Starting phenix.real_space_refine on Sat Feb 17 15:24:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7quq_14151/02_2024/7quq_14151_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7quq_14151/02_2024/7quq_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_2024/7quq_14151.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7quq_14151/02_2024/7quq_14151.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7quq_14151/02_2024/7quq_14151_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7quq_14151/02_2024/7quq_14151_updated.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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 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. 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 10.25, per 1000 atoms: 0.54 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: 8.26 Conformation dependent library (CDL) restraints added in 3.5 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: 3.70 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: 6.21 Time building geometry restraints manager: 8.78 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 - 17.36: 10572 17.36 - 34.72: 965 34.72 - 52.07: 133 52.07 - 69.43: 29 69.43 - 86.79: 22 Dihedral angle restraints: 11721 sinusoidal: 4677 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 11718 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 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: 3.850 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: 0.020 Extract box with map and model: 15.300 Check model and map are aligned: 0.280 Set scattering table: 0.190 Process input model: 52.670 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6355 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 : 13.757 86.788 7179 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 % Allowed : 0.10 % Favored : 99.80 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.003 TRP E 349 HIS 0.006 0.001 HIS E 141 PHE 0.058 0.002 PHE D 299 TYR 0.023 0.002 TYR F 422 ARG 0.007 0.001 ARG C 197 *********************** 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 : 2.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 MET cc_start: 0.6080 (mmt) cc_final: 0.5615 (mmp) REVERT: A 315 ARG cc_start: 0.5836 (tpp-160) cc_final: 0.4447 (ptt180) REVERT: A 354 PHE cc_start: 0.7904 (m-80) cc_final: 0.7513 (m-80) REVERT: B 88 GLU cc_start: 0.4830 (mp0) cc_final: 0.4558 (mp0) REVERT: B 193 ILE cc_start: 0.8040 (mt) cc_final: 0.7804 (mt) REVERT: C 403 TYR cc_start: 0.5373 (m-80) cc_final: 0.3917 (m-80) REVERT: D 88 GLU cc_start: 0.5457 (mp0) cc_final: 0.5218 (mp0) REVERT: D 299 PHE cc_start: 0.6615 (m-80) cc_final: 0.6201 (m-80) REVERT: E 219 TRP cc_start: 0.6205 (t-100) cc_final: 0.5990 (t-100) REVERT: E 245 ARG cc_start: 0.7869 (ttp80) cc_final: 0.7125 (ttp80) REVERT: F 73 VAL cc_start: 0.6496 (p) cc_final: 0.5766 (t) REVERT: F 388 MET cc_start: 0.5143 (ptm) cc_final: 0.3943 (mmm) outliers start: 2 outliers final: 2 residues processed: 483 average time/residue: 1.1949 time to fit residues: 654.2608 Evaluate side-chains 274 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 272 time to evaluate : 2.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain B residue 304 ASP 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: 0.9980 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: 1.3184 ------------------------------------------------------------------------------- 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** B 338 ASN 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 30 HIS ** 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: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 19485 Z= 0.287 Angle : 0.729 13.163 26472 Z= 0.361 Chirality : 0.048 0.272 2994 Planarity : 0.006 0.055 3399 Dihedral : 9.675 81.497 2824 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 21.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.97 % Favored : 94.95 % Rotamer: Outliers : 3.27 % Allowed : 14.63 % Favored : 82.09 % 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: -1.25 (0.17), residues: 2415 helix: -0.29 (0.15), residues: 1122 sheet: -0.38 (0.27), residues: 363 loop : -1.58 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 349 HIS 0.005 0.001 HIS E 30 PHE 0.040 0.002 PHE D 299 TYR 0.020 0.002 TYR B 398 ARG 0.005 0.001 ARG E 46 *********************** 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 365 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 299 time to evaluate : 2.