Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 15:59:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssz_25417/04_2023/7ssz_25417.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssz_25417/04_2023/7ssz_25417.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssz_25417/04_2023/7ssz_25417.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssz_25417/04_2023/7ssz_25417.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssz_25417/04_2023/7ssz_25417.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ssz_25417/04_2023/7ssz_25417.pdb" } resolution = 3.25 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= 0.003 sd= 0.062 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 K 3 8.98 5 S 60 5.16 5 C 9924 2.51 5 N 2564 2.21 5 O 2732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 135": "NH1" <-> "NH2" Residue "A GLU 146": "OE1" <-> "OE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A GLU 192": "OE1" <-> "OE2" Residue "A GLU 195": "OE1" <-> "OE2" Residue "A ARG 205": "NH1" <-> "NH2" Residue "A GLU 206": "OE1" <-> "OE2" Residue "A ARG 209": "NH1" <-> "NH2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A ARG 218": "NH1" <-> "NH2" Residue "A GLU 258": "OE1" <-> "OE2" Residue "A ARG 325": "NH1" <-> "NH2" Residue "A ARG 364": "NH1" <-> "NH2" Residue "A TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 490": "OE1" <-> "OE2" Residue "E ARG 32": "NH1" <-> "NH2" Residue "E ARG 39": "NH1" <-> "NH2" Residue "E ARG 46": "NH1" <-> "NH2" Residue "E ARG 51": "NH1" <-> "NH2" Residue "E ARG 53": "NH1" <-> "NH2" Residue "E ARG 72": "NH1" <-> "NH2" Residue "E ARG 100": "NH1" <-> "NH2" Residue "E GLU 105": "OE1" <-> "OE2" Residue "F ARG 32": "NH1" <-> "NH2" Residue "F ARG 39": "NH1" <-> "NH2" Residue "F ARG 46": "NH1" <-> "NH2" Residue "F ARG 51": "NH1" <-> "NH2" Residue "F ARG 53": "NH1" <-> "NH2" Residue "F ARG 72": "NH1" <-> "NH2" Residue "F ARG 100": "NH1" <-> "NH2" Residue "F GLU 105": "OE1" <-> "OE2" Residue "G ARG 32": "NH1" <-> "NH2" Residue "G ARG 39": "NH1" <-> "NH2" Residue "G ARG 46": "NH1" <-> "NH2" Residue "G ARG 51": "NH1" <-> "NH2" Residue "G ARG 53": "NH1" <-> "NH2" Residue "G ARG 72": "NH1" <-> "NH2" Residue "G ARG 100": "NH1" <-> "NH2" Residue "G GLU 105": "OE1" <-> "OE2" Residue "H ARG 32": "NH1" <-> "NH2" Residue "H ARG 39": "NH1" <-> "NH2" Residue "H ARG 46": "NH1" <-> "NH2" Residue "H ARG 51": "NH1" <-> "NH2" Residue "H ARG 53": "NH1" <-> "NH2" Residue "H ARG 72": "NH1" <-> "NH2" Residue "H ARG 100": "NH1" <-> "NH2" Residue "H GLU 105": "OE1" <-> "OE2" Residue "B ARG 135": "NH1" <-> "NH2" Residue "B GLU 146": "OE1" <-> "OE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B GLU 192": "OE1" <-> "OE2" Residue "B GLU 195": "OE1" <-> "OE2" Residue "B ARG 205": "NH1" <-> "NH2" Residue "B GLU 206": "OE1" <-> "OE2" Residue "B ARG 209": "NH1" <-> "NH2" Residue "B ARG 213": "NH1" <-> "NH2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B ARG 218": "NH1" <-> "NH2" Residue "B GLU 258": "OE1" <-> "OE2" Residue "B ARG 325": "NH1" <-> "NH2" Residue "B ARG 364": "NH1" <-> "NH2" Residue "B TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 490": "OE1" <-> "OE2" Residue "C ARG 135": "NH1" <-> "NH2" Residue "C GLU 146": "OE1" <-> "OE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C GLU 192": "OE1" <-> "OE2" Residue "C GLU 195": "OE1" <-> "OE2" Residue "C ARG 205": "NH1" <-> "NH2" Residue "C GLU 206": "OE1" <-> "OE2" Residue "C ARG 209": "NH1" <-> "NH2" Residue "C ARG 213": "NH1" <-> "NH2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C ARG 218": "NH1" <-> "NH2" Residue "C GLU 258": "OE1" <-> "OE2" Residue "C ARG 325": "NH1" <-> "NH2" Residue "C ARG 364": "NH1" <-> "NH2" Residue "C TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 490": "OE1" <-> "OE2" Residue "D ARG 135": "NH1" <-> "NH2" Residue "D GLU 146": "OE1" <-> "OE2" Residue "D GLU 191": "OE1" <-> "OE2" Residue "D GLU 192": "OE1" <-> "OE2" Residue "D GLU 195": "OE1" <-> "OE2" Residue "D ARG 205": "NH1" <-> "NH2" Residue "D GLU 206": "OE1" <-> "OE2" Residue "D ARG 209": "NH1" <-> "NH2" Residue "D ARG 213": "NH1" <-> "NH2" Residue "D ARG 214": "NH1" <-> "NH2" Residue "D ARG 218": "NH1" <-> "NH2" Residue "D GLU 258": "OE1" <-> "OE2" Residue "D ARG 325": "NH1" <-> "NH2" Residue "D ARG 364": "NH1" <-> "NH2" Residue "D TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 490": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 15283 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2935 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 20, 'TRANS': 341} Chain breaks: 2 Chain: "E" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 885 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "F" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 885 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "G" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 