Starting phenix.real_space_refine on Sat Jul 4 04:09:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qb2_52983/07_2026/9qb2_52983.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qb2_52983/07_2026/9qb2_52983.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qb2_52983/07_2026/9qb2_52983.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qb2_52983/07_2026/9qb2_52983.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qb2_52983/07_2026/9qb2_52983.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qb2_52983/07_2026/9qb2_52983.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.005 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 202 5.49 5 S 86 5.16 5 C 10506 2.51 5 N 3156 2.21 5 O 3857 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 107 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17807 Number of models: 1 Model: "" Number of chains: 11 Chain: "C" Number of atoms: 3129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3129 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 16, 'TRANS': 377} Chain breaks: 1 Chain: "D" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 780 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 7, 'TRANS': 86} Chain: "E" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1035 Classifications: {'peptide': 130} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 119} Chain: "F" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 542 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 58} Chain: "G" Number of atoms: 2792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2792 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 13, 'TRANS': 339} Chain: "H" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 9, 'TRANS': 87} Chain: "I" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1035 Classifications: {'peptide': 130} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 119} Chain: "J" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 542 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 58} Chain: "K" Number of atoms: 2724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2724 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 23, 'TRANS': 324} Chain breaks: 3 Chain: "b" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 1129 Inner-chain residues flagged as termini: ['pdbres=" G b 322 "'] Classifications: {'RNA': 53} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 24, 'rna3p_pyr': 27} Link IDs: {'rna2p': 1, 'rna3p': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 3297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 3297 Inner-chain residues flagged as termini: ['pdbres=" U B 195 "', 'pdbres=" A B 340 "', 'pdbres=" G B 362 "'] Classifications: {'RNA': 154} Modifications used: {'5*END': 4, 'rna2p_pur': 14, 'rna2p_pyr': 9, 'rna3p_pur': 68, 'rna3p_pyr': 59} Link IDs: {'rna2p': 22, 'rna3p': 131} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 3.37, per 1000 atoms: 0.19 Number of scatterers: 17807 At special positions: 0 Unit cell: (109.077, 156.732, 156.732, 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 86 16.00 P 202 15.00 O 3857 8.00 N 3156 7.00 C 10506 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 583.4 milliseconds 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3138 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 17 sheets defined 30.1% alpha, 19.2% beta 69 base pairs and 137 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'C' and resid 23 through 34 removed outlier: 3.646A pdb=" N HIS C 32 " --> pdb=" O ALA C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 57 Processing helix chain 'C' and resid 77 through 81 removed outlier: 3.761A pdb=" N ARG C 81 " --> pdb=" O PRO C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 89 Processing helix chain 'C' and resid 101 through 113 Processing helix chain 'C' and resid 138 through 141 removed outlier: 3.635A pdb=" N ARG C 141 " --> pdb=" O ARG C 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 138 through 141' Processing helix chain 'C' and resid 142 through 148 Processing helix chain 'C' and resid 165 through 176 removed outlier: 4.057A pdb=" N LEU C 169 " --> pdb=" O GLY C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 238 Processing helix chain 'C' and resid 262 through 277 Processing helix chain 'C' and resid 281 through 286 Processing helix chain 'C' and resid 290 through 292 No H-bonds generated for 'chain 'C' and resid 290 through 292' Processing helix chain 'C' and resid 305 through 311 Processing helix chain 'C' and resid 351 through 358 removed outlier: 3.559A pdb=" N THR C 357 " --> pdb=" O ALA C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 395 Processing helix chain 'C' and resid 409 through 416 Processing helix chain 'D' and resid 90 through 94 Processing helix chain 'D' and resid 134 through 138 removed outlier: 3.948A pdb=" N PHE D 138 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 149 No H-bonds generated for 'chain 'D' and resid 147 through 149' Processing helix chain 'D' and resid 153 through 157 Processing helix chain 'E' and resid 24 through 28 removed outlier: 3.738A pdb=" N LEU E 28 " --> pdb=" O TYR E 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 24 through 28' Processing helix chain 'E' and resid 40 through 57 Processing helix chain 'E' and resid 63 through 74 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 93 through 101 removed outlier: 3.763A pdb=" N ARG E 101 " --> pdb=" O MET E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 118 Processing helix chain 'E' and resid 135 through 148 Processing helix chain 'F' and resid 41 through 52 removed outlier: 3.518A pdb=" N ARG F 51 " --> pdb=" O THR F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 59 removed outlier: 3.571A pdb=" N GLN F 59 " --> pdb=" O MET F 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 52 Processing helix chain 'G' and resid 53 through 57 Processing helix chain 'G' and resid 58 through 62 Processing helix chain 'G' and resid 77 through 81 removed outlier: 3.751A pdb=" N ARG G 81 " --> pdb=" O PRO G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 89 Processing helix chain 'G' and resid 101 through 113 Processing helix chain 'G' and resid 138 through 141 Processing helix chain 'G' and resid 142 through 148 Processing helix chain 'G' and resid 165 through 176 removed outlier: 3.799A pdb=" N LEU G 169 " --> pdb=" O GLY G 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 238 Processing helix chain 'G' and resid 263 through 277 Processing helix chain 'G' and resid 281 through 286 Processing helix chain 'G' and resid 290 through 294 removed outlier: 3.924A pdb=" N THR G 294 " --> pdb=" O LYS G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 302 through 311 removed outlier: 3.507A pdb=" N VAL G 306 " --> pdb=" O LYS G 302 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASN G 307 " --> pdb=" O ASP G 303 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ALA G 308 " --> pdb=" O SER G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 358 Processing helix chain 'G' and resid 383 through 395 Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.616A pdb=" N LYS H 94 " --> pdb=" O ASP H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 134 through 138 removed outlier: 3.906A pdb=" N PHE H 138 " --> pdb=" O ALA H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 157 Processing helix chain 'I' and resid 24 through 28 Processing helix chain 'I' and resid 29 through 31 No H-bonds generated for 'chain 'I' and resid 29 through 31' Processing helix chain 'I' and resid 40 through 57 Processing helix chain 'I' and resid 63 through 74 removed outlier: 3.515A pdb=" N LYS I 69 " --> pdb=" O LYS I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.543A pdb=" N VAL I 90 " --> pdb=" O PRO I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 