Starting phenix.real_space_refine (version: dev) on Thu Feb 23 03:25:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7quq_14151/02_2023/7quq_14151_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7quq_14151/02_2023/7quq_14151.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7quq_14151/02_2023/7quq_14151.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7quq_14151/02_2023/7quq_14151.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7quq_14151/02_2023/7quq_14151_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7quq_14151/02_2023/7quq_14151_updated.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.115 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 Process input model Symmetric amino acids flipped Residue "A TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 235": "OE1" <-> "OE2" Residue "A ASP 334": "OD1" <-> "OD2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 360": "OE1" <-> "OE2" Residue "A TYR 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 288": "OD1" <-> "OD2" Residue "B PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 99": "OE1" <-> "OE2" Residue "C PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 209": "OE1" <-> "OE2" Residue "C ASP 227": "OD1" <-> "OD2" Residue "C GLU 253": "OE1" <-> "OE2" Residue "C PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 320": "OD1" <-> "OD2" Residue "D TYR 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 185": "OE1" <-> "OE2" Residue "E PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 18": "OD1" <-> "OD2" Residue "F TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 249": "OD1" <-> "OD2" Residue "F PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 399": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 19095 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3168 Classifications: {'peptide': 414} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 391} Chain breaks: 2 Chain: "B" Number of atoms: 3133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3133 Classifications: {'peptide': 405} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 389} Chain breaks: 3 Chain: "C" Number of atoms: 3168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3168 Classifications: {'peptide': 414} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 391} Chain breaks: 2 Chain: "D" Number of atoms: 3133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3133 Classifications: {'peptide': 405} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 389} Chain breaks: 3 Chain: "E" Number of atoms: 3168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3168 Classifications: {'peptide': 414} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 391} Chain breaks: 2 Chain: "F" Number of atoms: 3133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3133 Classifications: {'peptide': 405} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 389} Chain breaks: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.92, per 1000 atoms: 0.57 Number of scatterers: 19095 At special positions: 0 Unit cell: (71.74, 67.52, 270.08, 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 84 16.00 P 18 15.00 O 3615 8.00 N 3276 7.00 C 12102 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=9, symmetry=0 Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.14 Conformation dependent library (CDL) restraints added in 2.9 seconds 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4542 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 100 helices and 18 sheets defined 44.2% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'A' and resid 12 through 30 Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 75 through 85 Processing helix chain 'A' and resid 105 through 109 Processing helix chain 'A' and resid 112 through 129 Proline residue: A 118 - end of helix Processing helix chain 'A' and resid 146 through 162 Processing helix chain 'A' and resid 185 through 198 removed outlier: 3.837A pdb=" N THR A 195 " --> pdb=" O PHE A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 216 Processing helix chain 'A' and resid 226 through 241 Processing helix chain 'A' and resid 256 through 263 Processing helix chain 'A' and resid 293 through 299 Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 330 through 343 removed outlier: 3.811A pdb=" N GLU A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LYS A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 395 removed outlier: 3.656A pdb=" N GLN A 395 " --> pdb=" O ASP A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 406 Processing helix chain 'A' and resid 410 through 427 Processing helix chain 'B' and resid 11 through 28 removed outlier: 4.327A pdb=" N ARG B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 50 No H-bonds generated for 'chain 'B' and resid 48 through 50' Processing helix chain 'B' and resid 74 through 77 No H-bonds generated for 'chain 'B' and resid 74 through 77' Processing helix chain 'B' and resid 102 through 106 Processing helix chain 'B' and resid 114 through 126 Processing helix chain 'B' and resid 144 through 