885 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "H" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 885 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "B" Number of atoms: 2935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2935 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 20, 'TRANS': 341} Chain breaks: 2 Chain: "C" Number of atoms: 2935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2935 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 20, 'TRANS': 341} Chain breaks: 2 Chain: "D" Number of atoms: 2935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2935 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 20, 'TRANS': 341} Chain breaks: 2 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 8.17, per 1000 atoms: 0.53 Number of scatterers: 15283 At special positions: 0 Unit cell: (120.132, 120.132, 152.508, 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) K 3 19.00 S 60 16.00 O 2732 8.00 N 2564 7.00 C 9924 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 96 " distance=2.05 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 96 " distance=2.05 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 96 " distance=2.05 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 96 " distance=2.05 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: 5.90 Conformation dependent library (CDL) restraints added in 2.3 seconds 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3520 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 20 sheets defined 52.6% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 132 through 138 removed outlier: 3.879A pdb=" N ARG A 138 " --> pdb=" O LYS A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 165 removed outlier: 3.895A pdb=" N PHE A 156 " --> pdb=" O ASN A 152 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASP A 157 " --> pdb=" O ARG A 153 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ALA A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 188 Processing helix chain 'A' and resid 190 through 201 Processing helix chain 'A' and resid 216 through 226 removed outlier: 3.790A pdb=" N TYR A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 256 removed outlier: 3.778A pdb=" N THR A 255 " --> pdb=" O PHE A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 removed outlier: 4.302A pdb=" N GLU A 262 " --> pdb=" O PHE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 316 removed outlier: 3.507A pdb=" N VAL A 297 " --> pdb=" O ASP A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 347 Proline residue: A 338 - end of helix Processing helix chain 'A' and resid 361 through 367 removed outlier: 4.200A pdb=" N VAL A 365 " --> pdb=" O ALA A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 379 removed outlier: 3.711A pdb=" N VAL A 371 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE A 372 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG A 373 " --> pdb=" O ARG A 370 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 374 " --> pdb=" O VAL A 371 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG A 379 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 393 Processing helix chain 'A' and resid 394 through 419 Processing helix chain 'A' and resid 430 through 433 removed outlier: 3.619A pdb=" N ASP A 433 " --> pdb=" O SER A 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 430 through 433' Processing helix chain 'A' and resid 434 through 444 Processing helix chain 'A' and resid 454 through 473 removed outlier: 3.863A pdb=" N VAL A 469 " --> pdb=" O ALA A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 489 removed outlier: 3.888A pdb=" N ILE A 479 " --> pdb=" O PRO A 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 132 through 138 removed outlier: 3.880A pdb=" N ARG B 138 " --> pdb=" O LYS B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 165 removed outlier: 3.895A pdb=" N PHE B 156 " --> pdb=" O ASN B 152 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASP B 157 " --> pdb=" O ARG B 153 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ALA B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 188 Processing helix chain 'B' and resid 190 through 201 Processing helix chain 'B' and resid 216 through 226 removed outlier: 3.790A pdb=" N TYR B 226 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 256 removed outlier: 3.778A pdb=" N THR B 255 " --> pdb=" O PHE B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 removed outlier: 4.301A pdb=" N GLU B 262 " --> pdb=" O PHE B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 316 removed outlier: 3.507A pdb=" N VAL B 297 " --> pdb=" O ASP B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 347 Proline residue: B 338 - end of helix Processing helix chain 'B' and resid 361 through 367 removed outlier: 4.200A pdb=" N VAL