102 removed outlier: 3.575A pdb=" N ARG I 101 " --> pdb=" O MET I 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 110 through 118 removed outlier: 3.545A pdb=" N ALA I 118 " --> pdb=" O LEU I 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 132 through 134 No H-bonds generated for 'chain 'I' and resid 132 through 134' Processing helix chain 'I' and resid 135 through 148 Processing helix chain 'J' and resid 41 through 52 Processing helix chain 'J' and resid 55 through 59 Processing helix chain 'K' and resid 163 through 167 removed outlier: 4.020A pdb=" N GLN K 167 " --> pdb=" O PHE K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 199 through 204 removed outlier: 4.455A pdb=" N TYR K 203 " --> pdb=" O PRO K 199 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 63 through 64 removed outlier: 6.758A pdb=" N VAL C 300 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N TYR C 323 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ARG C 298 " --> pdb=" O TYR C 323 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LYS C 297 " --> pdb=" O GLU C 332 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE C 333 " --> pdb=" O MET C 345 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N MET C 345 " --> pdb=" O ILE C 333 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL C 335 " --> pdb=" O ILE C 343 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N ILE C 343 " --> pdb=" O VAL C 369 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N VAL C 369 " --> pdb=" O ILE C 343 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N MET C 345 " --> pdb=" O LYS C 367 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ILE C 315 " --> pdb=" O VAL C 363 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 90 through 96 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 90 through 96 current: chain 'C' and resid 129 through 136 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 129 through 136 current: chain 'C' and resid 195 through 208 removed outlier: 5.434A pdb=" N SER C 202 " --> pdb=" O SER C 219 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N SER C 219 " --> pdb=" O SER C 202 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N MET C 204 " --> pdb=" O TRP C 217 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TRP C 217 " --> pdb=" O MET C 204 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU C 206 " --> pdb=" O ILE C 215 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 213 through 220 current: chain 'C' and resid 254 through 255 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 254 through 255 current: chain 'D' and resid 83 through 88 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 83 through 88 current: chain 'D' and resid 109 through 119 removed outlier: 5.319A pdb=" N VAL D 113 " --> pdb=" O LYS D 128 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LYS D 128 " --> pdb=" O VAL D 113 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU D 115 " --> pdb=" O SER D 126 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 95 through 96 Processing sheet with id=AA4, first strand: chain 'E' and resid 61 through 62 Processing sheet with id=AA5, first strand: chain 'F' and resid 13 through 16 Processing sheet with id=AA6, first strand: chain 'G' and resid 63 through 64 removed outlier: 6.746A pdb=" N VAL G 300 " --> pdb=" O LEU G 321 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N TYR G 323 " --> pdb=" O ARG G 298 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ARG G 298 " --> pdb=" O TYR G 323 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LYS G 297 " --> pdb=" O VAL G 334 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ILE G 336 " --> pdb=" O LYS G 297 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU G 299 " --> pdb=" O ILE G 336 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N ILE G 343 " --> pdb=" O VAL G 369 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N VAL G 369 " --> pdb=" O ILE G 343 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N MET G 345 " --> pdb=" O LYS G 367 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE G 315 " --> pdb=" O VAL G 363 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 90 through 96 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 90 through 96 current: chain 'G' and resid 129 through 136 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 129 through 136 current: chain 'G' and resid 195 through 208 removed outlier: 5.409A pdb=" N SER G 202 " --> pdb=" O SER G 219 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N SER G 219 " --> pdb=" O SER G 202 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N MET G 204 " --> pdb=" O TRP G 217 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N TRP G 217 " --> pdb=" O MET G 204 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU G 206 " --> pdb=" O ILE G 215 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 213 through 220 current: chain 'G' and resid 254 through 255 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 254 through 255 current: chain 'H' and resid 84 through 88 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 84 through 88 current: chain 'H' and resid 109 through 119 removed outlier: 5.635A pdb=" N VAL H 113 " --> pdb=" O LYS H 128 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LYS H 128 " --> pdb=" O VAL H 113 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU H 115 " --> pdb=" O SER H 126 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN H 119 " --> pdb=" O ASP H 122 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 95 through 96 Processing sheet with id=AA9, first strand: chain 'I' and resid 60 through 61 Processing sheet with id=AB1, first strand: chain 'J' and resid 13 through 16 Processing sheet with id=AB2, first strand: chain 'K' and resid 155 through 160 removed outlier: 3.582A pdb=" N LEU K 516 " --> pdb=" O LEU K 157 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLY K 159 " --> pdb=" O LEU K 514 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU K 514 " --> pdb=" O GLY K 159 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 172 through 177 removed outlier: 4.417A pdb=" N GLY K 174 " --> pdb=" O ASN K 187 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN K 187 " --> pdb=" O GLY K 174 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER K 188 " --> pdb=" O ILE K 192 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE K 192 " --> pdb=" O SER K 188 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU K 218 " --> pdb=" O ILE K 195 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 226 through 231 removed outlier: 3.683A pdb=" N ASP K 228 " --> pdb=" O SER K 248 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE K 254 " --> pdb=" O SER K 267 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N SER K 267 " --> pdb=" O ILE K 254 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE K 256 " --> pdb=" O ARG K 265 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 284 through 285 removed outlier: 3.666A pdb=" N THR K 299 " --> pdb=" O PHE K 296 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 328 through 333 removed outlier: 3.594A pdb=" N ALA K 361 " --> pdb=" O LEU K 351 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ALA K 353 " --> pdb=" O PRO K 359 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 370 through 375 removed outlier: 6.876A pdb=" N GLY K 385 " --> pdb=" O THR K 371 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LEU K 373 " --> pdb=" O PHE K 383 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N PHE K 383 " --> pdb=" O LEU K 373 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N PHE K 375 " --> pdb=" O ARG K 381 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ARG K 381 " --> pdb=" O PHE K 375 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ALA K 386 " --> pdb=" O GLU K 391 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLU K 391 " --> pdb=" O ALA K 386 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TRP K 405 " --> pdb=" O CYS K 394 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 419 through 421 removed outlier: 6.570A pdb=" N VAL K 437 " --> pdb=" O SER K 456 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N SER K 456 " --> pdb=" O VAL K 437 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL K 439 " --> pdb=" O VAL K 454 " (cutoff:3.500A) 397 hydrogen bonds defined for protein. 