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 VAL cc_start: 0.6902 (OUTLIER) cc_final: 0.6701 (t) REVERT: A 244 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7699 (mtm) REVERT: A 312 MET cc_start: 0.6209 (mmt) cc_final: 0.5700 (mmp) REVERT: A 315 ARG cc_start: 0.6071 (tpp-160) cc_final: 0.4607 (ptt180) REVERT: B 70 GLU cc_start: 0.6171 (OUTLIER) cc_final: 0.5815 (pp20) REVERT: B 398 TYR cc_start: 0.5969 (m-80) cc_final: 0.5465 (m-80) REVERT: C 403 TYR cc_start: 0.5762 (m-80) cc_final: 0.4202 (m-80) REVERT: D 76 ARG cc_start: 0.6123 (OUTLIER) cc_final: 0.5452 (mpp-170) REVERT: D 247 ASN cc_start: 0.6637 (m-40) cc_final: 0.6377 (m-40) REVERT: E 74 GLU cc_start: 0.5898 (OUTLIER) cc_final: 0.5645 (pt0) REVERT: E 245 ARG cc_start: 0.7970 (ttp80) cc_final: 0.7418 (ttp80) REVERT: E 341 ARG cc_start: 0.6081 (ttp-110) cc_final: 0.5851 (tmm-80) REVERT: F 175 LEU cc_start: 0.7427 (pt) cc_final: 0.7210 (pp) REVERT: F 182 GLU cc_start: 0.7284 (pp20) cc_final: 0.7031 (pp20) REVERT: F 228 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8247 (mp) REVERT: F 388 MET cc_start: 0.5505 (ptm) cc_final: 0.3777 (mmt) outliers start: 66 outliers final: 20 residues processed: 346 average time/residue: 1.0205 time to fit residues: 408.6511 Evaluate side-chains 270 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 244 time to evaluate : 2.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 126 TYR Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 401 ASN Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 224 ASP Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 228 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 122 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 183 optimal weight: 0.0020 chunk 150 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 221 optimal weight: 6.9990 chunk 238 optimal weight: 0.9980 chunk 196 optimal weight: 0.9980 chunk 219 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 chunk 177 optimal weight: 0.7980 overall best weight: 0.7188 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 HIS E 208 ASN E 302 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6598 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 19485 Z= 0.222 Angle : 0.667 13.200 26472 Z= 0.330 Chirality : 0.046 0.201 2994 Planarity : 0.005 0.053 3399 Dihedral : 9.357 82.153 2820 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 20.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.32 % Allowed : 19.05 % Favored : 77.63 % 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: -1.12 (0.17), residues: 2415 helix: -0.17 (0.15), residues: 1125 sheet: -0.28 (0.28), residues: 351 loop : -1.53 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 349 HIS 0.004 0.001 HIS D 371 PHE 0.023 0.002 PHE D 299 TYR 0.016 0.002 TYR D 342 ARG 0.010 0.000 ARG E 46 *********************** 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 355 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 288 time to evaluate : 2.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 PHE cc_start: 0.5926 (t80) cc_final: 0.5411 (t80) REVERT: A 244 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.7712 (mtm) REVERT: A 312 MET cc_start: 0.6289 (mmt) cc_final: 0.5816 (mmp) REVERT: A 315 ARG cc_start: 0.6151 (tpp-160) cc_final: 0.4625 (ptt180) REVERT: B 70 GLU cc_start: 0.6067 (OUTLIER) cc_final: 0.5726 (pp20) REVERT: B 355 GLU cc_start: 0.6605 (OUTLIER) cc_final: 0.5355 (pm20) REVERT: B 398 TYR cc_start: 0.5878 (m-80) cc_final: 0.5481 (m-80) REVERT: C 403 TYR cc_start: 0.5708 (m-80) cc_final: 0.4410 (m-80) REVERT: D 76 ARG cc_start: 0.6107 (OUTLIER) cc_final: 0.5675 (mpp-170) REVERT: D 382 ILE cc_start: 0.6045 (OUTLIER) cc_final: 0.5550 (mp) REVERT: E 341 ARG cc_start: 0.6248 (ttp-110) cc_final: 0.5925 (tmm-80) REVERT: F 158 GLN cc_start: 0.6282 (OUTLIER) cc_final: 0.5479 (pm20) REVERT: F 175 LEU cc_start: 0.7445 (pt) cc_final: 0.7229 (pp) REVERT: F 228 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8348 (mp) REVERT: F 310 TYR cc_start: 0.7255 (m-80) cc_final: 0.7030 (m-80) REVERT: F 388 MET cc_start: 0.5537 (ptm) cc_final: 0.3852 (mmt) outliers start: 67 outliers final: 23 residues processed: 329 average time/residue: 1.0443 time to fit residues: 397.3058 Evaluate side-chains 275 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 245 time to evaluate : 2.