B 365 " --> pdb=" O ALA B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 379 removed outlier: 3.710A pdb=" N VAL B 371 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE B 372 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG B 373 " --> pdb=" O ARG B 370 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE B 374 " --> pdb=" O VAL B 371 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG B 379 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 393 Processing helix chain 'B' and resid 394 through 419 Processing helix chain 'B' and resid 430 through 433 removed outlier: 3.619A pdb=" N ASP B 433 " --> pdb=" O SER B 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 430 through 433' Processing helix chain 'B' and resid 434 through 444 Processing helix chain 'B' and resid 454 through 473 removed outlier: 3.863A pdb=" N VAL B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 489 removed outlier: 3.888A pdb=" N ILE B 479 " --> pdb=" O PRO B 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 132 through 138 removed outlier: 3.879A pdb=" N ARG C 138 " --> pdb=" O LYS C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 165 removed outlier: 3.895A pdb=" N PHE C 156 " --> pdb=" O ASN C 152 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASP C 157 " --> pdb=" O ARG C 153 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ALA C 158 " --> pdb=" O PRO C 154 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR C 163 " --> pdb=" O ILE C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 188 Processing helix chain 'C' and resid 190 through 201 Processing helix chain 'C' and resid 216 through 226 removed outlier: 3.789A pdb=" N TYR C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 256 removed outlier: 3.779A pdb=" N THR C 255 " --> pdb=" O PHE C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 263 removed outlier: 4.302A pdb=" N GLU C 262 " --> pdb=" O PHE C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 316 removed outlier: 3.507A pdb=" N VAL C 297 " --> pdb=" O ASP C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 347 Proline residue: C 338 - end of helix Processing helix chain 'C' and resid 361 through 367 removed outlier: 4.200A pdb=" N VAL C 365 " --> pdb=" O ALA C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 379 removed outlier: 3.710A pdb=" N VAL C 371 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE C 372 " --> pdb=" O VAL C 369 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG C 373 " --> pdb=" O ARG C 370 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE C 374 " --> pdb=" O VAL C 371 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG C 379 " --> pdb=" O LYS C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 393 Processing helix chain 'C' and resid 394 through 419 Processing helix chain 'C' and resid 430 through 433 removed outlier: 3.619A pdb=" N ASP C 433 " --> pdb=" O SER C 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 430 through 433' Processing helix chain 'C' and resid 434 through 444 Processing helix chain 'C' and resid 454 through 473 removed outlier: 3.863A pdb=" N VAL C 469 " --> pdb=" O ALA C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 489 removed outlier: 3.888A pdb=" N ILE C 479 " --> pdb=" O PRO C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 124 Processing helix chain 'D' and resid 132 through 138 removed outlier: 3.879A pdb=" N ARG D 138 " --> pdb=" O LYS D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 165 removed outlier: 3.895A pdb=" N PHE D 156 " --> pdb=" O ASN D 152 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASP D 157 " --> pdb=" O ARG D 153 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ALA D 158 " --> pdb=" O PRO D 154 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR D 163 " --> pdb=" O ILE D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 188 Processing helix chain 'D' and resid 190 through 201 Processing helix chain 'D' and resid 216 through 226 removed outlier: 3.790A pdb=" N TYR D 226 " --> pdb=" O LEU D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 256 removed outlier: 3.779A pdb=" N THR D 255 " --> pdb=" O PHE D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 removed outlier: 4.303A pdb=" N GLU D 262 " --> pdb=" O PHE D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 316 removed outlier: 3.507A pdb=" N VAL D 297 " --> pdb=" O ASP D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 347 Proline residue: D 338 - end of helix Processing helix chain 'D' and resid 361 through 367 removed outlier: 4.200A pdb=" N VAL D 365 " --> pdb=" O ALA D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 379 removed outlier: 3.711A pdb=" N VAL D 371 " --> pdb=" O LEU D 368 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE D 372 " --> pdb=" O VAL D 369 