157 removed outlier: 3.671A pdb=" N GLY B 149 " --> pdb=" O GLY B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 196 removed outlier: 4.241A pdb=" N ARG B 192 " --> pdb=" O LEU B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 215 Processing helix chain 'B' and resid 222 through 236 Processing helix chain 'B' and resid 238 through 241 No H-bonds generated for 'chain 'B' and resid 238 through 241' Processing helix chain 'B' and resid 250 through 257 Processing helix chain 'B' and resid 286 through 293 Processing helix chain 'B' and resid 323 through 327 Processing helix chain 'B' and resid 331 through 335 Processing helix chain 'B' and resid 373 through 391 removed outlier: 5.382A pdb=" N PHE B 389 " --> pdb=" O ASP B 386 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ASP B 390 " --> pdb=" O ILE B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 401 removed outlier: 3.823A pdb=" N ALA B 401 " --> pdb=" O TRP B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 424 Processing helix chain 'C' and resid 13 through 30 Processing helix chain 'C' and resid 49 through 51 No H-bonds generated for 'chain 'C' and resid 49 through 51' Processing helix chain 'C' and resid 75 through 85 Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 105 through 109 Processing helix chain 'C' and resid 112 through 130 Proline residue: C 118 - end of helix Processing helix chain 'C' and resid 146 through 162 Processing helix chain 'C' and resid 185 through 198 removed outlier: 3.910A pdb=" N THR C 195 " --> pdb=" O PHE C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 216 Processing helix chain 'C' and resid 226 through 242 Processing helix chain 'C' and resid 256 through 263 Processing helix chain 'C' and resid 293 through 299 Processing helix chain 'C' and resid 311 through 313 No H-bonds generated for 'chain 'C' and resid 311 through 313' Processing helix chain 'C' and resid 330 through 343 removed outlier: 3.535A pdb=" N GLU C 342 " --> pdb=" O ALA C 338 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS C 343 " --> pdb=" O ALA C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 393 removed outlier: 3.577A pdb=" N LEU C 393 " --> pdb=" O PHE C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 406 Processing helix chain 'C' and resid 410 through 427 Processing helix chain 'D' and resid 10 through 28 removed outlier: 3.970A pdb=" N ARG D 26 " --> pdb=" O ARG D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 50 No H-bonds generated for 'chain 'D' and resid 48 through 50' Processing helix chain 'D' and resid 73 through 77 Processing helix chain 'D' and resid 102 through 106 Processing helix chain 'D' and resid 114 through 126 Processing helix chain 'D' and resid 144 through 157 removed outlier: 3.669A pdb=" N GLY D 149 " --> pdb=" O GLY D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 196 removed outlier: 4.156A pdb=" N ARG D 192 " --> pdb=" O LEU D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 215 Processing helix chain 'D' and resid 222 through 236 Processing helix chain 'D' and resid 238 through 241 No H-bonds generated for 'chain 'D' and resid 238 through 241' Processing helix chain 'D' and resid 250 through 257 Processing helix chain 'D' and resid 286 through 293 Processing helix chain 'D' and resid 323 through 328 Processing helix chain 'D' and resid 331 through 335 Processing helix chain 'D' and resid 373 through 391 removed outlier: 5.247A pdb=" N PHE D 389 " --> pdb=" O ASP D 386 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASP D 390 " --> pdb=" O ILE D 387 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN D 391 " --> pdb=" O MET D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 399 Processing helix chain 'D' and resid 405 through 424 Processing helix chain 'E' and resid 12 through 30 Processing helix chain 'E' and resid 49 through 51 No H-bonds generated for 'chain 'E' and resid 49 through 51' Processing helix chain 'E' and resid 75 through 88 removed outlier: 7.345A pdb=" N SER E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N LEU E 88 " --> pdb=" O THR E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 93 No H-bonds generated for 'chain 'E' and resid 91 through 93' Processing helix chain 'E' and resid 105 through 109 Processing helix chain 'E' and resid 112 through 130 Proline residue: E 118 - end of helix Processing helix chain 'E' and resid 146 through 162 Processing helix chain 'E' and resid 183 through 198 Proline residue: E 186 - end of helix removed outlier: 3.556A pdb=" N ALA E 192 " --> pdb=" O THR E 189 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN E 194 " --> pdb=" O PHE E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 216 Processing helix chain 'E' and resid 226 through 241 Processing helix chain 'E' and resid 256 through 263 Processing helix chain 'E' and resid 293 through 299 Processing helix chain 'E' and resid 311 through 313 No H-bonds generated for 'chain 'E' and resid 311 through 313' Processing helix chain 'E' and resid 330 through 343 removed outlier: 3.590A pdb=" N GLU E 