1050 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 192 hydrogen bonds 360 hydrogen bond angles 0 basepair planarities 69 basepair parallelities 137 stacking parallelities Total time for adding SS restraints: 3.38 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3009 1.33 - 1.45: 5964 1.45 - 1.58: 9122 1.58 - 1.70: 400 1.70 - 1.82: 125 Bond restraints: 18620 Sorted by residual: bond pdb=" CG HIS J 44 " pdb=" CD2 HIS J 44 " ideal model delta sigma weight residual 1.354 1.299 0.055 1.10e-02 8.26e+03 2.48e+01 bond pdb=" O5' G B 412 " pdb=" C5' G B 412 " ideal model delta sigma weight residual 1.420 1.475 -0.055 1.50e-02 4.44e+03 1.36e+01 bond pdb=" O5' A B 372 " pdb=" C5' A B 372 " ideal model delta sigma weight residual 1.424 1.478 -0.054 1.50e-02 4.44e+03 1.29e+01 bond pdb=" O5' C B 408 " pdb=" C5' C B 408 " ideal model delta sigma weight residual 1.420 1.472 -0.052 1.50e-02 4.44e+03 1.19e+01 bond pdb=" CE1 HIS J 44 " pdb=" NE2 HIS J 44 " ideal model delta sigma weight residual 1.321 1.287 0.034 1.00e-02 1.00e+04 1.16e+01 ... (remaining 18615 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 25160 2.75 - 5.50: 996 5.50 - 8.25: 36 8.25 - 11.00: 1 11.00 - 13.75: 2 Bond angle restraints: 26195 Sorted by residual: angle pdb=" C2' G B 345 " pdb=" C1' G B 345 " pdb=" N9 G B 345 " ideal model delta sigma weight residual 112.00 125.75 -13.75 1.50e+00 4.44e-01 8.40e+01 angle pdb=" C2' G b 345 " pdb=" C1' G b 345 " pdb=" N9 G b 345 " ideal model delta sigma weight residual 112.00 125.62 -13.62 1.50e+00 4.44e-01 8.24e+01 angle pdb=" C1' G b 345 " pdb=" N9 G b 345 " pdb=" C8 G b 345 " ideal model delta sigma weight residual 127.00 135.33 -8.33 1.30e+00 5.92e-01 4.11e+01 angle pdb=" C1' G B 345 " pdb=" N9 G B 345 " pdb=" C8 G B 345 " ideal model delta sigma weight residual 127.00 135.24 -8.24 1.30e+00 5.92e-01 4.02e+01 angle pdb=" C1' G b 345 " pdb=" N9 G b 345 " pdb=" C4 G b 345 " ideal model delta sigma weight residual 126.50 119.39 7.11 1.30e+00 5.92e-01 2.99e+01 ... (remaining 26190 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.45: 10500 20.45 - 40.89: 607 40.89 - 61.34: 304 61.34 - 81.78: 265 81.78 - 102.23: 2 Dihedral angle restraints: 11678 sinusoidal: 6807 harmonic: 4871 Sorted by residual: dihedral pdb=" C4' A B 340 " pdb=" C3' A B 340 " pdb=" C2' A B 340 " pdb=" C1' A B 340 " ideal model delta sinusoidal sigma weight residual 36.35 -34.27 70.62 1 3.10e+00 1.04e-01 6.67e+02 dihedral pdb=" O4' A B 340 " pdb=" C4' A B 340 " pdb=" C3' A B 340 " pdb=" C2' A B 340 " ideal model delta sinusoidal sigma weight residual -35.15 24.98 -60.13 1 4.00e+00 6.25e-02 3.01e+02 dihedral pdb=" O4' A B 340 " pdb=" C2' A B 340 " pdb=" C1' A B 340 " pdb=" C3' A B 340 " ideal model delta sinusoidal sigma weight residual 25.59 -32.67 58.26 3 3.80e+00 6.93e-02 1.47e+02 ... (remaining 11675 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.139: 2724 0.139 - 0.278: 333 0.278 - 0.417: 9 0.417 - 0.556: 3 0.556 - 0.696: 3 Chirality restraints: 3072 Sorted by residual: chirality pdb=" C1' G b 345 " pdb=" O4' G b 345 " pdb=" C2' G b 345 " pdb=" N9 G b 345 " both_signs ideal model delta sigma weight residual False 2.46 1.76 0.70 2.00e-01 2.50e+01 1.21e+01 chirality pdb=" C1' G B 345 " pdb=" O4' G B 345 " pdb=" C2' G B 345 " pdb=" N9 G B 345 " both_signs ideal model delta sigma weight residual False 2.46 1.77 0.68 2.00e-01 2.50e+01 1.17e+01 chirality pdb=" P G B 440 " pdb=" OP1 G B 440 " pdb=" OP2 G B 440 " pdb=" O5' G B 440 " both_signs ideal model delta sigma weight residual True 2.41 -2.99 -0.58 2.00e-01 2.50e+01 8.38e+00 ... (remaining 3069 not shown) Planarity restraints: 2569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A B 374 " 0.002 2.00e-02 2.50e+03 5.02e-02 6.93e+01 pdb=" N9 A B 374 " 0.055 2.00e-02 2.50e+03 pdb=" C8 A B 374 " -0.019 2.00e-02 2.50e+03 pdb=" N7 A B 374 " -0.088 2.00e-02 2.50e+03 pdb=" C5 A B 374 " -0.008 2.00e-02 2.50e+03 pdb=" C6 A B 374 " 0.059 2.00e-02 2.50e+03 pdb=" N6 A B 374 " 0.014 2.00e-02 2.50e+03 pdb=" N1 A B 374 " 0.013 2.00e-02 2.50e+03 pdb=" C2 A B 374 " -0.075 2.00e-02 2.50e+03 pdb=" N3 A B 374 " -0.032 2.00e-02 2.50e+03 pdb=" C4 A B 374 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 283 " -0.104 9.50e-02 1.11e+02 6.07e-02 2.04e+01 pdb=" NE ARG G 283 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG G 283 " 0.077 2.00e-02 2.50e+03 pdb=" NH1 ARG G 283 " -0.024 2.00e-02 2.50e+03 pdb=" NH2 ARG G 283 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 372 " 0.060 2.00e-02 2.50e+03 2.64e-02 1.91e+01 pdb=" N9 A B 372 " -0.020 2.00e-02 2.50e+03 pdb=" C8 A B 372 " -0.012 2.00e-02 2.50e+03 pdb=" N7 A B 372 " -0.019 2.00e-02 2.50e+03 pdb=" C5 A B 372 " -0.027 2.00e-02 2.50e+03 pdb=" C6 A B 372 " 0.017 2.00e-02 2.50e+03 pdb=" N6 A B 372 " 0.038 2.00e-02 2.50e+03 pdb=" N1 A B 372 " 0.004 2.00e-02 2.50e+03 pdb=" C2 A B 372 " -0.016 2.00e-02 2.50e+03 pdb=" N3 A B 372 " -0.011 2.00e-02 2.50e+03 pdb=" C4 A B 372 " -0.015 2.00e-02 2.50e+03 ... (remaining 2566 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.13: 1 2.13 - 2.82: 4126 2.82 - 3.52: 22004 3.52 - 4.21: 47811 4.21 - 4.90: 73516 Nonbonded interactions: 147458 Sorted by model distance: nonbonded pdb=" NH1 ARG E 62 " pdb=" OG SER E 120 " model vdw 1.439 3.120 nonbonded pdb=" NH2 ARG E 62 " pdb=" O2' C b 236 " model vdw 2.203 3.120 nonbonded pdb=" O ARG I 62 " pdb=" O VAL I 126 " model vdw 2.313 3.040 nonbonded pdb=" O ASN H 93 " pdb=" OD1 ASN H 93 " model vdw 2.318 3.040 nonbonded pdb=" O2' C B 394 " pdb=" O2 C B 394 " model vdw 2.331 3.040 ... (remaining 147453 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and resid 43 through 395) selection = (chain 'G' and (resid 43 through 186 or resid 192 through 395)) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 66 through 159) } ncs_group { reference = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'F' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 16.380 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 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 0.070 18620 Z= 0.628 Angle : 1.240 13.748 26195 Z= 0.855 Chirality : 0.090 0.696 3072 Planarity : 0.008 0.105 2569 Dihedral : 18.533 102.227 8540 Min Nonbonded Distance : 1.439 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.27 % Allowed : 1.56 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.18), residues: 1648 helix: -1.49 (0.21), residues: 378 sheet: -1.89 (0.27), residues: 298 loop : -0.50 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.076 0.003 ARG G 283 TYR 0.049 0.006 TYR J 41 PHE 0.028 0.006 PHE K 318 TRP 0.039 0.007 TRP C 217 HIS 0.028 0.004 HIS G 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00947 / 0.63 (18620) covalent geometry : angle 1.23979 / 0.85 (26195) hydrogen bonds : bond 0.21237 / 14.13 ( 589) hydrogen bonds : angle 7.48282 / 5.28 ( 1410) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 361 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 LYS cc_start: 0.7977 (mtpt) cc_final: 0.7639 (mmtm) REVERT: C 46 LYS cc_start: 0.8258 (tttt) cc_final: 0.8038 (tppt) REVERT: C 111 ARG cc_start: 0.7746 (ttm170) cc_final: 0.7477 (mpp80) REVERT: C 116 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7915 (mp0) REVERT: C 137 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7667 (mm-30) REVERT: C 138 ARG cc_start: 0.7434 (mtm110) cc_final: 0.7214 (ttp-110) REVERT: C 144 LYS cc_start: 0.8117 (tttt) cc_final: 0.7788 (mptt) REVERT: C 174 GLU cc_start: 0.7177 (mt-10) cc_final: 0.6962 (tm-30) REVERT: C 193 GLN cc_start: 0.6736 (mt0) cc_final: 0.5692 (tt0) REVERT: C 195 ARG cc_start: 0.6665 (mtt180) cc_final: 0.6403 (mtt-85) REVERT: C 196 VAL cc_start: 0.8088 (t) cc_final: 0.7874 (p) REVERT: C 201 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7278 (tp30) REVERT: C 203 LYS cc_start: 0.8166 (tttt) cc_final: 0.7908 (ttmm) REVERT: C 212 ARG cc_start: 0.7314 (mtm110) cc_final: 0.6981 (mtm110) REVERT: C 258 ASP cc_start: 0.6607 (m-30) cc_final: 0.6343 (t70) REVERT: C 280 SER cc_start: 0.8379 (t) cc_final: 0.7888 (p) REVERT: C 284 ARG cc_start: 0.8137 (mmt-90) cc_final: 0.7785 (mmm-85) REVERT: C 290 GLU cc_start: 0.8084 (mp0) cc_final: 0.7838 (mp0) REVERT: C 328 GLU cc_start: 0.7460 (mt-10) cc_final: 0.6987 (mm-30) REVERT: C 391 LEU cc_start: 0.6232 (tp) cc_final: 0.6001 (tp) REVERT: C 394 LYS cc_start: 0.8014 (tttt) cc_final: 0.7758 (tmmm) REVERT: D 73 LEU cc_start: 0.6515 (OUTLIER) cc_final: 0.6313 (tt) REVERT: D 102 VAL cc_start: 0.7889 (t) cc_final: 0.7595 (p) REVERT: D 104 LEU cc_start: 0.6622 (mt) cc_final: 0.6187 (mm) REVERT: D 119 GLN cc_start: 0.6855 (mt0) cc_final: 0.6631 (mt0) REVERT: D 122 ASP cc_start: 0.7007 (m-30) cc_final: 0.6386 (p0) REVERT: D 157 PHE cc_start: 0.7214 (m-80) cc_final: 0.6891 (m-80) REVERT: E 36 GLN cc_start: 0.7668 (mt0) cc_final: 0.7365 (mm110) REVERT: E 45 ARG cc_start: 0.7565 (tpp80) cc_final: 0.7298 (ttm-80) REVERT: E 48 TYR cc_start: 0.7407 (m-10) cc_final: 0.7077 (m-10) REVERT: E 66 GLU cc_start: 0.7676 (tt0) cc_final: 0.7090 (tt0) REVERT: E 69 LYS cc_start: 0.7562 (ttpt) cc_final: 0.7264 (mttp) REVERT: E 75 GLU cc_start: 0.6751 (mp0) cc_final: 0.6371 (pt0) REVERT: E 86 LEU cc_start: 0.8148 (mt) cc_final: 0.7865 (mm) REVERT: E 97 MET cc_start: 0.8343 (mtp) cc_final: 0.8116 (mtp) REVERT: E 132 HIS cc_start: 0.6322 (t-170) cc_final: 0.5806 (t70) REVERT: E 134 GLU cc_start: 0.8446 (tp30) cc_final: 0.8172 (tt0) REVERT: E 135 TYR cc_start: 0.6785 (p90) cc_final: 0.6510 (p90) REVERT: E 145 GLU cc_start: 0.7102 (tt0) cc_final: 0.6779 (tp30) REVERT: E 151 LEU cc_start: 0.7603 (mm) cc_final: 0.7280 (pt) REVERT: F 1 MET cc_start: 0.7403 (mmt) cc_final: 0.7123 (mmt) REVERT: F 18 LYS cc_start: 0.6879 (mttm) cc_final: 0.6650 (mmtt) REVERT: F 23 MET cc_start: 0.8100 (mmm) cc_final: 0.7873 (mtp) REVERT: F 25 GLN cc_start: 0.8112 (pm20) cc_final: 0.7677 (pm20) REVERT: F 28 CYS cc_start: 0.8560 (t) cc_final: 0.8133 (m) REVERT: F 34 ARG cc_start: 0.8304 (mmt-90) cc_final: 0.7893 (mmm-85) REVERT: F 50 LYS cc_start: 0.7696 (mttt) cc_final: 0.7329 (mtmt) REVERT: G 88 ARG cc_start: 0.7684 (mmt-90) cc_final: 0.7477 (mmm160) REVERT: G 127 LYS cc_start: 0.8247 (mttt) cc_final: 0.7721 (mppt) REVERT: G 167 THR cc_start: 0.7745 (p) cc_final: 0.7397 (t) REVERT: G 168 GLN cc_start: 0.8198 (tt0) cc_final: 0.7800 (mp10) REVERT: G 183 ARG cc_start: 0.8479 (ttm110) cc_final: 0.7836 (ttt180) REVERT: G 210 GLU cc_start: 0.8210 (mp0) cc_final: 0.7729 (pt0) REVERT: G 211 ARG cc_start: 0.7511 (mtt-85) cc_final: 0.6778 (mtm180) REVERT: G 280 SER cc_start: 0.8985 (t) cc_final: 0.8661 (p) REVERT: G 287 TYR cc_start: 0.8141 (m-80) cc_final: 0.7772 (m-80) REVERT: G 388 GLN cc_start: 0.7000 (mt0) cc_final: 0.6724 (mm-40) REVERT: H 71 VAL cc_start: 0.7277 (t) cc_final: 0.6932 (p) REVERT: H 147 ASP cc_start: 0.8009 (t70) cc_final: 0.7803 (t70) REVERT: I 36 GLN cc_start: 0.8043 (mt0) cc_final: 0.7228 (mm110) REVERT: I 41 ARG cc_start: 0.7587 (ttt-90) cc_final: 0.7092 (ttp80) REVERT: I 42 ARG cc_start: 0.8393 (ptm-80) cc_final: 0.8028 (ptm160) REVERT: I 48 TYR cc_start: 0.8544 (m-10) cc_final: 0.8321 (m-10) REVERT: I 57 GLN cc_start: 0.7875 (tp40) cc_final: 0.7629 (tp40) REVERT: I 58 LYS cc_start: 0.7277 (tttt) cc_final: 0.7010 (tmtt) REVERT: I 62 ARG cc_start: 0.8408 (mtt-85) cc_final: 0.8025 (mtt180) REVERT: I 102 ASN cc_start: 0.7699 (m-40) cc_final: 0.7470 (t0) REVERT: I 128 MET cc_start: 0.7831 (ttp) cc_final: 0.7631 (ttp) REVERT: I 131 PRO cc_start: 0.8077 (Cg_endo) cc_final: 0.7850 (Cg_exo) REVERT: I 134 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8515 (mp0) REVERT: I 141 GLU cc_start: 0.7544 (tt0) cc_final: 0.6999 (tp30) REVERT: J 16 THR cc_start: 0.8341 (t) cc_final: 0.8060 (p) REVERT: J 21 ASP cc_start: 0.8015 (p0) cc_final: 0.7802 (p0) REVERT: K 169 GLU cc_start: 0.7679 (tt0) cc_final: 0.7299 (mm-30) REVERT: K 182 SER cc_start: 0.8565 (t) cc_final: 0.8321 (p) REVERT: K 214 MET cc_start: 0.8580 (mtm) cc_final: 0.8238 (mtp) REVERT: K 224 ASP cc_start: 0.8102 (t0) cc_final: 0.7899 (m-30) REVERT: K 263 GLU cc_start: 0.8304 (pt0) cc_final: 0.8098 (pp20) REVERT: K 307 ARG cc_start: 0.7959 (ttm170) cc_final: 0.7528 (tpm170) REVERT: K 322 GLN cc_start: 0.7464 (tm-30) cc_final: 0.6704 (pp30) REVERT: K 337 GLN cc_start: 0.7965 (mm-40) cc_final: 0.7367 (mp10) REVERT: K 347 ARG cc_start: 0.7473 (mpt180) cc_final: 0.7021 (mpp80) REVERT: K 374 CYS cc_start: 0.8489 (m) cc_final: 0.8246 (t) outliers start: 4 outliers final: 1 residues processed: 365 average time/residue: 0.6589 time to fit residues: 264.1099 Evaluate side-chains 245 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 243 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain I residue 91 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 32 HIS C 99 ASN C 147 GLN C 360 HIS D 106 ASN F 8 ASN F 44 HIS ** F 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 242 GLN G 270 GLN J 31 HIS J 44 HIS K 167 GLN K 273 HIS K 297 ASN K 366 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.166752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.123325 restraints weight = 23635.538| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.33 r_work: 0.3375 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18620 Z= 0.176 Angle : 0.631 20.796 26195 Z= 0.341 Chirality : 0.043 0.291 3072 Planarity : 0.005 0.074 2569 Dihedral : 19.963 108.217 5172 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.96 % Allowed : 9.47 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.19), residues: 1648 helix: 0.10 (0.25), residues: 381 sheet: -1.53 (0.25), residues: 337 loop : -0.21 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 43 TYR 0.020 0.002 TYR E 48 PHE 0.019 0.002 PHE K 382 TRP 0.015 0.002 TRP G 380 HIS 0.007 0.002 HIS G 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.18 (18620) covalent geometry : angle 0.63075 / 0.34 (26195) hydrogen bonds : bond 0.05971 / 4.18 ( 589) hydrogen bonds : angle 5.00817 / 3.48 ( 1410) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 261 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 193 GLN cc_start: 0.6819 (mt0) cc_final: 0.6337 (tt0) REVERT: D 73 LEU cc_start: 0.6613 (OUTLIER) cc_final: 0.6378 (tt) REVERT: D 157 PHE cc_start: 0.7320 (m-80) cc_final: 0.6894 (m-80) REVERT: E 66 GLU cc_start: 0.7561 (tt0) cc_final: 0.7301 (tt0) REVERT: E 89 GLU cc_start: 0.8039 (mp0) cc_final: 0.7793 (mp0) REVERT: E 128 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7628 (ttm) REVERT: E 132 HIS cc_start: 0.6181 (t-170) cc_final: 0.5856 (t70) REVERT: F 50 LYS cc_start: 0.7519 (mttt) cc_final: 0.7182 (mtmt) REVERT: G 244 GLN cc_start: 0.8530 (tp40) cc_final: 0.8255 (tp-100) REVERT: G 301 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7378 (mmm) REVERT: H 128 LYS cc_start: 0.8159 (tttt) cc_final: 0.7949 (ttpp) REVERT: I 36 GLN cc_start: 0.8187 (mt0) cc_final: 0.7845 (mm110) REVERT: I 38 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8296 (tp) REVERT: I 53 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7891 (mttt) REVERT: I 57 GLN cc_start: 0.8421 (tp40) cc_final: 