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG D 373 " --> pdb=" O ARG D 370 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE D 374 " --> pdb=" O VAL D 371 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG D 379 " --> pdb=" O LYS D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 393 Processing helix chain 'D' and resid 394 through 419 Processing helix chain 'D' and resid 430 through 433 removed outlier: 3.620A pdb=" N ASP D 433 " --> pdb=" O SER D 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 430 through 433' Processing helix chain 'D' and resid 434 through 444 Processing helix chain 'D' and resid 454 through 473 removed outlier: 3.863A pdb=" N VAL D 469 " --> pdb=" O ALA D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 489 removed outlier: 3.887A pdb=" N ILE D 479 " --> pdb=" O PRO D 475 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 118 removed outlier: 9.532A pdb=" N TYR A 147 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL A 107 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N PHE A 149 " --> pdb=" O VAL A 107 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASN A 109 " --> pdb=" O PHE A 149 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU A 146 " --> pdb=" O ASP A 141 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 4 through 8 removed outlier: 3.948A pdb=" N GLN E 4 " --> pdb=" O SER E 26 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER E 26 " --> pdb=" O GLN E 4 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 4 through 8 removed outlier: 3.948A pdb=" N GLN E 4 " --> pdb=" O SER E 26 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER E 26 " --> pdb=" O GLN E 4 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 11 through 13 removed outlier: 3.662A pdb=" N SER E 34 " --> pdb=" O TRP E 99 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA E 35 " --> pdb=" O ILE E 52 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ARG E 39 " --> pdb=" O PHE E 48 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N PHE E 48 " --> pdb=" O ARG E 39 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 11 through 13 Processing sheet with id=AA6, first strand: chain 'F' and resid 4 through 8 removed outlier: 3.948A pdb=" N GLN F 4 " --> pdb=" O SER F 26 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER F 26 " --> pdb=" O GLN F 4 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 4 through 8 removed outlier: 3.948A pdb=" N GLN F 4 " --> pdb=" O SER F 26 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER F 26 " --> pdb=" O GLN F 4 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 11 through 13 removed outlier: 3.663A pdb=" N SER F 34 " --> pdb=" O TRP F 99 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA F 35 " --> pdb=" O ILE F 52 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ARG F 39 " --> pdb=" O PHE F 48 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N PHE F 48 " --> pdb=" O ARG F 39 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 11 through 13 Processing sheet with id=AB1, first strand: chain 'G' and resid 4 through 8 removed outlier: 3.947A pdb=" N GLN G 4 " --> pdb=" O SER G 26 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER G 26 " --> pdb=" O GLN G 4 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 4 through 8 removed outlier: 3.947A pdb=" N GLN G 4 " --> pdb=" O SER G 26 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER G 26 " --> pdb=" O GLN G 4 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 11 through 13 removed outlier: 3.662A pdb=" N SER G 34 " --> pdb=" O TRP G 99 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA G 35 " --> pdb=" O ILE G 52 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ARG G 39 " --> pdb=" O PHE G 48 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N PHE G 48 " --> pdb=" O ARG G 39 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 11 through 13 Processing sheet with id=AB5, first strand: chain 'H' and resid 4 through 8 removed outlier: 3.947A pdb=" N GLN H 4 " --> pdb=" O SER H 26 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER H 26 " --> pdb=" O GLN H 4 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 4 through 8 removed outlier: 3.947A pdb=" N GLN H 4 " --> pdb=" O SER H 26 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER H 26 " --> pdb=" O GLN H 4 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 11 through 13 removed outlier: 3.662A pdb=" N SER H 34 " --> pdb=" O TRP H 99 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA H 35 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ARG H 39 " --> pdb=" O PHE H 48 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N PHE H 48 " --> pdb=" O ARG H 39 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 11 through 13 Processing sheet with id=AB9, first strand: chain 'B' and