342 " --> pdb=" O ALA E 338 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS E 343 " --> pdb=" O ALA E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 395 removed outlier: 3.723A pdb=" N GLN E 395 " --> pdb=" O ASP E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 406 Processing helix chain 'E' and resid 410 through 427 Processing helix chain 'F' and resid 11 through 28 removed outlier: 3.815A pdb=" N ARG F 26 " --> pdb=" O ARG F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 77 No H-bonds generated for 'chain 'F' and resid 74 through 77' Processing helix chain 'F' and resid 102 through 106 Processing helix chain 'F' and resid 111 through 126 removed outlier: 4.584A pdb=" N ASP F 115 " --> pdb=" O GLU F 111 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLN F 116 " --> pdb=" O LYS F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 157 Processing helix chain 'F' and resid 182 through 196 removed outlier: 3.869A pdb=" N ARG F 192 " --> pdb=" O LEU F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 215 Processing helix chain 'F' and resid 222 through 236 Processing helix chain 'F' and resid 238 through 241 No H-bonds generated for 'chain 'F' and resid 238 through 241' Processing helix chain 'F' and resid 250 through 257 Processing helix chain 'F' and resid 286 through 293 Processing helix chain 'F' and resid 323 through 327 Processing helix chain 'F' and resid 330 through 335 Processing helix chain 'F' and resid 373 through 385 Processing helix chain 'F' and resid 396 through 401 removed outlier: 3.598A pdb=" N ALA F 401 " --> pdb=" O TRP F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 424 Processing sheet with id= A, first strand: chain 'A' and resid 94 through 96 removed outlier: 7.975A pdb=" N ILE A 95 " --> pdb=" O ALA A 68 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N MET A 70 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL A 8 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N VAL A 71 " --> pdb=" O VAL A 8 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N SER A 10 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ALA A 202 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ALA A 172 " --> pdb=" O ALA A 202 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU A 204 " --> pdb=" O ALA A 172 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU A 174 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N PHE A 206 " --> pdb=" O LEU A 174 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 53 through 56 Processing sheet with id= C, first strand: chain 'A' and resid 273 through 277 removed outlier: 3.585A pdb=" N SER A 318 " --> pdb=" O ASN A 375 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 4 through 8 removed outlier: 6.991A pdb=" N GLY B 133 " --> pdb=" O LEU B 5 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ILE B 7 " --> pdb=" O GLY B 133 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU B 135 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ARG B 164 " --> pdb=" O PHE B 134 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N MET B 136 " --> pdb=" O ARG B 164 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N PHE B 166 " --> pdb=" O MET B 136 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N HIS B 138 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N PHE B 168 " --> pdb=" O HIS B 138 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N GLY B 199 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N SER B 169 " --> pdb=" O GLY B 199 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL B 201 " --> pdb=" O SER B 169 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL B 171 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LEU B 203 " --> pdb=" O VAL B 171 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 52 through 54 Processing sheet with id= F, first strand: chain 'B' and resid 266 through 271 Processing sheet with id= G, first strand: chain 'C' and resid 94 through 96 removed outlier: 8.333A pdb=" N ILE C 95 " --> pdb=" O ALA C 68 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N MET C 70 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL C 8 " --> pdb=" O ILE C 69 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N VAL C 71 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N SER C 10 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ALA C 202 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ALA C 172 " --> pdb=" O ALA C 202 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU C 204 " --> pdb=" O ALA C 172 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU C 174 " --> pdb=" O LEU C 204 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N PHE C 206 " --> pdb=" O LEU C 174 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 53 through 56 Processing sheet with id= I, first strand: chain 'C' and resid 272 through 277 removed outlier: 3.625A pdb=" N SER C 318 " --> pdb=" O ASN C 375 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 64 through 67 removed outlier: 8.972A pdb=" N VAL D 65 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N