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 219 TRP Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 401 ASN Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 158 GLN Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 224 ASP Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 237 THR Chi-restraints excluded: chain F residue 285 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 218 optimal weight: 0.9990 chunk 166 optimal weight: 0.0010 chunk 114 optimal weight: 3.9990 chunk 24 optimal weight: 0.0020 chunk 105 optimal weight: 7.9990 chunk 148 optimal weight: 4.9990 chunk 221 optimal weight: 4.9990 chunk 234 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 210 optimal weight: 10.0000 chunk 63 optimal weight: 0.0570 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN E 401 ASN F 247 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6555 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19485 Z= 0.187 Angle : 0.631 11.758 26472 Z= 0.311 Chirality : 0.045 0.192 2994 Planarity : 0.005 0.048 3399 Dihedral : 9.043 81.748 2820 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.72 % Allowed : 20.24 % Favored : 76.04 % 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: 0.09 (0.16), residues: 1119 sheet: -0.29 (0.27), residues: 372 loop : -1.43 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 102 HIS 0.003 0.001 HIS D 371 PHE 0.024 0.001 PHE E 191 TYR 0.020 0.002 TYR D 342 ARG 0.012 0.000 ARG E 46 *********************** 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 347 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 272 time to evaluate : 2.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 PHE cc_start: 0.5710 (t80) cc_final: 0.5280 (t80) REVERT: A 129 ASP cc_start: 0.6829 (m-30) cc_final: 0.6385 (m-30) REVERT: A 312 MET cc_start: 0.6215 (mmt) cc_final: 0.5984 (mmt) REVERT: A 315 ARG cc_start: 0.6084 (tpp-160) cc_final: 0.4611 (ptt180) REVERT: A 330 LYS cc_start: 0.7348 (OUTLIER) cc_final: 0.7111 (pmtt) REVERT: B 70 GLU cc_start: 0.5955 (OUTLIER) cc_final: 0.5660 (pp20) REVERT: B 355 GLU cc_start: 0.6447 (OUTLIER) cc_final: 0.5172 (pm20) REVERT: B 361 PHE cc_start: 0.5463 (OUTLIER) cc_final: 0.4448 (m-80) REVERT: B 398 TYR cc_start: 0.5796 (m-80) cc_final: 0.5411 (m-80) REVERT: C 151 PHE cc_start: 0.6135 (t80) cc_final: 0.5921 (t80) REVERT: C 403 TYR cc_start: 0.5604 (m-80) cc_final: 0.4443 (m-80) REVERT: D 382 ILE cc_start: 0.5980 (OUTLIER) cc_final: 0.5548 (mp) REVERT: E 70 MET cc_start: 0.5123 (OUTLIER) cc_final: 0.4870 (mpt) REVERT: E 341 ARG cc_start: 0.6126 (ttp-110) cc_final: 0.5793 (tmm-80) REVERT: F 228 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8291 (mp) REVERT: F 310 TYR cc_start: 0.7229 (m-80) cc_final: 0.6939 (m-80) REVERT: F 388 MET cc_start: 0.5525 (ptm) cc_final: 0.3985 (mmt) outliers start: 75 outliers final: 28 residues processed: 327 average time/residue: 1.0125 time to fit residues: 385.5039 Evaluate side-chains 274 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 239 time to evaluate : 2.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 219 TRP Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 361 PHE Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 405 ASN Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 401 ASN Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 224 ASP Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 237 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 195 optimal weight: 0.9990 chunk 133 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 174 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 200 optimal weight: 6.9990 chunk 162 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 119 optimal weight: 4.9990 chunk 210 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 GLN ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 HIS B 400 ASN ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 ASN ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 ASN ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 ASN ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.117 19485 Z= 0.632 Angle : 1.000 14.841 26472 Z= 0.507 Chirality : 0.059 0.384 2994 Planarity : 0.007 0.068 3399 Dihedral : 10.481 87.379 2820 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 32.53 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.80 % Favored : 94.08 % Rotamer: Outliers : 6.10 % Allowed : 20.34 % Favored : 73.56 % 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: -1.79 (0.16), residues: 2415 helix: -0.73 (0.15), residues: 1101 sheet: -0.61 (0.30), residues: 315 loop : -1.80 (0.18), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP A 219 HIS 0.010 0.003 HIS A 366 PHE 0.039 0.004 PHE E 151 TYR 0.034 0.004 TYR C 323 ARG 0.014 0.001 ARG E 46 *********************** 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 378 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 255 time to evaluate : 2.