resid 113 through 118 removed outlier: 9.532A pdb=" N TYR B 147 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL B 107 " --> pdb=" O TYR B 147 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N PHE B 149 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ASN B 109 " --> pdb=" O PHE B 149 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU B 146 " --> pdb=" O ASP B 141 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 113 through 118 removed outlier: 9.532A pdb=" N TYR C 147 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL C 107 " --> pdb=" O TYR C 147 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N PHE C 149 " --> pdb=" O VAL C 107 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASN C 109 " --> pdb=" O PHE C 149 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU C 146 " --> pdb=" O ASP C 141 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 113 through 118 removed outlier: 9.532A pdb=" N TYR D 147 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N VAL D 107 " --> pdb=" O TYR D 147 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N PHE D 149 " --> pdb=" O VAL D 107 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASN D 109 " --> pdb=" O PHE D 149 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU D 146 " --> pdb=" O ASP D 141 " (cutoff:3.500A) 860 hydrogen bonds defined for protein. 2364 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: 5.18 Time building geometry restraints manager: 6.36 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: 2408 1.31 - 1.43: 4505 1.43 - 1.56: 8647 1.56 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 15652 Sorted by residual: bond pdb=" CA SER B 426 " pdb=" CB SER B 426 " ideal model delta sigma weight residual 1.528 1.451 0.077 1.61e-02 3.86e+03 2.28e+01 bond pdb=" CA SER A 426 " pdb=" CB SER A 426 " ideal model delta sigma weight residual 1.528 1.452 0.076 1.61e-02 3.86e+03 2.23e+01 bond pdb=" CA SER D 426 " pdb=" CB SER D 426 " ideal model delta sigma weight residual 1.528 1.452 0.076 1.61e-02 3.86e+03 2.22e+01 bond pdb=" CA SER C 426 " pdb=" CB SER C 426 " ideal model delta sigma weight residual 1.528 1.452 0.076 1.61e-02 3.86e+03 2.21e+01 bond pdb=" N TYR C 265 " pdb=" CA TYR C 265 " ideal model delta sigma weight residual 1.453 1.491 -0.038 8.30e-03 1.45e+04 2.09e+01 ... (remaining 15647 not shown) Histogram of bond angle deviations from ideal: 99.07 - 106.13: 494 106.13 - 113.19: 7501 113.19 - 120.26: 7699 120.26 - 127.32: 5378 127.32 - 134.38: 120 Bond angle restraints: 21192 Sorted by residual: angle pdb=" N VAL B 445 " pdb=" CA VAL B 445 " pdb=" C VAL B 445 " ideal model delta sigma weight residual 110.42 100.34 10.08 9.60e-01 1.09e+00 1.10e+02 angle pdb=" N VAL A 445 " pdb=" CA VAL A 445 " pdb=" C VAL A 445 " ideal model delta sigma weight residual 110.42 100.35 10.07 9.60e-01 1.09e+00 1.10e+02 angle pdb=" N VAL D 445 " pdb=" CA VAL D 445 " pdb=" C VAL D 445 " ideal model delta sigma weight residual 110.42 100.37 10.05 9.60e-01 1.09e+00 1.10e+02 angle pdb=" N VAL C 445 " pdb=" CA VAL C 445 " pdb=" C VAL C 445 " ideal model delta sigma weight residual 110.42 100.39 10.03 9.60e-01 1.09e+00 1.09e+02 angle pdb=" N GLU B 262 " pdb=" CA GLU B 262 " pdb=" C GLU B 262 " ideal model delta sigma weight residual 113.28 104.88 8.40 1.22e+00 6.72e-01 4.74e+01 ... (remaining 21187 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 8180 17.92 - 35.85: 801 35.85 - 53.77: 211 53.77 - 71.70: 24 71.70 - 89.62: 4 Dihedral angle restraints: 9220 sinusoidal: 3728 harmonic: 5492 Sorted by residual: dihedral pdb=" C THR D 444 " pdb=" N THR D 444 " pdb=" CA THR D 444 " pdb=" CB THR D 444 " ideal model delta harmonic sigma weight residual -122.00 -144.18 22.18 0 2.50e+00 1.60e-01 7.87e+01 dihedral pdb=" C THR B 444 " pdb=" N THR B 444 " pdb=" CA THR B 444 " pdb=" CB THR B 444 " ideal model delta harmonic sigma weight residual -122.00 -144.16 22.16 0 2.50e+00 1.60e-01 7.86e+01 dihedral pdb=" C THR C 444 " pdb=" N THR C 444 " pdb=" CA THR C 444 " pdb=" CB THR C 444 " ideal model delta harmonic sigma weight residual -122.00 -144.14 22.14 0 2.50e+00 1.60e-01 7.84e+01 ... (remaining 9217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.167: 2014 0.167 - 0.334: 298 0.334 - 0.501: 12 0.501 - 0.669: 4 0.669 - 0.836: 4 Chirality restraints: 2332 Sorted by residual: chirality pdb=" CA THR D 444 " pdb=" N THR D 444 " pdb=" C THR D 444 " pdb=" CB THR D 444 " both_signs ideal model delta sigma weight residual False 2.53 1.69 0.84 2.00e-01 2.50e+01 1.75e+01 chirality pdb=" CA THR C 444 " pdb=" N THR C 444 " pdb=" C THR C 444 " pdb=" CB THR C 444 " both_signs ideal model delta sigma weight residual False 2.53 1.69 0.83 2.00e-01 2.50e+01 1.74e+01 chirality pdb=" CA THR A 444 " pdb=" N THR A 444 " pdb=" C THR A 444 " pdb=" CB THR A 444 " both_signs ideal model delta