SER D 6 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N VAL D 67 " --> pdb=" O SER D 6 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N HIS D 8 " --> pdb=" O VAL D 67 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N LEU D 5 " --> pdb=" O GLN D 132 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N PHE D 134 " --> pdb=" O LEU D 5 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE D 7 " --> pdb=" O PHE D 134 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N MET D 136 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N VAL D 9 " --> pdb=" O MET D 136 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N HIS D 138 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ARG D 164 " --> pdb=" O PHE D 134 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N MET D 136 " --> pdb=" O ARG D 164 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N PHE D 166 " --> pdb=" O MET D 136 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N HIS D 138 " --> pdb=" O PHE D 166 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N PHE D 168 " --> pdb=" O HIS D 138 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N GLY D 199 " --> pdb=" O THR D 167 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N SER D 169 " --> pdb=" O GLY D 199 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL D 201 " --> pdb=" O SER D 169 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL D 171 " --> pdb=" O VAL D 201 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LEU D 203 " --> pdb=" O VAL D 171 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 52 through 54 Processing sheet with id= L, first strand: chain 'D' and resid 266 through 271 Processing sheet with id= M, first strand: chain 'E' and resid 94 through 96 removed outlier: 8.180A pdb=" N ILE E 95 " --> pdb=" O ALA E 68 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N MET E 70 " --> pdb=" O ILE E 95 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL E 8 " --> pdb=" O ILE E 69 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N VAL E 71 " --> pdb=" O VAL E 8 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N SER E 10 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALA E 202 " --> pdb=" O SER E 170 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ALA E 172 " --> pdb=" O ALA E 202 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU E 204 " --> pdb=" O ALA E 172 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 53 through 56 Processing sheet with id= O, first strand: chain 'E' and resid 272 through 277 removed outlier: 3.796A pdb=" N SER E 318 " --> pdb=" O ASN E 375 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 4 through 8 removed outlier: 6.851A pdb=" N GLY F 133 " --> pdb=" O LEU F 5 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N ILE F 7 " --> pdb=" O GLY F 133 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU F 135 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG F 164 " --> pdb=" O PHE F 134 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N MET F 136 " --> pdb=" O ARG F 164 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE F 166 " --> pdb=" O MET F 136 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N HIS F 138 " --> pdb=" O PHE F 166 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N PHE F 168 " --> pdb=" O HIS F 138 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N GLY F 199 " --> pdb=" O THR F 167 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N SER F 169 " --> pdb=" O GLY F 199 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL F 201 " --> pdb=" O SER F 169 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N VAL F 171 " --> pdb=" O VAL F 201 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU F 203 " --> pdb=" O VAL F 171 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'F' and resid 52 through 54 Processing sheet with id= R, first strand: chain 'F' and resid 266 through 271 821 hydrogen bonds defined for protein. 2277 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.72 Time building geometry restraints manager: 9.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6287 1.34 - 1.46: 4434 1.46 - 1.59: 8584 1.59 - 1.71: 18 1.71 - 1.83: 162 Bond restraints: 19485 Sorted by residual: bond pdb=" C6 G2P D 501 " pdb=" O6 G2P D 501 " ideal model delta sigma weight residual 1.223 1.463 -0.240 2.00e-02 2.50e+03 1.44e+02 bond pdb=" C6 G2P F 501 " pdb=" O6 G2P F 501 " ideal model delta sigma weight residual 1.223 1.459 -0.236 2.00e-02 2.50e+03 1.40e+02 bond pdb=" C6 G2P B 501 " pdb=" O6 G2P B 501 " ideal model delta sigma weight residual 1.223 1.457 -0.234 2.00e-02 2.50e+03 1.37e+02 bond pdb=" C2' G2P D 501 " pdb=" C3' G2P D 501 " ideal model delta sigma weight residual 1.528 1.300 0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" C2' G2P B 501 " pdb=" C3' G2P B 501 " ideal model delta sigma weight residual 1.528 1.301 0.227 2.00e-02 2.50e+03 1.29e+02 ... (remaining 19480 not shown) Histogram of bond angle deviations from ideal: 96.85 - 105.22: 394 105.22 - 113.58: 10999 113.58 - 121.94: 11061 121.94 - 130.31: 3926 130.31 - 138.67: 92 Bond angle restraints: 26472 Sorted by residual: angle pdb=" C ASN D 298 " pdb=" N PHE D 299 " pdb=" CA PHE D 299 " ideal model delta sigma weight residual 120.71 126.27 -5.56 1.42e+00 4.96e-01 1.53e+01 angle pdb=" C ALA B 99 " pdb=" CA ALA B 99 " pdb=" CB ALA B 99 " ideal model delta sigma weight residual 115.79 111.14 4.65 1.19e+00 7.06e-01 1.53e+01 angle pdb=" C5 G2P E 501 " pdb=" C6 G2P E 501 " pdb=" N1 G2P E 501 " ideal model delta sigma weight residual 110.74 122.25 -11.51 3.00e+00 1.11e-01 1.47e+01 angle pdb=" C3A G2P F 501 " pdb=" PB G2P F 501 " pdb=" O3B G2P F 501 " ideal model delta sigma weight residual 99.71 110.75 -11.04 3.00e+00 1.11e-01 1.35e+01 angle pdb=" C5 G2P E 501 " pdb=" C6 G2P E 501 " pdb=" O6 G2P E 501 " ideal model delta sigma weight residual 129.13 118.25 10.88 3.00e+00 1.11e-01 1.31e+01 ... (remaining 26467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.89: 10369 15.89 - 31.78: 959 31.78 - 47.66: 186 47.66 - 63.55: 25 63.55 - 79.44: 14 Dihedral angle restraints: 11553 sinusoidal: 4509 harmonic: 7044 Sorted by residual: dihedral pdb=" CA TRP E 349 " pdb=" C TRP E 349 " pdb=" N ILE E 350 " pdb=" CA ILE E 350 " ideal model delta harmonic sigma weight residual 180.00 151.77 28.23 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA VAL B 369 " pdb=" C VAL B 369 " pdb=" N ASN B 370 " pdb=" CA ASN B 370 " ideal model delta harmonic sigma weight residual 180.00 156.05 23.95 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA LYS D 163 " pdb=" C LYS D 163 " pdb=" N ARG D 164 " pdb=" CA ARG D 164 " ideal model delta harmonic sigma weight residual -180.00 -157.72 -22.28 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 11550 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2493 0.068 - 0.135: 447 0.135 - 0.203: 46 0.203 - 0.270: 5 0.270 - 0.338: 3 Chirality restraints: 2994 Sorted by residual: chirality pdb=" CB ILE A 350 " pdb=" CA ILE A 350 " pdb=" CG1 ILE A 350 " pdb=" CG2 ILE A 350 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" C3' G2P C 501 " pdb=" C2' G2P C 501 " pdb=" C4' G2P C 501 " pdb=" O3' G2P C 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.41 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" C3' G2P A 501 " pdb=" C2' G2P A 501 " pdb=" C4' G2P A 501 " pdb=" O3' G2P A 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.43 -0.27 2.00e-01 2.50e+01 1.89e+00 ... (remaining 2991 not shown) Planarity restraints: 3399 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 349 " -0.028 2.00e-02 2.50e+03 2.98e-02 2.21e+01 pdb=" CG TRP E 349 " 0.080 2.00e-02 2.50e+03 pdb=" CD1 TRP E 349 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TRP E 349 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 349 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E 349 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 349 " -0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 349 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 349 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP E 349 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 299 " 0.018 2.00e-02 2.50e+03 2.57e-02 1.16e+01 pdb=" CG PHE D 299 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE D 299 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE D 299 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE D 299 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE D 299 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE D 299 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU F 182 " 0.051 5.00e-02 4.00e+02 7.67e-02 9.42e+00 pdb=" N PRO F 183 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO F 183 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO F 183 " 0.043 5.00e-02 4.00e+02 ... (remaining 3396 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 621 2.70 - 3.25: 19525 3.25 - 3.80: 34238 3.80 - 4.35: 45249 4.35 - 4.90: 72492 Nonbonded interactions: 172125 Sorted by model distance: nonbonded pdb=" OG SER D 146 " pdb=" OG1 THR D 189 " model vdw 2.144 2.440 nonbonded pdb=" OG SER B 146 " pdb=" OG1 THR B 189 " model vdw 2.158 2.440 nonbonded pdb=" OG SER F 146 " pdb=" OG1 THR F 189 " model vdw 2.184 2.440 nonbonded pdb=" OG SER E 180 " pdb=" O LEU F 349 " model vdw 2.187 2.440 nonbonded pdb=" OD1 ASN E 188 " pdb=" OH TYR E 403 " model vdw 2.188 2.440 ... (remaining 172120 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 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 18 5.49 5 S 84 5.16 5 C 12102 2.51 5 N 3276 2.21 5 O 3615 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.870 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: 15.490 Check model and map are aligned: 0.290 Process input model: 52.560 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.150 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:12.