight: 8.9990 chunk 168 optimal weight: 0.8980 chunk 131 optimal weight: 0.9990 chunk 192 optimal weight: 2.9990 chunk 289 optimal weight: 0.8980 chunk 266 optimal weight: 3.9990 chunk 230 optimal weight: 0.0870 chunk 23 optimal weight: 3.9990 chunk 178 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 HIS ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 23707 Z= 0.143 Angle : 0.549 11.924 32047 Z= 0.275 Chirality : 0.041 0.242 3544 Planarity : 0.004 0.082 4130 Dihedral : 4.431 46.829 3236 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer Outliers : 0.04 % 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: 1.47 (0.16), residues: 2907 helix: 1.84 (0.15), residues: 1368 sheet: 0.39 (0.27), residues: 408 loop : 0.25 (0.20), residues: 1131 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 135 time to evaluate : 2.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 135 average time/residue: 0.4184 time to fit residues: 87.8077 Evaluate side-chains 136 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 135 time to evaluate : 2.906 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2729 time to fit residues: 4.2829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 183 optimal weight: 1.9990 chunk 245 optimal weight: 0.0470 chunk 70 optimal weight: 30.0000 chunk 212 optimal weight: 0.9990 chunk 34 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 231 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 237 optimal weight: 0.9980 chunk 29 optimal weight: 0.0070 chunk 42 optimal weight: 8.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.077354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.048762 restraints weight = 77371.391| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.52 r_work: 0.2763 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.050 23707 Z= 0.136 Angle : 0.548 11.923 32047 Z= 0.274 Chirality : 0.041 0.242 3544 Planarity : 0.003 0.065 4130 Dihedral : 4.321 41.879 3236 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer Outliers : 0.04 % 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: 1.53 (0.16), residues: 2907 helix: 1.86 (0.15), residues: 1368 sheet: 0.39 (0.27), residues: 418 loop : 0.33 (0.20), residues: 1121 =============================================================================== Job complete usr+sys time: 4203.06 seconds wall clock time: 77 minutes 42.95 seconds (4662.95 seconds total)