Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 09:33:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x16_21990/04_2023/6x16_21990_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x16_21990/04_2023/6x16_21990.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x16_21990/04_2023/6x16_21990.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x16_21990/04_2023/6x16_21990.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x16_21990/04_2023/6x16_21990_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x16_21990/04_2023/6x16_21990_updated.pdb" } resolution = 3.39 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= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 54 5.16 5 C 6222 2.51 5 N 1503 2.21 5 O 1656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 48": "OD1" <-> "OD2" Residue "B PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B GLU 181": "OE1" <-> "OE2" Residue "B ASP 185": "OD1" <-> "OD2" Residue "B TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 257": "OD1" <-> "OD2" Residue "B ASP 267": "OD1" <-> "OD2" Residue "B PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 291": "OE1" <-> "OE2" Residue "B PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 394": "OD1" <-> "OD2" Residue "A ASP 48": "OD1" <-> "OD2" Residue "A PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 172": "OE1" <-> "OE2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A ASP 185": "OD1" <-> "OD2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 257": "OD1" <-> "OD2" Residue "A ASP 267": "OD1" <-> "OD2" Residue "A PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 291": "OE1" <-> "OE2" Residue "A PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 394": "OD1" <-> "OD2" Residue "C ASP 48": "OD1" <-> "OD2" Residue "C PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 172": "OE1" <-> "OE2" Residue "C GLU 181": "OE1" <-> "OE2" Residue "C ASP 185": "OD1" <-> "OD2" Residue "C TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 257": "OD1" <-> "OD2" Residue "C ASP 267": "OD1" <-> "OD2" Residue "C PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 291": "OE1" <-> "OE2" Residue "C PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 394": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 9438 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 3087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3087 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 18, 'TRANS': 397} Chain: "A" Number of atoms: 3087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3087 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 18, 'TRANS': 397} Chain: "C" Number of atoms: 3087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3087 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 18, 'TRANS': 397} Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'6OU': 1, 'TB1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'6OU': 1, 'TB1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "C" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'6OU': 1, 'TB1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Time building chain proxies: 5.91, per 1000 atoms: 0.63 Number of scatterers: 9438 At special positions: 0 Unit cell: (110.545, 109.472, 74.0543, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 54 16.00 P 3 15.00 O 1656 8.00 N 1503 7.00 C 6222 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: 3.94 Conformation dependent library (CDL) restraints added in 1.6 seconds 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2238 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 0 sheets defined 75.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'B' and resid 3 through 9 Processing helix chain 'B' and resid 12 through 32 Processing helix chain 'B' and resid 36 through 72 Proline residue: B 45 - end of helix removed outlier: 4.716A pdb=" N MET B 59 " --> pdb=" O CYS B 55 " (cutoff:3.500A) Proline residue: B 60 - end of helix Processing helix chain 'B' and resid 80 through 106 removed outlier: 3.808A pdb=" N TYR B 88 " --> pdb=" O LYS B 84 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 136 Processing helix chain 'B' and resid 142 through 147 Processing helix chain 'B' and resid 151 through 170 removed outlier: 4.016A pdb=" N ASN B 170 " --> pdb=" O THR B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 219 Proline residue: B 206 - end of helix Processing helix chain 'B' and resid 222 through 253 removed outlier: 4.248A pdb=" N GLY B 226 " --> pdb=" O HIS B 223 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL B 237 " --> pdb=" O ALA B 234 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 241 " --> pdb=" O GLY B 238 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 244 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU B 245 " --> pdb=" O GLN B 242 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL B 246 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TYR B 247 