sigma weight residual False 2.53 1.69 0.83 2.00e-01 2.50e+01 1.73e+01 ... (remaining 2329 not shown) Planarity restraints: 2700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 201 " -0.022 2.00e-02 2.50e+03 4.51e-02 2.03e+01 pdb=" C GLU C 201 " 0.078 2.00e-02 2.50e+03 pdb=" O GLU C 201 " -0.029 2.00e-02 2.50e+03 pdb=" N GLY C 202 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 201 " 0.022 2.00e-02 2.50e+03 4.50e-02 2.03e+01 pdb=" C GLU A 201 " -0.078 2.00e-02 2.50e+03 pdb=" O GLU A 201 " 0.029 2.00e-02 2.50e+03 pdb=" N GLY A 202 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 418 " 0.023 2.00e-02 2.50e+03 4.49e-02 2.01e+01 pdb=" C PHE A 418 " -0.078 2.00e-02 2.50e+03 pdb=" O PHE A 418 " 0.028 2.00e-02 2.50e+03 pdb=" N ALA A 419 " 0.026 2.00e-02 2.50e+03 ... (remaining 2697 not shown) Histogram of nonbonded interaction distances: 0.47 - 1.40: 24 1.40 - 2.34: 36 2.34 - 3.27: 15754 3.27 - 4.21: 42056 4.21 - 5.14: 83500 Warning: very small nonbonded interaction distances. Nonbonded interactions: 141370 Sorted by model distance: nonbonded pdb=" CZ ARG E 53 " pdb=" OD2 ASP B 261 " model vdw 0.467 3.270 nonbonded pdb=" OD2 ASP A 261 " pdb=" CZ ARG H 53 " model vdw 0.475 3.270 nonbonded pdb=" CZ ARG G 53 " pdb=" OD2 ASP D 261 " model vdw 0.475 3.270 nonbonded pdb=" CZ ARG F 53 " pdb=" OD2 ASP C 261 " model vdw 0.485 3.270 nonbonded pdb=" NH1 ARG E 53 " pdb=" CG ASP B 261 " model vdw 0.950 3.350 ... (remaining 141365 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 103 through 491) selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 5.030 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: 16.240 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 40.700 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 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 : 0.014 0.092 15652 Z= 0.890 Angle : 1.699 10.644 21192 Z= 1.181 Chirality : 0.119 0.836 2332 Planarity : 0.009 0.078 2700 Dihedral : 14.901 89.621 5688 Min Nonbonded Distance : 0.467 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer Outliers : 6.31 % Cbeta Deviations : 1.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.17), residues: 1876 helix: -1.92 (0.14), residues: 928 sheet: 1.08 (0.53), residues: 120 loop : -1.26 (0.19), residues: 828 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 272 time to evaluate : 1.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 104 outliers final: 28 residues processed: 345 average time/residue: 0.3462 time to fit residues: 162.7237 Evaluate side-chains 201 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 173 time to evaluate : 1.764 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.2247 time to fit residues: 12.1427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 0.6980 chunk 142 optimal weight: 0.5980 chunk 79 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 109 optimal weight: 0.6980 chunk 170 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN A 145 ASN A 164 GLN A 217 GLN E 33 ASN E 84 ASN F 33 ASN F 84 ASN G 33 ASN G 84 ASN H 33 ASN H 84 ASN B 124 GLN B 164 GLN B 217 GLN C 124 GLN C 164 GLN C 217 GLN D 124 GLN D 145 ASN D 217 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 15652 Z= 0.218 Angle : 0.659 7.540 21192 Z= 0.356 Chirality : 0.044 0.198 2332 Planarity : 0.006 0.057 2700 Dihedral : 4.984 28.307 2120 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 2.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.19), residues: 1876 helix: -0.05 (0.17), residues: 956 sheet: 1.54 (0.45), residues: 136 loop : -1.07 (0.20), residues: 784 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 206 time to evaluate : 1.601 Fit side-chains outliers start: 35 outliers final: 17 residues processed: 230 average time/residue: 0.2968 time to fit residues: 98.7623 Evaluate side-chains 178 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 161 time to evaluate : 1.737 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1428 time to fit residues: 6.8563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 0.9980 chunk 52 optimal weight: 0.0020 chunk 142 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 171 optimal weight: 0.8980 chunk 184 optimal weight: 0.5980 chunk 152 optimal weight: 0.2980 chunk 169 optimal weight: 0.5980 chunk 58 optimal weight: 5.9990 chunk 137 optimal weight: 0.6980 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 15652 Z= 0.168 Angle : 0.564 6.290 21192 Z= 0.300 Chirality : 0.042 0.270 2332 Planarity : 0.005 0.051 2700 Dihedral : 4.494 23.295 2120 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer Outliers : 1.76 % 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: 0.41 (0.19), residues: 1876 helix: 0.99 (0.18), residues: 920 sheet: 1.97 (0.46), residues: 136 loop : -0.84 (0.20), residues: 820 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 