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.6199 (ptp-170) cc_final: 0.5373 (ptm160) REVERT: A 70 MET cc_start: 0.6567 (OUTLIER) cc_final: 0.5991 (mtp) REVERT: A 244 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.7491 (mtm) REVERT: A 312 MET cc_start: 0.6619 (mmt) cc_final: 0.6370 (mmp) REVERT: A 315 ARG cc_start: 0.6636 (tpp-160) cc_final: 0.5160 (ptt180) REVERT: B 127 LYS cc_start: 0.4512 (OUTLIER) cc_final: 0.2657 (pptt) REVERT: B 355 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.5900 (pm20) REVERT: B 398 TYR cc_start: 0.6263 (m-80) cc_final: 0.5905 (m-80) REVERT: D 94 LYS cc_start: 0.4232 (OUTLIER) cc_final: 0.4024 (tppt) REVERT: D 349 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7143 (mm) REVERT: E 166 ILE cc_start: 0.6881 (OUTLIER) cc_final: 0.6457 (mm) REVERT: E 178 GLN cc_start: 0.7853 (tt0) cc_final: 0.7620 (tt0) REVERT: E 312 MET cc_start: 0.6953 (mmt) cc_final: 0.6673 (mmm) REVERT: E 341 ARG cc_start: 0.6505 (ttp-110) cc_final: 0.6210 (tmm-80) REVERT: F 158 GLN cc_start: 0.6569 (OUTLIER) cc_final: 0.5476 (pm20) REVERT: F 173 SER cc_start: 0.7937 (OUTLIER) cc_final: 0.7356 (p) REVERT: F 240 LEU cc_start: 0.8007 (tt) cc_final: 0.7356 (mt) REVERT: F 388 MET cc_start: 0.6802 (ptm) cc_final: 0.4679 (mmt) REVERT: F 418 LEU cc_start: 0.5388 (OUTLIER) cc_final: 0.5121 (tp) outliers start: 123 outliers final: 52 residues processed: 341 average time/residue: 1.1416 time to fit residues: 446.3021 Evaluate side-chains 286 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 224 time to evaluate : 2.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 219 TRP Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 405 ASN Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 185 ASN Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 355 GLU Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 310 SER Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 158 GLN Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 224 ASP Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 226 ASN Chi-restraints excluded: chain F residue 237 THR Chi-restraints excluded: chain F residue 267 THR Chi-restraints excluded: chain F residue 285 ASN Chi-restraints excluded: chain F residue 288 ASP Chi-restraints excluded: chain F residue 407 MET Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain F residue 426 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 79 optimal weight: 0.9990 chunk 211 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 235 optimal weight: 0.8980 chunk 195 optimal weight: 0.3980 chunk 108 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 123 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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** ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 HIS ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 ASN E 266 GLN E 270 HIS E 401 ASN F 247 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 19485 Z= 0.258 Angle : 0.722 12.958 26472 Z= 0.359 Chirality : 0.048 0.188 2994 Planarity : 0.005 0.049 3399 Dihedral : 9.622 89.422 2820 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 24.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 4.32 % Allowed : 23.07 % Favored : 72.62 % 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: -1.48 (0.16), residues: 2415 helix: -0.35 (0.15), residues: 1104 sheet: -0.60 (0.28), residues: 348 loop : -1.79 (0.19), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 102 HIS 0.007 0.001 HIS A 366 PHE 0.022 0.002 PHE E 191 TYR 0.017 0.002 TYR F 106 ARG 0.011 0.001 ARG E 46 *********************** 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 348 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 261 time to evaluate : 2.