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE B 248 " --> pdb=" O LEU B 245 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL B 249 " --> pdb=" O VAL B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 274 removed outlier: 3.986A pdb=" N LYS B 266 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ASP B 267 " --> pdb=" O LYS B 263 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ALA B 268 " --> pdb=" O HIS B 264 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA B 272 " --> pdb=" O ALA B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 292 removed outlier: 3.539A pdb=" N MET B 292 " --> pdb=" O VAL B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 299 No H-bonds generated for 'chain 'B' and resid 296 through 299' Processing helix chain 'B' and resid 302 through 309 removed outlier: 3.902A pdb=" N THR B 308 " --> pdb=" O PRO B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 329 removed outlier: 4.042A pdb=" N PHE B 323 " --> pdb=" O GLY B 319 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA B 326 " --> pdb=" O THR B 322 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU B 329 " --> pdb=" O ILE B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 346 Processing helix chain 'B' and resid 359 through 370 removed outlier: 3.677A pdb=" N CYS B 364 " --> pdb=" O ALA B 360 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER B 369 " --> pdb=" O MET B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 387 removed outlier: 3.648A pdb=" N ALA B 384 " --> pdb=" O ALA B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 415 removed outlier: 3.943A pdb=" N MET B 395 " --> pdb=" O ALA B 391 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N GLY B 396 " --> pdb=" O ILE B 392 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N MET B 399 " --> pdb=" O MET B 395 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL B 400 " --> pdb=" O GLY B 396 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASN B 401 " --> pdb=" O ARG B 397 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASP B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 406 " --> pdb=" O VAL B 402 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR B 415 " --> pdb=" O ILE B 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 3 through 9 Processing helix chain 'A' and resid 12 through 32 Processing helix chain 'A' and resid 36 through 72 Proline residue: A 45 - end of helix removed outlier: 4.716A pdb=" N MET A 59 " --> pdb=" O CYS A 55 " (cutoff:3.500A) Proline residue: A 60 - end of helix Processing helix chain 'A' and resid 80 through 106 removed outlier: 3.808A pdb=" N TYR A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 136 Processing helix chain 'A' and resid 142 through 147 Processing helix chain 'A' and resid 151 through 170 removed outlier: 4.015A pdb=" N ASN A 170 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 219 Proline residue: A 206 - end of helix Processing helix chain 'A' and resid 222 through 253 removed outlier: 4.248A pdb=" N GLY A 226 " --> pdb=" O HIS A 223 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL A 237 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A 241 " --> pdb=" O GLY A 238 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 244 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU A 245 " --> pdb=" O GLN A 242 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL A 246 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TYR A 247 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE A 248 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A 249 " --> pdb=" O VAL A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 274 removed outlier: 3.987A pdb=" N LYS A 266 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ASP A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ALA A 268 " --> pdb=" O HIS A 264 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA A 272 " --> pdb=" O ALA A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 292 removed outlier: 3.539A pdb=" N MET A 292 " --> pdb=" O VAL A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 299 No H-bonds generated for 'chain 'A' and resid 296 through 299' Processing helix chain 'A' and resid 302 through 309 removed outlier: 3.901A pdb=" N THR A 308 " --> pdb=" O PRO A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 329 removed outlier: 4.041A pdb=" N PHE A 323 " --> pdb=" O GLY A 319 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA A 326 " --> pdb=" O THR A 322 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU A 329 " --> pdb=" O ILE A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 346 Processing helix chain 'A' and resid 359 through 370 removed outlier: 3.677A pdb=" N CYS A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER A 369 " --> pdb=" O MET A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 387 removed outlier: 3.648A pdb=" N ALA A 384 " --> pdb=" O ALA A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 