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6500 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 : 0.009 0.240 19485 Z= 0.576 Angle : 0.938 12.467 26472 Z= 0.441 Chirality : 0.052 0.338 2994 Planarity : 0.006 0.077 3399 Dihedral : 12.926 79.439 7011 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.16), residues: 2415 helix: -0.45 (0.15), residues: 1119 sheet: -0.36 (0.27), residues: 375 loop : -1.61 (0.19), residues: 921 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 481 time to evaluate : 2.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 483 average time/residue: 1.1966 time to fit residues: 656.0137 Evaluate side-chains 275 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 273 time to evaluate : 2.360 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 3.2448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 7.9990 chunk 184 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 124 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 190 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 115 optimal weight: 0.9990 chunk 141 optimal weight: 0.7980 chunk 220 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 ASN A 208 ASN A 414 ASN ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 247 ASN B 263 ASN ** B 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 HIS ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 ASN E 220 ASN E 401 ASN F 298 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.081 19485 Z= 0.287 Angle : 0.737 13.092 26472 Z= 0.364 Chirality : 0.048 0.271 2994 Planarity : 0.006 0.057 3399 Dihedral : 6.130 58.655 2652 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 20.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.72 % Favored : 95.20 % Rotamer Outliers : 3.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -1.26 (0.17), residues: 2415 helix: -0.29 (0.15), residues: 1122 sheet: -0.37 (0.27), residues: 363 loop : -1.58 (0.19), residues: 930 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 303 time to evaluate : 2.308 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 18 residues processed: 350 average time/residue: 1.0636 time to fit residues: 431.0150 Evaluate side-chains 258 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 240 time to evaluate : 2.255 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 15 residues processed: 3 average time/residue: 0.3257 time to fit residues: 4.5834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 122 optimal weight: 0.1980 chunk 68 optimal weight: 3.9990 chunk 183 optimal weight: 0.5980 chunk 150 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 221 optimal weight: 5.9990 chunk 238 optimal weight: 0.9990 chunk 196 optimal weight: 2.9990 chunk 219 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 ASN A 208 ASN ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 ASN C 80 ASN ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 HIS ** E 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 19485 Z= 0.236 Angle : 0.679 13.672 26472 Z= 0.336 Chirality : 0.046 0.208 2994 Planarity : 0.005 0.056 3399 Dihedral : 5.982 58.853 2652 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 20.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer Outliers : 3.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -1.15 (0.17), residues: 2415 helix: -0.20 (0.15), residues: 1137 sheet: -0.25 (0.28), residues: 351 loop : -1.58 (0.19), residues: 927 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 284 time to evaluate : 2.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 27 residues processed: 337 average time/residue: 1.0756 time to fit residues: 419.0537 Evaluate side-chains 273 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 246 time to evaluate : 1.849 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 21 residues processed: 6 average time/residue: 0.2591 time to fit residues: 5.2580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 218 optimal weight: 0.6980 chunk 166 optimal weight: 4.9990 chunk 114 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 148 optimal weight: 4.9990 chunk 221 optimal weight: 2.9990 chunk 234 optimal weight: 0.7980 chunk 115 optimal weight: 0.6980 chunk 210 optimal weight: 8.9990 chunk 63 optimal weight: 0.7980 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 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN C 428 GLN ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 ASN ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN F 247 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 19485 Z= 0.216 Angle : 0.656 13.550 26472 Z= 0.323 Chirality : 0.046 0.182 2994 Planarity : 0.005 0.051 3399 Dihedral : 5.903 59.103 2652 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 19.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer Outliers : 4.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.17), residues: 2415 helix: -0.03 (0.16), residues: 1134 sheet: -0.30 (0.27), residues: 372 loop : -1.49 (0.20), residues: 909 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 276 time to evaluate : 2.