0.8048 (tp40) REVERT: I 140 ASP cc_start: 0.7147 (m-30) cc_final: 0.6940 (m-30) REVERT: I 144 GLU cc_start: 0.6679 (pp20) cc_final: 0.6304 (pp20) REVERT: J 40 LYS cc_start: 0.8075 (mttm) cc_final: 0.7839 (mmtp) REVERT: J 53 LYS cc_start: 0.8593 (mmmt) cc_final: 0.8350 (mmmt) REVERT: K 155 ARG cc_start: 0.6594 (mtp-110) cc_final: 0.6289 (mtp180) REVERT: K 182 SER cc_start: 0.8121 (t) cc_final: 0.7619 (m) outliers start: 29 outliers final: 10 residues processed: 281 average time/residue: 0.7212 time to fit residues: 221.7798 Evaluate side-chains 213 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 198 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain G residue 116 GLU Chi-restraints excluded: chain G residue 301 MET Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 53 LYS Chi-restraints excluded: chain I residue 91 TYR Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain K residue 367 GLN Chi-restraints excluded: chain K residue 424 THR Chi-restraints excluded: chain K residue 484 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 132 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 180 optimal weight: 10.0000 chunk 4 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 154 optimal weight: 8.9990 chunk 109 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 63 ASN C 259 HIS C 276 HIS ** F 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 146 GLN G 242 GLN I 68 GLN ** I 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 297 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.164847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.121177 restraints weight = 23607.000| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.35 r_work: 0.3346 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18620 Z= 0.146 Angle : 0.573 21.906 26195 Z= 0.302 Chirality : 0.040 0.227 3072 Planarity : 0.005 0.067 2569 Dihedral : 20.003 118.695 5172 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.57 % Allowed : 13.26 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.20), residues: 1648 helix: 0.46 (0.26), residues: 381 sheet: -1.34 (0.25), residues: 358 loop : -0.08 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 41 TYR 0.019 0.002 TYR H 145 PHE 0.015 0.002 PHE I 70 TRP 0.013 0.001 TRP K 395 HIS 0.006 0.001 HIS G 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (18620) covalent geometry : angle 0.57283 / 0.30 (26195) hydrogen bonds : bond 0.04728 / 3.25 ( 589) hydrogen bonds : angle 4.51919 / 3.12 ( 1410) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 215 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 114 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.8081 (mtp180) REVERT: C 117 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8169 (ttmm) REVERT: C 193 GLN cc_start: 0.6906 (mt0) cc_final: 0.6438 (tt0) REVERT: C 260 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8555 (mtp) REVERT: C 372 GLU cc_start: 0.7398 (mm-30) cc_final: 0.7111 (mt-10) REVERT: E 25 GLN cc_start: 0.7567 (tp40) cc_final: 0.6985 (tm-30) REVERT: E 89 GLU cc_start: 0.7993 (mp0) cc_final: 0.7711 (mp0) REVERT: F 50 LYS cc_start: 0.7382 (mttt) cc_final: 0.7033 (mtmt) REVERT: G 167 THR cc_start: 0.8181 (p) cc_final: 0.7963 (t) REVERT: I 26 GLU cc_start: 0.6787 (OUTLIER) cc_final: 0.6317 (mp0) REVERT: I 36 GLN cc_start: 0.8149 (mt0) cc_final: 0.7781 (mt0) REVERT: I 53 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7855 (mtpt) REVERT: I 57 GLN cc_start: 0.8300 (tp40) cc_final: 0.7944 (tp40) REVERT: I 62 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.8311 (mtt180) REVERT: J 23 MET cc_start: 0.6949 (mmm) cc_final: 0.6655 (tmm) REVERT: J 40 LYS cc_start: 0.8049 (mttm) cc_final: 0.7810 (mmtp) REVERT: K 182 SER cc_start: 0.8132 (t) cc_final: 0.7698 (m) REVERT: K 239 GLN cc_start: 0.7467 (OUTLIER) cc_final: 0.7003 (mt0) outliers start: 38 outliers final: 10 residues processed: 241 average time/residue: 0.7132 time to fit residues: 188.1378 Evaluate side-chains 212 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 195 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 195 ARG Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain I residue 26 GLU Chi-restraints excluded: chain I residue 53 LYS Chi-restraints excluded: chain I residue 62 ARG Chi-restraints excluded: chain I residue 91 TYR Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain K residue 233 SER Chi-restraints excluded: chain K residue 239 GLN Chi-restraints excluded: chain K residue 424 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 48 optimal weight: 1.9990 chunk 77 optimal weight: 0.0270 chunk 41 optimal weight: 0.0270 chunk 183 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 166 optimal weight: 30.0000 chunk 174 optimal weight: 50.0000 chunk 117 optimal weight: 1.9990 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 GLN F 58 GLN G 242 GLN G 388 GLN H 93 ASN K 297 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.165060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.121634 restraints weight = 23663.560| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.32 r_work: 0.3348 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18620 Z= 0.113 Angle : 0.524 21.459 26195 Z= 0.275 Chirality : 0.038 0.197 3072 Planarity : 0.004 0.068 2569 Dihedral : 19.934 105.432 5170 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.23 % Allowed : 15.29 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.20), residues: 1648 helix: 0.58 (0.26), residues: 385 sheet: -1.30 (0.24), residues: 360 loop : -0.00 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 298 TYR 0.017 0.001 TYR K 244 PHE 0.012 0.001 PHE D 123 TRP 0.011 0.001 TRP K 395 HIS 0.006 0.001 HIS E 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (18620) covalent geometry : angle 0.52425 / 0.27 (26195) hydrogen bonds : bond 0.04128 / 2.82 ( 589) hydrogen bonds : angle 4.33486 / 3.00 ( 1410) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 209 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 111 ARG cc_start: 0.8288 (mpp80) cc_final: 0.8006 (mmt90) REVERT: C 114 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.8056 (mtp180) REVERT: C 118 THR cc_start: 0.8334 (m) cc_final: 0.8092 (t) REVERT: C 148 SER cc_start: 0.9243 (OUTLIER) cc_final: 0.9038 (t) REVERT: C 193 GLN cc_start: 0.7066 (mt0) cc_final: 0.6565 (tt0) REVERT: C 260 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8587 (ttp) REVERT: E 25 GLN cc_start: 0.7372 (tp40) cc_final: 0.6753 (tm130) REVERT: E 89 GLU cc_start: 0.8013 (mp0) cc_final: 0.7694 (mp0) REVERT: E 128 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7664 (ttm) REVERT: E 133 GLU cc_start: 0.7362 (pm20) cc_final: 0.6939 (mp0) REVERT: F 10 GLN cc_start: 0.6262 (mp10) cc_final: 0.5970 (mt0) REVERT: F 50 LYS cc_start: 0.7381 (mttt) cc_final: 0.7006 (mtmt) REVERT: G 244 GLN cc_start: 0.8566 (tp40) cc_final: 0.8186 (tp-100) REVERT: I 36 GLN cc_start: 0.8203 (mt0) cc_final: 0.7846 (mt0) REVERT: I 53 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7798 (mtpt) REVERT: I 57 GLN cc_start: 0.8301 (tp40) cc_final: 0.7951 (tp40) REVERT: I 62 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8328 (mtt180) REVERT: J 28 CYS cc_start: 0.8724 (m) cc_final: 0.8478 (t) REVERT: J 40 LYS cc_start: 0.8017 (mttm) cc_final: 0.7787 (mmtp) REVERT: K 155 ARG cc_start: 0.6649 (mtm-85) cc_final: 0.6358 (mtm180) REVERT: K 182 SER cc_start: 0.8127 (t) cc_final: 0.7708 (m) REVERT: K 218 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7925 (tp) REVERT: K 239 GLN cc_start: 0.7476 (OUTLIER) cc_final: 0.7012 (mt0) outliers start: 33 outliers final: 8 residues processed: 231 average time/residue: 0.6972 time to fit residues: 176.8637 Evaluate side-chains 206 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 190 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain I residue 53 LYS Chi-restraints excluded: chain I residue 62 ARG Chi-restraints excluded: chain I residue 91 TYR Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain K residue 218 LEU Chi-restraints excluded: chain K residue 239 GLN Chi-restraints excluded: chain K residue 424 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 105 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 GLN D 142 GLN F 58 GLN G 242 GLN G 388 GLN J 10 GLN K 415 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.157078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.110376 restraints weight = 23581.565| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.49 r_work: 0.3184 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 18620 Z= 0.163 Angle : 0.570 21.268 26195 Z= 0.295 Chirality : 0.039 0.202 3072 Planarity : 0.005 0.071 2569 Dihedral : 19.927 105.056 5170 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.04 % Allowed : 14.82 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.20), residues: 1648 helix: 0.58 (0.27), residues: 384 sheet: -1.54 (0.24), residues: 376 loop : 0.08 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 298 TYR 0.027 0.002 TYR K 244 PHE 0.018 0.002 PHE I 70 TRP 0.010 0.001 TRP C 380 HIS 0.006 0.001 HIS G 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (18620) covalent geometry : angle 0.57031 / 0.30 (26195) hydrogen bonds : bond 0.04366 / 2.97 ( 589) hydrogen bonds : angle 4.36572 / 3.02 ( 1410) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 209 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: C 111 ARG cc_start: 0.8425 (mpp80) cc_final: 0.8048 (mmt90) REVERT: C 114 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8258 (mtp180) REVERT: C 118 THR cc_start: 0.8555 (OUTLIER) cc_final: 0.8290 (t) REVERT: C 193 GLN cc_start: 0.6915 (mt0) cc_final: 0.6290 (tt0) REVERT: C 260 MET cc_start: 0.9036 (OUTLIER) cc_final: 0.8727 (ttp) REVERT: E 25 GLN cc_start: 0.7606 (tp40) cc_final: 0.6830 (tm130) REVERT: E 89 GLU cc_start: 0.8076 (mp0) cc_final: 0.7727 (mp0) REVERT: E 128 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7632 (ttm) REVERT: F 18 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.8114 (mmmt) REVERT: F 50 LYS cc_start: 0.7603 (mttt) cc_final: 0.7263 (mtmt) REVERT: I 36 GLN cc_start: 0.8320 (mt0) cc_final: 0.8051 (mt0) REVERT: I 53 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7781 (mtpt) REVERT: I 57 GLN cc_start: 0.8281 (tp40) cc_final: 0.7948 (tp40) REVERT: I 62 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8431 (mmt180) REVERT: J 40 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7956 (mmtp) REVERT: K 155 ARG cc_start: 0.6775 (mtm-85) cc_final: 0.6464 (mtm180) REVERT: K 182 SER cc_start: 0.8337 (t) cc_final: 0.7782 (m) REVERT: K 218 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7968 (tp) REVERT: K 239 GLN cc_start: 0.7428 (OUTLIER) cc_final: 0.6933 (mt0) outliers start: 45 outliers final: 17 residues processed: 237 average time/residue: 0.6607 time to fit residues: 171.8566 Evaluate side-chains 219 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 192 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 195 ARG Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain F residue 18 LYS Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain I residue 53 LYS Chi-restraints excluded: chain I residue 62 ARG Chi-restraints excluded: chain I residue 91 TYR Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 40 LYS Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain K residue 218 LEU Chi-restraints excluded: chain K residue 239 GLN Chi-restraints excluded: chain K residue 400 SER Chi-restraints excluded: chain K residue 424 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 147 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 166 optimal weight: 30.0000 chunk 97 optimal weight: 5.9990 chunk 6 optimal weight: 0.5980 chunk 68 optimal weight: 0.4980 chunk 92 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 141 optimal weight: 2.9990 chunk 173 optimal weight: 30.0000 chunk 82 optimal weight: 5.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 160 HIS ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 GLN G 242 GLN G 388 GLN H 93 ASN J 10 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.156815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.109401 restraints weight = 23374.341| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.47 r_work: 0.3187 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 18620 Z= 0.149 Angle : 0.540 21.001 26195 Z= 0.282 Chirality : 0.038 0.182 3072 Planarity : 0.005 0.052 2569 Dihedral : 19.915 104.673 5170 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.38 % Allowed : 15.97 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.20), residues: 1648 helix: 0.61 (0.27), residues: 384 sheet: -1.47 (0.24), residues: 361 loop : 0.06 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 298 TYR 0.023 0.001 TYR K 244 PHE 0.013 0.002 PHE I 70 TRP 0.010 0.001 TRP C 380 HIS 0.005 0.001 HIS E 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (18620) covalent geometry : angle 0.53992 / 0.28 (26195) hydrogen bonds : bond 0.04157 / 2.80 ( 589) hydrogen bonds : angle 4.30077 / 2.97 ( 1410) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 202 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: C 118 THR cc_start: 0.8552 (OUTLIER) cc_final: 0.8314 (t) REVERT: C 193 GLN cc_start: 0.6999 (mt0) cc_final: 0.6315 (tt0) REVERT: C 258 ASP cc_start: 0.6589 (t70) cc_final: 0.6331 (t0) REVERT: C 260 MET cc_start: 0.9057 (OUTLIER) cc_final: 0.8740 (ttp) REVERT: E 25 GLN cc_start: 0.7655 (tp40) cc_final: 0.6901 (tm-30) REVERT: E 89 GLU cc_start: 0.8082 (mp0) cc_final: 0.7687 (mp0) REVERT: E 128 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7557 (ttm) REVERT: E 133 GLU cc_start: 0.7229 (pm20) cc_final: 0.6907 (pm20) REVERT: F 10 GLN cc_start: 0.6689 (mp10) cc_final: 0.6414 (mt0) REVERT: F 18 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8096 (mmmt) REVERT: F 34 ARG cc_start: 0.8150 (mpt180) cc_final: 0.7870 (mmm-85) REVERT: F 49 LYS cc_start: 0.8578 (mttm) cc_final: 0.8270 (mttp) REVERT: F 50 LYS cc_start: 0.7577 (mttt) cc_final: 0.7190 (mtmt) REVERT: H 158 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7941 (mp) REVERT: I 36 GLN cc_start: 0.8351 (mt0) cc_final: 0.8071 (mt0) REVERT: I 53 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7784 (mtpt) REVERT: I 57 GLN cc_start: 0.8299 (tp40) cc_final: 0.7975 (tp40) REVERT: J 40 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7981 (mmtp) REVERT: K 182 SER cc_start: 0.8509 (t) cc_final: 0.7920 (m) REVERT: K 218 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.7918 (tp) REVERT: K 239 GLN cc_start: 0.7426 (OUTLIER) cc_final: 0.6935 (mt0) outliers start: 50 outliers final: 19 residues processed: 231 average time/residue: 0.6625 time to fit residues: 168.1485 Evaluate side-chains 225 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 197 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 195 ARG Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 18 LYS Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain I residue 53 LYS Chi-restraints excluded: chain I residue 91 TYR Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 40 LYS Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain K residue 218 LEU Chi-restraints excluded: chain K residue 239 GLN Chi-restraints excluded: chain K residue 367 GLN Chi-restraints excluded: chain K residue 400 SER Chi-restraints excluded: chain K residue 424 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 108 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 48 optimal weight: 0.0980 chunk 71 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 174 optimal weight: 40.0000 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 