415 removed outlier: 3.943A pdb=" N MET A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N GLY A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N MET A 399 " --> pdb=" O MET A 395 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL A 400 " --> pdb=" O GLY A 396 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASN A 401 " --> pdb=" O ARG A 397 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 406 " --> pdb=" O VAL A 402 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR A 415 " --> pdb=" O ILE A 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 9 Processing helix chain 'C' and resid 12 through 32 Processing helix chain 'C' and resid 36 through 72 Proline residue: C 45 - end of helix removed outlier: 4.716A pdb=" N MET C 59 " --> pdb=" O CYS C 55 " (cutoff:3.500A) Proline residue: C 60 - end of helix Processing helix chain 'C' and resid 80 through 106 removed outlier: 3.808A pdb=" N TYR C 88 " --> pdb=" O LYS C 84 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE C 95 " --> pdb=" O LEU C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 136 Processing helix chain 'C' and resid 142 through 147 Processing helix chain 'C' and resid 151 through 170 removed outlier: 4.016A pdb=" N ASN C 170 " --> pdb=" O THR C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 219 Proline residue: C 206 - end of helix Processing helix chain 'C' and resid 222 through 253 removed outlier: 4.249A pdb=" N GLY C 226 " --> pdb=" O HIS C 223 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL C 237 " --> pdb=" O ALA C 234 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU C 241 " --> pdb=" O GLY C 238 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU C 244 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU C 245 " --> pdb=" O GLN C 242 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL C 246 " --> pdb=" O ILE C 243 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TYR C 247 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE C 248 " --> pdb=" O LEU C 245 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL C 249 " --> pdb=" O VAL C 246 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU C 250 " --> pdb=" O TYR C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 274 removed outlier: 3.987A pdb=" N LYS C 266 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ASP C 267 " --> pdb=" O LYS C 263 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ALA C 268 " --> pdb=" O HIS C 264 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA C 272 " --> pdb=" O ALA C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 292 removed outlier: 3.538A pdb=" N MET C 292 " --> pdb=" O VAL C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 299 No H-bonds generated for 'chain 'C' and resid 296 through 299' Processing helix chain 'C' and resid 302 through 309 removed outlier: 3.902A pdb=" N THR C 308 " --> pdb=" O PRO C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 329 removed outlier: 4.042A pdb=" N PHE C 323 " --> pdb=" O GLY C 319 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA C 326 " --> pdb=" O THR C 322 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU C 329 " --> pdb=" O ILE C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 346 Processing helix chain 'C' and resid 359 through 370 removed outlier: 3.676A pdb=" N CYS C 364 " --> pdb=" O ALA C 360 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER C 369 " --> pdb=" O MET C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 387 removed outlier: 3.648A pdb=" N ALA C 384 " --> pdb=" O ALA C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 415 removed outlier: 3.943A pdb=" N MET C 395 " --> pdb=" O ALA C 391 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N GLY C 396 " --> pdb=" O ILE C 392 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N MET C 399 " --> pdb=" O MET C 395 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL C 400 " --> pdb=" O GLY C 396 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN C 401 " --> pdb=" O ARG C 397 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASP C 405 " --> pdb=" O ASN C 401 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU C 406 " --> pdb=" O VAL C 402 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR C 415 " --> pdb=" O ILE C 411 " (cutoff:3.500A) 602 hydrogen bonds defined for protein. 1629 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: 2.40 Time building geometry restraints manager: 4.