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7667 (mtm) REVERT: A 315 ARG cc_start: 0.6479 (tpp-160) cc_final: 0.5172 (ptt180) REVERT: B 355 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.5511 (pm20) REVERT: B 398 TYR cc_start: 0.5898 (m-80) cc_final: 0.5455 (m-80) REVERT: C 403 TYR cc_start: 0.5815 (m-80) cc_final: 0.4763 (m-80) REVERT: D 77 ILE cc_start: 0.6327 (OUTLIER) cc_final: 0.6124 (mp) REVERT: D 94 LYS cc_start: 0.3937 (OUTLIER) cc_final: 0.3709 (tppt) REVERT: D 382 ILE cc_start: 0.5961 (OUTLIER) cc_final: 0.5686 (mp) REVERT: E 166 ILE cc_start: 0.7039 (OUTLIER) cc_final: 0.6444 (mp) REVERT: E 341 ARG cc_start: 0.6397 (ttp-110) cc_final: 0.6097 (tmm-80) REVERT: F 173 SER cc_start: 0.7556 (OUTLIER) cc_final: 0.7062 (p) REVERT: F 228 ILE cc_start: 0.8827 (OUTLIER) cc_final: 0.8524 (mp) REVERT: F 240 LEU cc_start: 0.7844 (tt) cc_final: 0.7284 (mp) REVERT: F 310 TYR cc_start: 0.7384 (m-80) cc_final: 0.7107 (m-80) REVERT: F 388 MET cc_start: 0.6167 (ptm) cc_final: 0.4654 (mmt) outliers start: 87 outliers final: 34 residues processed: 323 average time/residue: 1.0977 time to fit residues: 407.5096 Evaluate side-chains 259 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 217 time to evaluate : 2.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 322 LYS Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 405 ASN Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 401 ASN Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 158 GLN Chi-restraints excluded: chain F residue 160 TYR Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 224 ASP Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 237 THR Chi-restraints excluded: chain F residue 285 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 226 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 133 optimal weight: 0.5980 chunk 171 optimal weight: 0.5980 chunk 197 optimal weight: 4.9990 chunk 131 optimal weight: 0.5980 chunk 234 optimal weight: 3.9990 chunk 146 optimal weight: 0.8980 chunk 142 optimal weight: 0.6980 chunk 108 optimal weight: 0.0020 chunk 144 optimal weight: 0.8980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 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** E 302 ASN E 401 ASN F 247 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19485 Z= 0.222 Angle : 0.682 12.613 26472 Z= 0.340 Chirality : 0.047 0.187 2994 Planarity : 0.005 0.046 3399 Dihedral : 9.228 89.619 2820 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 22.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.87 % Allowed : 24.55 % Favored : 71.58 % 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: -1.22 (0.17), residues: 2415 helix: -0.11 (0.16), residues: 1092 sheet: -0.67 (0.28), residues: 357 loop : -1.58 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 102 HIS 0.006 0.001 HIS A 366 PHE 0.022 0.002 PHE E 191 TYR 0.024 0.002 TYR F 106 ARG 0.012 0.000 ARG E 46 *********************** 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 328 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 250 time to evaluate : 2.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7683 (mtm) REVERT: A 315 ARG cc_start: 0.6282 (tpp-160) cc_final: 0.4986 (ptt180) REVERT: B 60 TYR cc_start: 0.4542 (m-80) cc_final: 0.4185 (m-80) REVERT: B 175 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7845 (tp) REVERT: B 178 ASP cc_start: 0.6765 (t0) cc_final: 0.6541 (t70) REVERT: B 355 GLU cc_start: 0.6761 (OUTLIER) cc_final: 0.5414 (pm20) REVERT: B 398 TYR cc_start: 0.5837 (m-80) cc_final: 0.5337 (m-80) REVERT: C 245 ARG cc_start: 0.7335 (ttp80) cc_final: 0.7133 (ttp80) REVERT: C 403 TYR cc_start: 0.5411 (m-80) cc_final: 0.4555 (m-80) REVERT: D 77 ILE cc_start: 0.6245 (OUTLIER) cc_final: 0.5858 (mp) REVERT: D 184 TYR cc_start: 0.6994 (m-10) cc_final: 0.6739 (m-10) REVERT: D 382 ILE cc_start: 0.6149 (OUTLIER) cc_final: 0.5818 (mp) REVERT: E 341 ARG cc_start: 0.6290 (ttp-110) cc_final: 0.5974 (tmm-80) REVERT: F 158 GLN cc_start: 0.6062 (OUTLIER) cc_final: 0.5098 (pm20) REVERT: F 173 SER cc_start: 0.7457 (OUTLIER) cc_final: 0.6948 (p) REVERT: F 228 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8425 (mp) REVERT: F 240 LEU cc_start: 0.7738 (tt) cc_final: 0.7227 (mp) REVERT: F 380 ARG cc_start: 0.6028 (OUTLIER) cc_final: 0.5738 (ptt90) REVERT: F 388 MET cc_start: 0.6106 (ptm) cc_final: 0.4531 (mmt) outliers start: 78 outliers final: 33 residues processed: 301 average time/residue: 1.0737 time to fit residues: 372.5617 Evaluate side-chains 264 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 222 time to evaluate : 2.