GLN G 242 GLN G 388 GLN H 93 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.158253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.111070 restraints weight = 23745.530| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.50 r_work: 0.3220 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18620 Z= 0.105 Angle : 0.510 19.683 26195 Z= 0.265 Chirality : 0.037 0.164 3072 Planarity : 0.004 0.059 2569 Dihedral : 19.869 102.184 5170 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.64 % Allowed : 16.98 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.20), residues: 1648 helix: 0.80 (0.27), residues: 384 sheet: -1.41 (0.25), residues: 360 loop : 0.08 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 298 TYR 0.022 0.001 TYR K 244 PHE 0.011 0.001 PHE H 123 TRP 0.011 0.001 TRP C 380 HIS 0.004 0.001 HIS G 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (18620) covalent geometry : angle 0.51038 / 0.27 (26195) hydrogen bonds : bond 0.03700 / 2.45 ( 589) hydrogen bonds : angle 4.13156 / 2.86 ( 1410) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 206 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: C 111 ARG cc_start: 0.8360 (mpp80) cc_final: 0.8033 (mmt90) REVERT: C 118 THR cc_start: 0.8482 (m) cc_final: 0.8274 (t) REVERT: C 212 ARG cc_start: 0.7770 (mpp80) cc_final: 0.7159 (mtp85) REVERT: C 258 ASP cc_start: 0.6550 (t70) cc_final: 0.6315 (t0) REVERT: C 260 MET cc_start: 0.9027 (OUTLIER) cc_final: 0.8712 (ttp) REVERT: C 372 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7304 (mt-10) REVERT: E 25 GLN cc_start: 0.7706 (tp40) cc_final: 0.6961 (tm-30) REVERT: E 89 GLU cc_start: 0.8099 (mp0) cc_final: 0.7635 (mp0) REVERT: E 128 MET cc_start: 0.8007 (OUTLIER) cc_final: 0.7593 (ttm) REVERT: E 145 GLU cc_start: 0.7748 (tp30) cc_final: 0.7547 (tp30) REVERT: F 18 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.8062 (mmmt) REVERT: F 34 ARG cc_start: 0.8089 (mpt180) cc_final: 0.7884 (mmm-85) REVERT: F 49 LYS cc_start: 0.8532 (mttm) cc_final: 0.8263 (mttp) REVERT: F 50 LYS cc_start: 0.7573 (mttt) cc_final: 0.7235 (mtmt) REVERT: G 388 GLN cc_start: 0.7285 (mm-40) cc_final: 0.6992 (mm-40) REVERT: H 134 LYS cc_start: 0.8019 (mtmm) cc_final: 0.7359 (mmtm) REVERT: H 155 GLN cc_start: 0.8517 (mm-40) cc_final: 0.8268 (tp-100) REVERT: I 36 GLN cc_start: 0.8303 (mt0) cc_final: 0.8026 (mt0) REVERT: I 53 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7733 (mtpt) REVERT: I 57 GLN cc_start: 0.8226 (tp40) cc_final: 0.7909 (tp40) REVERT: J 40 LYS cc_start: 0.8145 (mttm) cc_final: 0.7934 (mmtp) REVERT: K 182 SER cc_start: 0.8499 (t) cc_final: 0.7908 (m) REVERT: K 218 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7891 (tp) REVERT: K 239 GLN cc_start: 0.7421 (OUTLIER) cc_final: 0.6927 (mt0) REVERT: K 400 SER cc_start: 0.7747 (OUTLIER) cc_final: 0.7536 (p) outliers start: 39 outliers final: 16 residues processed: 228 average time/residue: 0.7226 time to fit residues: 180.8405 Evaluate side-chains 212 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 189 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 195 ARG Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 18 LYS Chi-restraints excluded: chain F residue 58 GLN Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain I residue 53 LYS Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain K residue 218 LEU Chi-restraints excluded: chain K residue 239 GLN Chi-restraints excluded: chain K residue 400 SER Chi-restraints excluded: chain K residue 424 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 132 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 169 optimal weight: 50.0000 chunk 159 optimal weight: 0.3980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN F 58 GLN G 242 GLN ** H 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 136 GLN K 415 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.156817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.109555 restraints weight = 23423.382| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.49 r_work: 0.3194 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18620 Z= 0.150 Angle : 0.535 19.868 26195 Z= 0.279 Chirality : 0.038 0.165 3072 Planarity : 0.005 0.056 2569 Dihedral : 19.874 101.911 5168 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.44 % Allowed : 17.52 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.20), residues: 1648 helix: 0.81 (0.27), residues: 382 sheet: -1.34 (0.25), residues: 369 loop : 0.14 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 121 TYR 0.023 0.001 TYR K 244 PHE 0.012 0.002 PHE K 485 TRP 0.009 0.001 TRP C 380 HIS 0.005 0.001 HIS G 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (18620) covalent geometry : angle 0.53524 / 0.28 (26195) hydrogen bonds : bond 0.03967 / 2.63 ( 589) hydrogen bonds : angle 4.18272 / 2.90 ( 1410) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 198 time to evaluate : 0.600 Fit side-chains revert: symmetry clash REVERT: C 111 ARG cc_start: 0.8417 (mpp80) cc_final: 0.8044 (mmt90) REVERT: C 118 THR cc_start: 0.8546 (OUTLIER) cc_final: 0.8331 (t) REVERT: C 212 ARG cc_start: 0.7863 (mpp80) cc_final: 0.7250 (mtp85) REVERT: C 258 ASP cc_start: 0.6600 (t70) cc_final: 0.6347 (t0) REVERT: C 260 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8742 (ttp) REVERT: C 372 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7348 (mt-10) REVERT: E 25 GLN cc_start: 0.7741 (tp40) cc_final: 0.6868 (tm-30) REVERT: E 89 GLU cc_start: 0.8119 (mp0) cc_final: 0.7726 (mp0) REVERT: E 128 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7612 (ttm) REVERT: E 135 TYR cc_start: 0.6925 (p90) cc_final: 0.6701 (p90) REVERT: F 18 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.8083 (mmmt) REVERT: F 34 ARG cc_start: 0.8111 (mpt180) cc_final: 0.7905 (mmm-85) REVERT: F 49 LYS cc_start: 0.8570 (mttm) cc_final: 0.8248 (mttp) REVERT: F 50 LYS cc_start: 0.7542 (mttt) cc_final: 0.7205 (mtmt) REVERT: F 58 GLN cc_start: 0.7648 (OUTLIER) cc_final: 0.7445 (mt0) REVERT: G 388 GLN cc_start: 0.7306 (mm-40) cc_final: 0.7015 (mm-40) REVERT: H 134 LYS cc_start: 0.8117 (mtmm) cc_final: 0.7461 (mmtm) REVERT: I 53 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7781 (mtpt) REVERT: I 57 GLN cc_start: 0.8262 (tp40) cc_final: 0.7960 (tp40) REVERT: I 70 PHE cc_start: 0.7050 (m-80) cc_final: 0.6752 (m-10) REVERT: J 40 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7986 (mmtp) REVERT: K 182 SER cc_start: 0.8535 (t) cc_final: 0.8008 (m) REVERT: K 239 GLN cc_start: 0.7411 (OUTLIER) cc_final: 0.6915 (mt0) outliers start: 36 outliers final: 16 residues processed: 219 average time/residue: 0.7161 time to fit residues: 172.2979 Evaluate side-chains 217 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 195 ARG Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 18 LYS Chi-restraints excluded: chain F residue 58 GLN Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain I residue 53 LYS Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 40 LYS Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain K residue 239 GLN Chi-restraints excluded: chain K residue 367 GLN Chi-restraints excluded: chain K residue 424 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 4 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 135 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 87 optimal weight: 0.4980 chunk 76 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 GLN G 242 GLN H 93 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.157768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.110852 restraints weight = 23571.950| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.46 r_work: 0.3210 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18620 Z= 0.110 Angle : 0.525 19.588 26195 Z= 0.272 Chirality : 0.037 0.209 3072 Planarity : 0.004 0.059 2569 