165 time to evaluate : 1.799 Fit side-chains outliers start: 29 outliers final: 16 residues processed: 187 average time/residue: 0.2717 time to fit residues: 76.6981 Evaluate side-chains 160 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 144 time to evaluate : 1.648 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1279 time to fit residues: 6.3293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 114 optimal weight: 0.4980 chunk 171 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 162 optimal weight: 0.3980 chunk 48 optimal weight: 0.6980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 GLN C 164 GLN D 164 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 15652 Z= 0.256 Angle : 0.581 5.672 21192 Z= 0.311 Chirality : 0.044 0.148 2332 Planarity : 0.005 0.052 2700 Dihedral : 4.461 22.486 2120 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer Outliers : 1.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.20), residues: 1876 helix: 1.03 (0.18), residues: 936 sheet: 0.84 (0.38), residues: 196 loop : -0.73 (0.22), residues: 744 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 145 time to evaluate : 1.848 Fit side-chains outliers start: 24 outliers final: 13 residues processed: 163 average time/residue: 0.2729 time to fit residues: 66.8888 Evaluate side-chains 139 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 126 time to evaluate : 1.870 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1563 time to fit residues: 6.1512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 135 optimal weight: 0.3980 chunk 74 optimal weight: 5.9990 chunk 155 optimal weight: 0.0670 chunk 125 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 163 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 15652 Z= 0.176 Angle : 0.520 4.988 21192 Z= 0.279 Chirality : 0.041 0.153 2332 Planarity : 0.005 0.049 2700 Dihedral : 4.257 23.268 2120 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer Outliers : 0.49 % 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: 0.72 (0.20), residues: 1876 helix: 1.31 (0.18), residues: 936 sheet: 0.80 (0.39), residues: 200 loop : -0.65 (0.22), residues: 740 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 138 time to evaluate : 1.656 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 140 average time/residue: 0.3491 time to fit residues: 71.2860 Evaluate side-chains 135 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 129 time to evaluate : 1.775 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1438 time to fit residues: 4.1042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 0.9980 chunk 163 optimal weight: 0.0060 chunk 35 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 181 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 15 optimal weight: 0.4980 chunk 60 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 GLN ** F 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 15652 Z= 0.170 Angle : 0.505 4.859 21192 Z= 0.272 Chirality : 0.041 0.124 2332 Planarity : 0.005 0.048 2700 Dihedral : 4.171 23.971 2120 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer Outliers : 0.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.20), residues: 1876 helix: 1.44 (0.18), residues: 932 sheet: 0.82 (0.38), residues: 200 loop : -0.57 (0.23), residues: 744 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 127 time to evaluate : 1.806 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 140 average time/residue: 0.2970 time to fit residues: 61.5692 Evaluate side-chains 129 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 121 time to evaluate : 1.885 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1321 time to fit residues: 4.5755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 0.2980 chunk 20 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 132 optimal weight: 0.2980 chunk 102 optimal weight: 0.5980 chunk 153 optimal weight: 0.5980 chunk 101 optimal weight: 0.6980 chunk 181 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 15652 Z= 0.152 Angle : 0.492 4.843 21192 Z= 0.265 Chirality : 0.040 0.127 2332 Planarity : 0.005 0.047 2700 Dihedral : 4.074 23.193 2120 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer Outliers : 0.30 % 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: 1.02 (0.20), residues: 1876 helix: 1.55 (0.18), residues: 932 sheet: 0.93 (0.38), residues: 208 loop : -0.48 (0.23), residues: 736 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 131 time to evaluate : 1.864 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 136 average time/residue: 0.2935 time to fit residues: 59.4164 Evaluate side-chains 128 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 125 time to evaluate : 1.784 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1339 time to fit residues: 3.2871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 