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 322 LYS Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 405 ASN Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 185 ASN Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 158 GLN Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 224 ASP Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 226 ASN Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 285 ASN Chi-restraints excluded: chain F residue 380 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 93 optimal weight: 3.9990 chunk 139 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 184 optimal weight: 0.7980 chunk 213 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 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 302 ASN E 401 ASN ** F 28 HIS ** 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: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 19485 Z= 0.313 Angle : 0.735 12.926 26472 Z= 0.366 Chirality : 0.048 0.213 2994 Planarity : 0.005 0.059 3399 Dihedral : 9.429 82.349 2820 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 25.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.30 % Favored : 94.66 % Rotamer: Outliers : 3.77 % Allowed : 26.04 % Favored : 70.19 % 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: -1.33 (0.17), residues: 2415 helix: -0.21 (0.15), residues: 1101 sheet: -0.61 (0.28), residues: 354 loop : -1.69 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP D 102 HIS 0.007 0.001 HIS F 28 PHE 0.028 0.002 PHE E 151 TYR 0.021 0.002 TYR F 106 ARG 0.019 0.001 ARG B 423 *********************** 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 307 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 231 time to evaluate : 2.118 Fit side-chains revert: symmetry clash REVERT: A 232 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8178 (tp) REVERT: A 244 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7704 (mtm) REVERT: A 315 ARG cc_start: 0.6381 (tpp-160) cc_final: 0.5103 (ptt180) REVERT: B 56 ARG cc_start: 0.5125 (mmt90) cc_final: 0.4903 (mmt90) REVERT: B 178 ASP cc_start: 0.6817 (t0) cc_final: 0.6590 (t70) REVERT: B 353 TYR cc_start: 0.8419 (OUTLIER) cc_final: 0.7976 (m-10) REVERT: B 355 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.5590 (pm20) REVERT: B 398 TYR cc_start: 0.6053 (m-80) cc_final: 0.5491 (m-80) REVERT: C 245 ARG cc_start: 0.7376 (ttp80) cc_final: 0.7175 (ttp80) REVERT: C 403 TYR cc_start: 0.5860 (m-80) cc_final: 0.4813 (m-80) REVERT: D 4 ILE cc_start: 0.6786 (OUTLIER) cc_final: 0.6553 (mt) REVERT: D 77 ILE cc_start: 0.6329 (OUTLIER) cc_final: 0.5962 (mp) REVERT: D 382 ILE cc_start: 0.6253 (OUTLIER) cc_final: 0.5941 (mp) REVERT: E 341 ARG cc_start: 0.6417 (ttp-110) cc_final: 0.6119 (tmm-80) REVERT: F 129 LYS cc_start: 0.4939 (mppt) cc_final: 0.4208 (mptt) REVERT: F 158 GLN cc_start: 0.6172 (OUTLIER) cc_final: 0.5191 (pm20) REVERT: F 173 SER cc_start: 0.7563 (OUTLIER) cc_final: 0.7007 (p) REVERT: F 228 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8483 (mp) REVERT: F 240 LEU cc_start: 0.7907 (tt) cc_final: 0.7297 (mp) REVERT: F 388 MET cc_start: 0.6275 (ptm) cc_final: 0.4931 (mmt) outliers start: 76 outliers final: 44 residues processed: 278 average time/residue: 1.0840 time to fit residues: 348.2545 Evaluate side-chains 262 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 208 time to evaluate : 2.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 322 LYS Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 353 TYR Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 405 ASN Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 185 ASN Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 355 GLU Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain E residue 401 ASN Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 158 GLN Chi-restraints excluded: chain F residue 160 TYR Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 224 ASP Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 226 ASN Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 237 THR Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 285 ASN Chi-restraints excluded: chain F residue 426 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 224 optimal weight: 0.9980 chunk 204 optimal weight: 0.7980 chunk 218 optimal weight: 0.9990 chunk 131 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 171 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 197 optimal weight: 2.9990 chunk 206 optimal weight: 20.0000 chunk 217 optimal weight: 0.9980 chunk 143 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 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 302 ASN E 401 ASN ** F 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19485 Z= 0.251 Angle : 0.709 12.705 26472 Z= 0.351 Chirality : 0.047 0.190 2994 Planarity : 0.005 0.060 3399 Dihedral : 9.238 80.545 2820 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 23.