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1455 1.31 - 1.43: 2347 1.43 - 1.56: 5669 1.56 - 1.68: 45 1.68 - 1.80: 102 Bond restraints: 9618 Sorted by residual: bond pdb=" C16 6OU A 501 " pdb=" O18 6OU A 501 " ideal model delta sigma weight residual 1.327 1.414 -0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" C16 6OU C 501 " pdb=" O18 6OU C 501 " ideal model delta sigma weight residual 1.327 1.413 -0.086 2.00e-02 2.50e+03 1.87e+01 bond pdb=" C16 6OU B 501 " pdb=" O18 6OU B 501 " ideal model delta sigma weight residual 1.327 1.413 -0.086 2.00e-02 2.50e+03 1.87e+01 bond pdb=" C31 6OU B 501 " pdb=" O30 6OU B 501 " ideal model delta sigma weight residual 1.331 1.408 -0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" C31 6OU C 501 " pdb=" O30 6OU C 501 " ideal model delta sigma weight residual 1.331 1.408 -0.077 2.00e-02 2.50e+03 1.48e+01 ... (remaining 9613 not shown) Histogram of bond angle deviations from ideal: 99.43 - 105.92: 255 105.92 - 112.41: 4980 112.41 - 118.90: 2789 118.90 - 125.38: 4969 125.38 - 131.87: 90 Bond angle restraints: 13083 Sorted by residual: angle pdb=" O22 6OU C 501 " pdb=" P23 6OU C 501 " pdb=" O26 6OU C 501 " ideal model delta sigma weight residual 93.95 109.51 -15.56 3.00e+00 1.11e-01 2.69e+01 angle pdb=" O22 6OU B 501 " pdb=" P23 6OU B 501 " pdb=" O26 6OU B 501 " ideal model delta sigma weight residual 93.95 109.49 -15.54 3.00e+00 1.11e-01 2.68e+01 angle pdb=" O22 6OU A 501 " pdb=" P23 6OU A 501 " pdb=" O26 6OU A 501 " ideal model delta sigma weight residual 93.95 109.49 -15.54 3.00e+00 1.11e-01 2.68e+01 angle pdb=" N ALA A 205 " pdb=" CA ALA A 205 " pdb=" C ALA A 205 " ideal model delta sigma weight residual 109.81 121.12 -11.31 2.21e+00 2.05e-01 2.62e+01 angle pdb=" N ALA B 205 " pdb=" CA ALA B 205 " pdb=" C ALA B 205 " ideal model delta sigma weight residual 109.81 121.07 -11.26 2.21e+00 2.05e-01 2.59e+01 ... (remaining 13078 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.99: 5028 16.99 - 33.97: 468 33.97 - 50.96: 96 50.96 - 67.95: 18 67.95 - 84.93: 15 Dihedral angle restraints: 5625 sinusoidal: 2088 harmonic: 3537 Sorted by residual: dihedral pdb=" CA VAL B 58 " pdb=" C VAL B 58 " pdb=" N MET B 59 " pdb=" CA MET B 59 " ideal model delta harmonic sigma weight residual -180.00 -160.87 -19.13 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA VAL C 58 " pdb=" C VAL C 58 " pdb=" N MET C 59 " pdb=" CA MET C 59 " ideal model delta harmonic sigma weight residual -180.00 -160.90 -19.10 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA VAL A 58 " pdb=" C VAL A 58 " pdb=" N MET A 59 " pdb=" CA MET A 59 " ideal model delta harmonic sigma weight residual -180.00 -160.91 -19.09 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 5622 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1093 0.039 - 0.079: 378 0.079 - 0.118: 99 0.118 - 0.157: 32 0.157 - 0.196: 18 Chirality restraints: 1620 Sorted by residual: chirality pdb=" C20 6OU C 501 " pdb=" C19 6OU C 501 " pdb=" C21 6OU C 501 " pdb=" O30 6OU C 501 " both_signs ideal model delta sigma weight residual False 2.35 2.54 -0.20 2.00e-01 2.50e+01 9.63e-01 chirality pdb=" C20 6OU B 501 " pdb=" C19 6OU B 501 " pdb=" C21 6OU B 501 " pdb=" O30 6OU B 501 " both_signs ideal model delta sigma weight residual False 2.35 2.54 -0.19 2.00e-01 2.50e+01 9.24e-01 chirality pdb=" C20 6OU A 501 " pdb=" C19 6OU A 501 " pdb=" C21 6OU A 501 " pdb=" O30 6OU A 501 " both_signs ideal model delta sigma weight residual False 2.35 2.54 -0.19 2.00e-01 2.50e+01 9.11e-01 ... (remaining 1617 not shown) Planarity restraints: 1605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 44 " 0.045 5.00e-02 4.00e+02 6.68e-02 7.13e+00 pdb=" N PRO A 45 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 45 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 45 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 44 " -0.045 5.00e-02 4.00e+02 6.67e-02 7.13e+00 pdb=" N PRO C 45 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO C 45 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 45 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 44 " 0.045 5.00e-02 4.00e+02 6.67e-02 7.12e+00 pdb=" N PRO B 45 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 45 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 45 " 0.037 5.00e-02 4.00e+02 ... (remaining 1602 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 3015 2.84 - 3.35: 9032 3.35 - 3.87: 15610 3.87 - 4.38: 17855 4.38 - 4.90: 31453 Nonbonded interactions: 76965 Sorted by model distance: nonbonded pdb=" OG SER A 65 " pdb=" OH TYR A 195 " model vdw 2.322 2.440 nonbonded pdb=" OG SER C 65 " pdb=" OH TYR C 195 " model vdw 2.322 2.440 nonbonded pdb=" OG SER B 65 " pdb=" OH TYR B 195 " model vdw 2.322 2.440 nonbonded pdb=" OG SER C 278 " pdb=" O3 TB1 C 502 " model vdw 2.323 2.440 nonbonded pdb=" OG SER B 278 " pdb=" O3 TB1 B 502 " model vdw 2.323 2.440 ... (remaining 76960 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.730 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 28.640 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 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 : 0.006 0.087 9618 Z= 0.418 Angle : 0.994 15.560 13083 Z= 0.481 Chirality : 0.047 0.196 1620 Planarity : 0.008 0.067 1605 Dihedral : 14.757 84.933 3387 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer Outliers : 0.31 % 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: -3.86 (0.18), residues: 1242 helix: -2.31 (0.12), residues: 1005 sheet: None (None), residues: 0 loop : -2.56 (0.34), residues: 237 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 78 time to evaluate : 0.981 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 81 average time/residue: 0.1722 time to fit residues: 21.9655 Evaluate side-chains 74 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.936 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.7980 chunk 93 optimal weight: 0.0870 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 111 optimal weight: 0.0040 overall best weight: 0.4370 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 GLN B 132 HIS ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 14 GLN A 132 HIS ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 GLN C 318 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 9618 Z= 0.158 Angle : 0.528 7.965 13083 Z= 0.271 Chirality : 0.036 0.120 1620 Planarity : 0.006 0.055 1605 Dihedral : 9.991 86.863 1410 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer Outliers : 0.93 % 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: -1.18 (0.22), residues: 1242 helix: -0.34 (0.16), residues: 996 sheet: None (None), residues: 0 loop : -2.08 (0.34), residues: 246 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 82 time to evaluate : 1.086 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 86 average time/residue: 0.1623 time to fit residues: 22.3859 Evaluate side-chains 83 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 1.000 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0866 time to fit residues: 2.3986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 92 optimal weight: 0.0770 chunk 76 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 111 optimal weight: 0.0970 chunk 120 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 chunk 38 optimal weight: 0.0470 chunk 89 optimal weight: 0.0870 overall best weight: 0.1812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 9618 Z= 0.123 Angle : 0.491 7.833 13083 Z= 0.247 Chirality : 0.035 0.118 1620 Planarity : 0.005 0.051 1605 Dihedral : 8.755 83.726 1410 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 0.62 % 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: -0.17 (0.23), residues: 1242 helix: 0.31 (0.16), residues: 999 sheet: None (None), residues: 0 loop : -1.50 (0.34), residues: 243 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 81 time to evaluate : 1.047 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 86 average time/residue: 0.1670 time to fit residues: 22.9148 Evaluate side-chains 81 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 78 time to evaluate : 1.023 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0980 time to fit residues: 2.0278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 GLN C 310 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 9618 Z= 0.220 Angle : 0.547 7.778 13083 Z= 0.273 Chirality : 0.037 0.123 1620 Planarity : 0.005 0.052 1605 Dihedral : 9.151 84.623 1410 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.23), residues: 1242 helix: 0.43 (0.16), residues: 1011 sheet: None (None), residues: 0 loop : -1.27 (0.35), residues: 231 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 0.909 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 84 average time/residue: 0.1687 time to fit residues: 23.0059 Evaluate side-chains 82 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 1.034 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1115 time to fit residues: 2.3542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 101 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 0 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 9618 Z= 0.190 Angle : 0.525 7.820 13083 Z= 0.262 Chirality : 0.037 0.123 1620 Planarity : 0.005 0.053 1605 Dihedral : 9.036 83.999 1410 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer Outliers : 0.41 % 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: 0.30 (0.24), residues: 1242 helix: 0.59 (0.17), residues: 1014 sheet: None (None), residues: 0 loop : -1.20 (0.35), residues: 228 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 0.944 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 80 average time/residue: 0.1688 time to fit residues: 21.3683 Evaluate side-chains 82 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 0.972 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0963 time to fit residues: 2.1088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 98 optimal weight: 0.3980 chunk 55 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 9618 Z= 0.186 Angle : 0.522 7.880 13083 Z= 0.261 Chirality : 0.037 0.121 1620 Planarity : 0.004 0.053 1605 Dihedral : 8.813 83.615 1410 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer Outliers : 0.10 % 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: 0.48 (0.23), residues: 1242 helix: 0.68 (0.16), residues: 1017 sheet: None (None), residues: 0 loop : -0.97 (0.35), residues: 