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 32 residues processed: 334 average time/residue: 1.0926 time to fit residues: 422.2530 Evaluate side-chains 278 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 246 time to evaluate : 2.295 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 24 residues processed: 8 average time/residue: 0.4072 time to fit residues: 7.6346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 195 optimal weight: 0.0770 chunk 133 optimal weight: 0.0670 chunk 3 optimal weight: 6.9990 chunk 174 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 119 optimal weight: 5.9990 chunk 210 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 overall best weight: 1.4080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 270 HIS F 100 ASN F 247 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.084 19485 Z= 0.289 Angle : 0.711 14.246 26472 Z= 0.351 Chirality : 0.048 0.253 2994 Planarity : 0.005 0.048 3399 Dihedral : 6.149 59.373 2652 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 22.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.97 % Favored : 94.99 % Rotamer Outliers : 4.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -1.07 (0.17), residues: 2415 helix: -0.09 (0.16), residues: 1116 sheet: -0.31 (0.28), residues: 354 loop : -1.53 (0.20), residues: 945 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 257 time to evaluate : 2.424 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 94 outliers final: 37 residues processed: 319 average time/residue: 1.0304 time to fit residues: 382.8657 Evaluate side-chains 268 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 231 time to evaluate : 2.266 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 37 outliers final: 27 residues processed: 11 average time/residue: 0.3684 time to fit residues: 8.9376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 79 optimal weight: 0.0970 chunk 211 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 137 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 235 optimal weight: 2.9990 chunk 195 optimal weight: 0.0070 chunk 108 optimal weight: 4.9990 chunk 19 optimal weight: 0.4980 chunk 77 optimal weight: 0.5980 chunk 123 optimal weight: 5.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 ASN B 11 GLN ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN F 247 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 19485 Z= 0.193 Angle : 0.644 13.954 26472 Z= 0.317 Chirality : 0.045 0.191 2994 Planarity : 0.005 0.046 3399 Dihedral : 5.856 59.771 2652 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 20.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer Outliers : 3.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.98 (0.17), residues: 2415 helix: 0.03 (0.16), residues: 1128 sheet: -0.35 (0.27), residues: 366 loop : -1.52 (0.20), residues: 921 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 264 time to evaluate : 2.447 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 29 residues processed: 315 average time/residue: 1.0969 time to fit residues: 399.4680 Evaluate side-chains 262 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 233 time to evaluate : 2.294 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 24 residues processed: 6 average time/residue: 0.4652 time to fit residues: 7.2097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 226 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 133 optimal weight: 0.0010 chunk 171 optimal weight: 0.8980 chunk 197 optimal weight: 3.9990 chunk 131 optimal weight: 0.4980 chunk 234 optimal weight: 6.9990 chunk 146 optimal weight: 0.8980 chunk 142 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 GLN ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 ASN F 247 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 19485 Z= 0.212 Angle : 0.653 13.867 26472 Z= 0.321 Chirality : 0.045 0.207 2994 Planarity : 0.005 0.051 3399 Dihedral : 5.832 59.911 2652 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 20.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer Outliers : 3.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.93 (0.17), residues: 2415 helix: 0.10 (0.16), residues: 1128 sheet: -0.34 (0.28), residues: 354 loop : -1.54 (0.20), residues: 933 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 252 time to evaluate : 2.371 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 34 residues processed: 305 average time/residue: 1.1435 time to fit residues: 403.2175 Evaluate side-chains 256 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 222 time to evaluate : 2.376 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 34 outliers final: 29 residues processed: 6 average time/residue: 0.3216 time to fit residues: 6.1806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 93 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 148 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 chunk 21 optimal weight: 5.9990 chunk 184 optimal weight: 0.6980 chunk 213 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 GLN ** E 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 247 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 19485 Z= 0.252 Angle : 0.693 14.020 26472 Z= 0.341 Chirality : 0.047 0.195 2994 Planarity : 0.005 0.066 3399 Dihedral : 5.974 59.636 2652 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 21.