0.0980 chunk 72 optimal weight: 9.9990 chunk 108 optimal weight: 0.7980 chunk 54 optimal weight: 9.9990 chunk 35 optimal weight: 0.9980 chunk 115 optimal weight: 0.5980 chunk 123 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 142 optimal weight: 0.7980 chunk 164 optimal weight: 0.0670 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 GLN D 164 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 15652 Z= 0.149 Angle : 0.484 4.810 21192 Z= 0.260 Chirality : 0.040 0.127 2332 Planarity : 0.005 0.046 2700 Dihedral : 4.003 23.869 2120 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 0.18 % 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: 1.09 (0.20), residues: 1876 helix: 1.60 (0.18), residues: 936 sheet: 0.94 (0.37), residues: 208 loop : -0.45 (0.24), residues: 732 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 127 time to evaluate : 1.734 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 130 average time/residue: 0.2916 time to fit residues: 56.7865 Evaluate side-chains 126 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 125 time to evaluate : 1.881 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1407 time to fit residues: 2.8590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 1.9990 chunk 158 optimal weight: 0.8980 chunk 168 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 152 optimal weight: 3.9990 chunk 159 optimal weight: 0.9990 chunk 110 optimal weight: 0.7980 chunk 178 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 GLN C 164 GLN D 164 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 15652 Z= 0.261 Angle : 0.543 10.123 21192 Z= 0.291 Chirality : 0.043 0.131 2332 Planarity : 0.005 0.047 2700 Dihedral : 4.160 23.003 2120 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer Outliers : 0.49 % 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: 0.86 (0.20), residues: 1876 helix: 1.39 (0.18), residues: 936 sheet: 1.08 (0.38), residues: 200 loop : -0.59 (0.23), residues: 740 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 123 time to evaluate : 1.837 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 130 average time/residue: 0.2806 time to fit residues: 54.8887 Evaluate side-chains 125 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 118 time to evaluate : 1.665 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1739 time to fit residues: 4.4405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 187 optimal weight: 0.5980 chunk 172 optimal weight: 5.9990 chunk 149 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 115 optimal weight: 0.5980 chunk 91 optimal weight: 0.0980 chunk 118 optimal weight: 0.6980 chunk 158 optimal weight: 4.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 GLN ** F 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 15652 Z= 0.159 Angle : 0.500 8.204 21192 Z= 0.268 Chirality : 0.040 0.133 2332 Planarity : 0.005 0.046 2700 Dihedral : 4.048 24.314 2120 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.21), residues: 1876 helix: 1.57 (0.18), residues: 936 sheet: 1.24 (0.38), residues: 208 loop : -0.50 (0.24), residues: 732 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3752 Ramachandran restraints generated. 1876 Oldfield, 0 Emsley, 1876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 122 time to evaluate : 1.731 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 123 average time/residue: 0.3071 time to fit residues: 56.0331 Evaluate side-chains 121 residues out of total 1648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 1.679 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1377 time to fit residues: 2.8508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 9.9990 chunk 137 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 149 optimal weight: 0.7980 chunk 62 optimal weight: 9.9990 chunk 153 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 GLN C 164 GLN D 164 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.211605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.183643 restraints weight = 17302.122| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 1.34 r_work: 0.3704 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3585 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 15652 Z= 0.209 Angle : 0.523 8.196 21192 Z= 0.281 Chirality : 0.041 0.143 2332 Planarity : 0.005 0.052 2700 Dihedral : 4.086 23.700 2120 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer Outliers : 0.06 % 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: 1.04 (0.21), residues: 1876 helix: 1.52 (0.18), residues: 936 sheet: 1.28 (0.38), residues: 208 loop : -0.54 (0.24), residues: 732 =============================================================================== Job complete usr+sys time: 3030.55 seconds wall clock time: 55 minutes 52.77 seconds (3352.77 seconds total)