225 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 1.053 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 77 average time/residue: 0.1731 time to fit residues: 21.3653 Evaluate side-chains 75 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 1.044 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 chunk 66 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 54 optimal weight: 0.4980 chunk 73 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 318 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 9618 Z= 0.180 Angle : 0.520 7.939 13083 Z= 0.259 Chirality : 0.037 0.121 1620 Planarity : 0.004 0.053 1605 Dihedral : 8.654 83.539 1410 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer Outliers : 0.72 % 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: 0.61 (0.23), residues: 1242 helix: 0.76 (0.16), residues: 1020 sheet: None (None), residues: 0 loop : -0.89 (0.36), residues: 222 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 79 time to evaluate : 0.993 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 79 average time/residue: 0.1818 time to fit residues: 23.0346 Evaluate side-chains 83 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 78 time to evaluate : 1.055 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0984 time to fit residues: 2.4423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 93 optimal weight: 0.3980 chunk 107 optimal weight: 5.9990 chunk 113 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 338 GLN C 338 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 9618 Z= 0.181 Angle : 0.528 7.974 13083 Z= 0.263 Chirality : 0.037 0.120 1620 Planarity : 0.004 0.053 1605 Dihedral : 8.632 84.077 1410 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.23), residues: 1242 helix: 0.81 (0.16), residues: 1020 sheet: None (None), residues: 0 loop : -0.84 (0.36), residues: 222 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 77 time to evaluate : 0.911 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 79 average time/residue: 0.1664 time to fit residues: 20.9311 Evaluate side-chains 78 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 1.029 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1198 time to fit residues: 1.6134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 116 optimal weight: 0.1980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 9618 Z= 0.197 Angle : 0.539 7.935 13083 Z= 0.267 Chirality : 0.037 0.122 1620 Planarity : 0.004 0.053 1605 Dihedral : 8.722 85.616 1410 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 0.10 % 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: 0.67 (0.24), residues: 1242 helix: 0.79 (0.16), residues: 1023 sheet: None (None), residues: 0 loop : -0.80 (0.37), residues: 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 76 time to evaluate : 0.992 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 77 average time/residue: 0.1685 time to fit residues: 20.8647 Evaluate side-chains 76 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 1.013 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 1.9990 chunk 55 optimal weight: 0.4980 chunk 81 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 112 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 9618 Z= 0.185 Angle : 0.534 8.084 13083 Z= 0.265 Chirality : 0.037 0.124 1620 Planarity : 0.004 0.053 1605 Dihedral : 8.569 87.234 1410 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer Outliers : 0.10 % 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: 0.69 (0.23), residues: 1242 helix: 0.80 (0.16), residues: 1023 sheet: None (None), residues: 0 loop : -0.79 (0.36), residues: 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 76 time to evaluate : 0.980 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 77 average time/residue: 0.1786 time to fit residues: 21.8835 Evaluate side-chains 76 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 1.198 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 2.9990 chunk 89 optimal weight: 0.0010 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 5 optimal weight: 0.4980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.139667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.106139 restraints weight = 10984.580| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.10 r_work: 0.2895 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 9618 Z= 0.168 Angle : 0.528 8.029 13083 Z= 0.262 Chirality : 0.037 0.128 1620 Planarity : 0.004 0.053 1605 Dihedral : 8.413 86.945 1410 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer Outliers : 0.10 % 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: 0.74 (0.23), residues: 1242 helix: 0.83 (0.16), residues: 1023 sheet: None (None), residues: 0 loop : -0.75 (0.36), residues: 219 =============================================================================== Job complete usr+sys time: 1770.71 seconds wall clock time: 33 minutes 4.00 seconds (1984.00 seconds total)