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer Outliers : 3.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.95 (0.17), residues: 2415 helix: 0.13 (0.16), residues: 1104 sheet: -0.37 (0.28), residues: 354 loop : -1.55 (0.20), residues: 957 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 225 time to evaluate : 2.309 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 38 residues processed: 276 average time/residue: 1.1230 time to fit residues: 357.1832 Evaluate side-chains 255 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 217 time to evaluate : 2.119 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 38 outliers final: 33 residues processed: 6 average time/residue: 0.4368 time to fit residues: 6.5889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 224 optimal weight: 0.8980 chunk 204 optimal weight: 0.6980 chunk 218 optimal weight: 3.9990 chunk 131 optimal weight: 0.7980 chunk 95 optimal weight: 0.6980 chunk 171 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 206 optimal weight: 9.9990 chunk 217 optimal weight: 0.9980 chunk 143 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN ** C 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 247 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 19485 Z= 0.229 Angle : 0.685 14.001 26472 Z= 0.338 Chirality : 0.046 0.265 2994 Planarity : 0.005 0.061 3399 Dihedral : 5.971 59.967 2652 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 21.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer Outliers : 2.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.95 (0.17), residues: 2415 helix: 0.09 (0.16), residues: 1116 sheet: -0.38 (0.28), residues: 354 loop : -1.53 (0.20), residues: 945 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 238 time to evaluate : 2.268 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 35 residues processed: 276 average time/residue: 1.1019 time to fit residues: 355.5216 Evaluate side-chains 256 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 221 time to evaluate : 2.342 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 35 outliers final: 31 residues processed: 5 average time/residue: 0.3477 time to fit residues: 5.7407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 230 optimal weight: 2.9990 chunk 140 optimal weight: 0.6980 chunk 109 optimal weight: 0.0770 chunk 160 optimal weight: 0.5980 chunk 242 optimal weight: 1.9990 chunk 222 optimal weight: 0.7980 chunk 192 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 148 optimal weight: 0.7980 chunk 118 optimal weight: 0.5980 chunk 153 optimal weight: 0.8980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 19485 Z= 0.214 Angle : 0.682 13.915 26472 Z= 0.336 Chirality : 0.046 0.349 2994 Planarity : 0.005 0.081 3399 Dihedral : 5.902 59.987 2652 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 21.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer Outliers : 1.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.90 (0.17), residues: 2415 helix: 0.13 (0.16), residues: 1113 sheet: -0.36 (0.28), residues: 354 loop : -1.47 (0.20), residues: 948 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 238 time to evaluate : 2.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 31 residues processed: 271 average time/residue: 1.0632 time to fit residues: 334.5650 Evaluate side-chains 244 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 213 time to evaluate : 2.174 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 31 outliers final: 29 residues processed: 3 average time/residue: 0.3633 time to fit residues: 4.6274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 177 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 193 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 198 optimal weight: 0.8980 chunk 24 optimal weight: 0.0000 chunk 35 optimal weight: 3.9990 chunk 169 optimal weight: 0.9980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4788 r_free = 0.4788 target = 0.197870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.174296 restraints weight = 24358.666| |-----------------------------------------------------------------------------| r_work (start): 0.4532 rms_B_bonded: 1.92 r_work: 0.4418 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.4296 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.4296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 19485 Z= 0.211 Angle : 0.675 13.915 26472 Z= 0.333 Chirality : 0.046 0.373 2994 Planarity : 0.005 0.063 3399 Dihedral : 5.861 59.530 2652 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 20.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer Outliers : 1.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.17), residues: 2415 helix: 0.17 (0.16), residues: 1098 sheet: -0.35 (0.28), residues: 354 loop : -1.45 (0.20), residues: 963 =============================================================================== Job complete usr+sys time: 6997.44 seconds wall clock time: 125 minutes 14.24 seconds (7514.24 seconds total)