Dihedral : 19.857 100.477 5168 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.89 % Allowed : 18.27 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.20), residues: 1648 helix: 0.86 (0.27), residues: 382 sheet: -1.23 (0.25), residues: 362 loop : 0.11 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 298 TYR 0.022 0.001 TYR K 244 PHE 0.012 0.001 PHE H 123 TRP 0.010 0.001 TRP C 380 HIS 0.004 0.001 HIS G 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (18620) covalent geometry : angle 0.52455 / 0.27 (26195) hydrogen bonds : bond 0.03724 / 2.45 ( 589) hydrogen bonds : angle 4.08825 / 2.84 ( 1410) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 197 time to evaluate : 0.559 Fit side-chains revert: symmetry clash REVERT: C 111 ARG cc_start: 0.8406 (mpp80) cc_final: 0.8023 (mmt90) REVERT: C 118 THR cc_start: 0.8517 (m) cc_final: 0.8300 (t) REVERT: C 212 ARG cc_start: 0.7856 (mpp80) cc_final: 0.7193 (mtp85) REVERT: C 258 ASP cc_start: 0.6571 (t70) cc_final: 0.6325 (t0) REVERT: C 260 MET cc_start: 0.9033 (OUTLIER) cc_final: 0.8720 (ttp) REVERT: C 371 MET cc_start: 0.8276 (ttp) cc_final: 0.7980 (ttp) REVERT: D 157 PHE cc_start: 0.7369 (m-80) cc_final: 0.6998 (m-80) REVERT: E 25 GLN cc_start: 0.7918 (tp40) cc_final: 0.7004 (tm-30) REVERT: E 89 GLU cc_start: 0.8135 (mp0) cc_final: 0.7825 (mp0) REVERT: E 128 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7621 (ttm) REVERT: F 18 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.8070 (mmmt) REVERT: F 34 ARG cc_start: 0.8135 (mpt180) cc_final: 0.7913 (mmm-85) REVERT: F 49 LYS cc_start: 0.8545 (mttm) cc_final: 0.8227 (mttp) REVERT: F 50 LYS cc_start: 0.7537 (mttt) cc_final: 0.7325 (mtmt) REVERT: F 58 GLN cc_start: 0.7636 (OUTLIER) cc_final: 0.7421 (mt0) REVERT: G 388 GLN cc_start: 0.7261 (mm-40) cc_final: 0.6970 (mm-40) REVERT: H 134 LYS cc_start: 0.8057 (mtmm) cc_final: 0.7392 (mmtm) REVERT: I 53 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7740 (mtpt) REVERT: I 57 GLN cc_start: 0.8225 (tp40) cc_final: 0.7935 (tp40) REVERT: I 70 PHE cc_start: 0.7068 (m-80) cc_final: 0.6852 (m-10) REVERT: J 40 LYS cc_start: 0.8220 (mttm) cc_final: 0.8003 (mmtp) REVERT: K 182 SER cc_start: 0.8548 (t) cc_final: 0.8010 (m) REVERT: K 218 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7941 (tp) REVERT: K 239 GLN cc_start: 0.7419 (OUTLIER) cc_final: 0.6925 (mt0) outliers start: 28 outliers final: 15 residues processed: 214 average time/residue: 0.6709 time to fit residues: 157.8496 Evaluate side-chains 209 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 187 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 195 ARG Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 18 LYS Chi-restraints excluded: chain F residue 58 GLN Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain I residue 53 LYS Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain K residue 218 LEU Chi-restraints excluded: chain K residue 239 GLN Chi-restraints excluded: chain K residue 322 GLN Chi-restraints excluded: chain K residue 424 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 29 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 70 optimal weight: 0.5980 chunk 111 optimal weight: 0.0770 chunk 118 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 GLN G 242 GLN H 93 ASN K 152 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.158225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.111408 restraints weight = 23480.755| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.48 r_work: 0.3218 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18620 Z= 0.104 Angle : 0.517 19.539 26195 Z= 0.267 Chirality : 0.036 0.207 3072 Planarity : 0.004 0.055 2569 Dihedral : 19.836 99.045 5168 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.96 % Allowed : 18.27 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.20), residues: 1648 helix: 0.91 (0.27), residues: 381 sheet: -1.22 (0.25), residues: 361 loop : 0.14 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 298 TYR 0.021 0.001 TYR K 244 PHE 0.012 0.001 PHE H 123 TRP 0.010 0.001 TRP C 380 HIS 0.004 0.001 HIS G 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.10 (18620) covalent geometry : angle 0.51676 / 0.27 (26195) hydrogen bonds : bond 0.03622 / 2.36 ( 589) hydrogen bonds : angle 4.03351 / 2.80 ( 1410) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 193 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: C 111 ARG cc_start: 0.8388 (mpp80) cc_final: 0.8000 (mmt90) REVERT: C 212 ARG cc_start: 0.7842 (mpp80) cc_final: 0.7192 (mtp85) REVERT: C 258 ASP cc_start: 0.6568 (t70) cc_final: 0.6334 (t0) REVERT: C 260 MET cc_start: 0.9023 (OUTLIER) cc_final: 0.8714 (ttp) REVERT: D 157 PHE cc_start: 0.7442 (m-80) cc_final: 0.7116 (m-80) REVERT: E 25 GLN cc_start: 0.7928 (tp40) cc_final: 0.6959 (tm-30) REVERT: E 89 GLU cc_start: 0.8117 (mp0) cc_final: 0.7800 (mp0) REVERT: E 128 MET cc_start: 0.8016 (OUTLIER) cc_final: 0.7631 (ttm) REVERT: F 18 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.8063 (mmmt) REVERT: F 34 ARG cc_start: 0.8130 (mpt180) cc_final: 0.7894 (mmm-85) REVERT: F 49 LYS cc_start: 0.8529 (mttm) cc_final: 0.8233 (mttp) REVERT: F 50 LYS cc_start: 0.7537 (mttt) cc_final: 0.7259 (mtmt) REVERT: G 254 MET cc_start: 0.8920 (mmm) cc_final: 0.8682 (mmm) REVERT: G 388 GLN cc_start: 0.7278 (mm-40) cc_final: 0.6993 (mm-40) REVERT: H 134 LYS cc_start: 0.8039 (mtmm) cc_final: 0.7392 (mmtm) REVERT: H 150 LYS cc_start: 0.7490 (mmtt) cc_final: 0.7048 (mmpt) REVERT: I 53 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7766 (mtpt) REVERT: I 57 GLN cc_start: 0.8247 (tp40) cc_final: 0.7954 (tp40) REVERT: J 23 MET cc_start: 0.7108 (tpt) cc_final: 0.6735 (tmm) REVERT: K 182 SER cc_start: 0.8551 (t) cc_final: 0.8017 (m) REVERT: K 239 GLN cc_start: 0.7418 (OUTLIER) cc_final: 0.6922 (mt0) outliers start: 29 outliers final: 14 residues processed: 210 average time/residue: 0.6905 time to fit residues: 159.3353 Evaluate side-chains 199 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 180 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 195 ARG Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 18 LYS Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain I residue 53 LYS Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain K residue 239 GLN Chi-restraints excluded: chain K residue 322 GLN Chi-restraints excluded: chain K residue 424 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 133 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 80 optimal weight: 8.9990 chunk 87 optimal weight: 6.9990 chunk 68 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 157 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 242 GLN H 93 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.157658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.110116 restraints weight = 23526.984| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.49 r_work: 0.3203 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18620 Z= 0.125 Angle : 0.533 19.908 26195 Z= 0.275 Chirality : 0.037 0.170 3072 Planarity : 0.004 0.055 2569 Dihedral : 19.835 97.994 5168 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.89 % Allowed : 18.34 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.20), residues: 1648 helix: 0.82 (0.27), residues: 386 sheet: -1.27 (0.25), residues: 371 loop : 0.17 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 138 TYR 0.023 0.001 TYR K 244 PHE 0.011 0.001 PHE H 123 TRP 0.009 0.001 TRP C 380 HIS 0.004 0.001 HIS G 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (18620) covalent geometry : angle 0.53339 / 0.27 (26195) hydrogen bonds : bond 0.03788 / 2.48 ( 589) hydrogen bonds : angle 4.06506 / 2.82 ( 1410) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6487.83 seconds wall clock time: 111 minutes 15.76 seconds (6675.76 seconds total)