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.27 % Allowed : 26.49 % Favored : 70.24 % 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: -0.12 (0.16), residues: 1095 sheet: -0.55 (0.28), residues: 351 loop : -1.71 (0.19), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP E 23 HIS 0.006 0.001 HIS F 28 PHE 0.021 0.002 PHE A 191 TYR 0.021 0.002 TYR F 106 ARG 0.014 0.001 ARG E 46 *********************** 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 298 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 232 time to evaluate : 2.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7697 (mtm) REVERT: A 315 ARG cc_start: 0.6310 (tpp-160) cc_final: 0.5055 (ptt180) REVERT: B 56 ARG cc_start: 0.5207 (mmt90) cc_final: 0.4984 (mmt90) REVERT: B 118 MET cc_start: 0.6683 (mmm) cc_final: 0.5696 (mmt) REVERT: B 175 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7782 (tp) REVERT: B 353 TYR cc_start: 0.8404 (OUTLIER) cc_final: 0.7881 (m-10) REVERT: B 355 GLU cc_start: 0.6699 (OUTLIER) cc_final: 0.5418 (pm20) REVERT: B 398 TYR cc_start: 0.5917 (m-80) cc_final: 0.5404 (m-80) REVERT: C 403 TYR cc_start: 0.5519 (m-80) cc_final: 0.4643 (m-80) REVERT: D 4 ILE cc_start: 0.6682 (OUTLIER) cc_final: 0.6413 (mt) REVERT: D 77 ILE cc_start: 0.6266 (OUTLIER) cc_final: 0.5871 (mp) REVERT: D 355 GLU cc_start: 0.6454 (OUTLIER) cc_final: 0.6070 (pm20) REVERT: D 382 ILE cc_start: 0.6265 (OUTLIER) cc_final: 0.5959 (mp) REVERT: E 341 ARG cc_start: 0.6372 (ttp-110) cc_final: 0.6059 (tmm-80) REVERT: F 31 THR cc_start: 0.5858 (OUTLIER) cc_final: 0.5415 (t) REVERT: F 129 LYS cc_start: 0.4544 (mppt) cc_final: 0.4110 (mptt) REVERT: F 158 GLN cc_start: 0.6148 (OUTLIER) cc_final: 0.5112 (pm20) REVERT: F 173 SER cc_start: 0.7487 (OUTLIER) cc_final: 0.6969 (p) REVERT: F 228 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8465 (mp) REVERT: F 240 LEU cc_start: 0.7775 (tt) cc_final: 0.7212 (mp) REVERT: F 388 MET cc_start: 0.6242 (ptm) cc_final: 0.4684 (mmt) outliers start: 66 outliers final: 36 residues processed: 272 average time/residue: 1.0491 time to fit residues: 331.6011 Evaluate side-chains 263 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 215 time to evaluate : 2.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 322 LYS Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 353 TYR Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 405 ASN Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 185 ASN Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 355 GLU Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain E residue 401 ASN Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 158 GLN Chi-restraints excluded: chain F residue 160 TYR Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 224 ASP Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 226 ASN Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 285 ASN Chi-restraints excluded: chain F residue 426 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 230 optimal weight: 0.8980 chunk 140 optimal weight: 0.5980 chunk 109 optimal weight: 4.9990 chunk 160 optimal weight: 0.8980 chunk 242 optimal weight: 0.7980 chunk 222 optimal weight: 4.9990 chunk 192 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 148 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 153 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: ** A 208 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 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN E 401 ASN ** F 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19485 Z= 0.244 Angle : 0.711 12.548 26472 Z= 0.351 Chirality : 0.047 0.188 2994 Planarity : 0.005 0.064 3399 Dihedral : 9.115 80.610 2820 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 23.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.83 % Allowed : 27.68 % Favored : 69.49 % 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: -1.28 (0.17), residues: 2415 helix: -0.08 (0.16), residues: 1092 sheet: -0.44 (0.30), residues: 306 loop : -1.79 (0.18), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP D 102 HIS 0.004 0.001 HIS F 28 PHE 0.020 0.002 PHE A 191 TYR 0.026 0.002 TYR F 106 ARG 0.015 0.001 ARG E 46 ********************** 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 293 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 236 time to evaluate : 2.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7700 (mtm) REVERT: A 315 ARG cc_start: 0.6242 (tpp-160) cc_final: 0.4955 (ptt180) REVERT: B 118 MET cc_start: 0.6589 (mmm) cc_final: 0.6388 (mtt) REVERT: B 175 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7764 (tp) REVERT: B 353 TYR cc_start: 0.8384 (OUTLIER) cc_final: 0.7872 (m-10) REVERT: B 355 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.5525 (pm20) REVERT: B 398 TYR cc_start: 0.5867 (m-80) cc_final: 0.5351 (m-80) REVERT: C 403 TYR cc_start: 0.5437 (m-80) cc_final: 0.4596 (m-80) REVERT: D 77 ILE cc_start: 0.6235 (OUTLIER) cc_final: 0.5864 (mp) REVERT: D 355 GLU cc_start: 0.6461 (OUTLIER) cc_final: 0.6095 (pm20) REVERT: D 382 ILE cc_start: 0.6193 (OUTLIER) cc_final: 0.5897 (mp) REVERT: E 341 ARG cc_start: 0.6340 (ttp-110) cc_final: 0.6037 (tmm-80) REVERT: F 31 THR cc_start: 0.5952 (OUTLIER) cc_final: 0.5501 (t) REVERT: F 90 SER cc_start: 0.4749 (m) cc_final: 0.4525 (m) REVERT: F 129 LYS cc_start: 0.4420 (mppt) cc_final: 0.4038 (mptt) REVERT: F 158 GLN cc_start: 0.6022 (OUTLIER) cc_final: 0.5267 (pm20) REVERT: F 173 SER cc_start: 0.7438 (OUTLIER) cc_final: 0.6928 (p) REVERT: F 228 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8462 (mp) REVERT: F 240 LEU cc_start: 0.7750 (tt) cc_final: 0.7145 (mp) REVERT: F 388 MET cc_start: 0.6255 (ptm) cc_final: 0.4709 (mmt) outliers start: 57 outliers final: 33 residues processed: 269 average time/residue: 1.0868 time to fit residues: 337.9878 Evaluate side-chains 270 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 226 time to evaluate : 2.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 322 LYS Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 353 TYR Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 405 ASN Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 185 ASN Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 355 GLU Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 48 MET Chi-restraints excluded: chain F residue 158 GLN Chi-restraints excluded: chain F residue 160 TYR Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 224 ASP Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 226 ASN Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 285 ASN Chi-restraints excluded: chain F residue 426 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 177 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 193 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 169 optimal weight: 0.1980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN B 400 ASN ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 GLN ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN E 401 ASN ** F 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 247 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.195237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.170857 restraints weight = 24152.520| |-----------------------------------------------------------------------------| r_work (start): 0.4488 rms_B_bonded: 1.98 r_work: 0.4356 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.4356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 19485 Z= 0.236 Angle : 0.708 12.422 26472 Z= 0.348 Chirality : 0.047 0.193 2994 Planarity : 0.005 0.063 3399 Dihedral : 8.922 80.714 2820 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 23.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.83 % Allowed : 27.78 % Favored : 69.39 % 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: -1.14 (0.17), residues: 2415 helix: -0.01 (0.16), residues: 1101 sheet: -0.56 (0.28), residues: 351 loop : -1.62 (0.19), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 102 HIS 0.005 0.001 HIS A 366 PHE 0.024 0.001 PHE E 191 TYR 0.022 0.002 TYR F 106 ARG 0.015 0.001 ARG E 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6737.75 seconds wall clock time: 121 minutes 16.74 seconds (7276.74 seconds total)