Starting phenix.real_space_refine on Fri Aug 7 00:24:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qb2_52983/08_2026/9qb2_52983.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qb2_52983/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9qb2_52983/08_2026/9qb2_52983.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qb2_52983/08_2026/9qb2_52983.map" model { file = "/net/cci-nas-00/data/ceres_data/9qb2_52983/08_2026/9qb2_52983.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qb2_52983/08_2026/9qb2_52983.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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: 3.48, per 1000 atoms: 0.20 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: 1.22 Conformation dependent library (CDL) restraints added in 624.4 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: 1.90 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: 3.07 Time building geometry restraints manager: 1.73 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=" 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 bond pdb=" CG HIS G 120 " pdb=" CD2 HIS G 120 " ideal model delta sigma weight residual 1.354 1.317 0.037 1.10e-02 8.26e+03 1.13e+01 bond pdb=" O5' A B 372 " pdb=" C5' A B 372 " ideal model delta sigma weight residual 1.424 1.478 -0.054 1.60e-02 3.91e+03 1.13e+01 bond pdb=" CG HIS F 44 " pdb=" CD2 HIS F 44 " ideal model delta sigma weight residual 1.354 1.317 0.037 1.10e-02 8.26e+03 1.13e+01 ... (remaining 18615 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 25233 2.75 - 5.50: 924 5.50 - 8.25: 33 8.25 - 11.00: 3 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 1.10e+00 8.26e-01 1.56e+02 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 1.10e+00 8.26e-01 1.53e+02 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=" O4' G b 345 " pdb=" C1' G b 345 " pdb=" N9 G b 345 " ideal model delta sigma weight residual 108.50 112.70 -4.20 7.00e-01 2.04e+00 3.60e+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 - 0.142: 2789 0.142 - 0.284: 270 0.284 - 0.425: 7 0.425 - 0.567: 3 0.567 - 0.709: 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 2.47 1.76 0.71 2.00e-01 2.50e+01 1.26e+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 2.47 1.77 0.70 2.00e-01 2.50e+01 1.21e+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: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 16.570 Find NCS groups from input model: 0.200 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:6.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.770 ------------------------------------------------------------------------------- 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= 0.639 Angle : 1.216 13.748 26195 Z= 0.859 Chirality : 0.087 0.709 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 0.00941 / 0.64 (18620) covalent geometry : angle 1.21562 / 0.86 (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 : 0.470 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: 0.6477 time to fit residues: 260.3395 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 : 0.469 ------------------------------------------------------------------------------- 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 = 0.166708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.123299 restraints weight = 23647.896| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.33 r_work: 0.3375 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 18620 Z= 0.176 Angle : 0.646 20.394 26195 Z= 0.350 Chirality : 0.044 0.317 3072 Planarity : 0.005 0.069 2569 Dihedral : 19.912 107.084 5172 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.83 % Allowed : 9.81 % Favored : 88.36 % 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: -0.80 (0.19), residues: 1648 helix: 0.06 (0.25), residues: 377 sheet: -1.59 (0.25), residues: 360 loop : -0.19 (0.20), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 283 TYR 0.018 0.002 TYR K 196 PHE 0.019 0.002 PHE K 382 TRP 0.014 0.002 TRP C 108 HIS 0.006 0.001 HIS H 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.18 (18620) covalent geometry : angle 0.64592 / 0.35 (26195) hydrogen bonds : bond 0.06249 / 4.36 ( 589) hydrogen bonds : angle 5.04211 / 3.51 ( 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 285 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 258 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 193 GLN cc_start: 0.6802 (mt0) cc_final: 0.6345 (tt0) REVERT: D 73 LEU cc_start: 0.6601 (OUTLIER) cc_final: 0.6396 (tt) REVERT: D 157 PHE cc_start: 0.7315 (m-80) cc_final: 0.6875 (m-80) REVERT: E 66 GLU cc_start: 0.7563 (tt0) cc_final: 0.7309 (tt0) REVERT: E 89 GLU cc_start: 0.8010 (mp0) cc_final: 0.7766 (mp0) REVERT: E 128 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7622 (ttm) REVERT: E 132 HIS cc_start: 0.6170 (t-170) cc_final: 0.5843 (t70) REVERT: F 50 LYS cc_start: 0.7519 (mttt) cc_final: 0.7185 (mtmt) REVERT: G 244 GLN cc_start: 0.8531 (tp40) cc_final: 0.8255 (tp-100) REVERT: I 36 GLN cc_start: 0.8152 (mt0) cc_final: 0.7856 (mm110) REVERT: I 53 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7876 (mttt) REVERT: I 57 GLN cc_start: 0.8435 (tp40) cc_final: 0.8083 (tp40) REVERT: I 140 ASP cc_start: 0.7145 (m-30) cc_final: 0.6943 (m-30) REVERT: I 144 GLU cc_start: 0.6712 (pp20) cc_final: 0.6360 (pp20) REVERT: J 40 LYS cc_start: 0.8074 (mttm) cc_final: 0.7840 (mmtp) REVERT: J 53 LYS cc_start: 0.8575 (mmmt) cc_final: 0.8347 (mmmt) REVERT: K 155 ARG cc_start: 0.6558 (mtp-110) cc_final: 0.6278 (mtp180) REVERT: K 182 SER cc_start: 0.8144 (t) cc_final: 0.7659 (m) outliers start: 27 outliers final: 9 residues processed: 277 average time/residue: 0.7299 time to fit residues: 221.1093 Evaluate side-chains 211 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 199 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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 H residue 126 SER Chi-restraints excluded: chain H residue 141 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 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: 0.8980 chunk 75 optimal weight: 4.9990 chunk 180 optimal weight: 20.0000 chunk 4 optimal weight: 0.8980 chunk 18 optimal weight: 0.4980 chunk 141 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 154 optimal weight: 7.9990 chunk 109 optimal weight: 4.9990 chunk 134 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 276 HIS ** F 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 242 GLN I 68 GLN K 297 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.166726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.123784 restraints weight = 23696.454| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.34 r_work: 0.3383 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18620 Z= 0.118 Angle : 0.553 21.512 26195 Z= 0.292 Chirality : 0.038 0.188 3072 Planarity : 0.005 0.063 2569 Dihedral : 19.917 104.388 5172 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.17 % Allowed : 13.60 % Favored : 84.24 % 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: -0.47 (0.20), residues: 1648 helix: 0.49 (0.26), residues: 380 sheet: -1.34 (0.25), residues: 358 loop : -0.08 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 219 TYR 0.014 0.001 TYR E 135 PHE 0.013 0.002 PHE I 70 TRP 0.013 0.001 TRP K 395 HIS 0.005 0.001 HIS E 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (18620) covalent geometry : angle 0.55309 / 0.29 (26195) hydrogen bonds : bond 0.04705 / 3.25 ( 589) hydrogen bonds : angle 4.47558 / 3.10 ( 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 247 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 215 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 114 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.8078 (mtp180) REVERT: C 117 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8147 (ttmm) REVERT: C 193 GLN cc_start: 0.6886 (mt0) cc_final: 0.6424 (tt0) REVERT: C 260 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8547 (mtp) REVERT: E 25 GLN cc_start: 0.7447 (tp40) cc_final: 0.6847 (tm130) REVERT: E 45 ARG cc_start: 0.7026 (ttm-80) cc_final: 0.6808 (ttm-80) REVERT: E 66 GLU cc_start: 0.7581 (tt0) cc_final: 0.7321 (tt0) REVERT: E 89 GLU cc_start: 0.7975 (mp0) cc_final: 0.7703 (mp0) REVERT: E 128 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7745 (ttm) REVERT: F 50 LYS cc_start: 0.7320 (mttt) cc_final: 0.6981 (mtmt) REVERT: G 254 MET cc_start: 0.8955 (mmm) cc_final: 0.8686 (mmm) REVERT: H 141 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8087 (mt) REVERT: I 36 GLN cc_start: 0.8151 (mt0) cc_final: 0.7880 (mm110) REVERT: I 53 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7861 (mtpt) REVERT: I 57 GLN cc_start: 0.8302 (tp40) cc_final: 0.7916 (tp40) REVERT: I 62 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8340 (mtt180) REVERT: J 40 LYS cc_start: 0.7989 (mttm) cc_final: 0.7739 (mmtp) REVERT: J 53 LYS cc_start: 0.8551 (mmmt) cc_final: 0.8329 (mmmt) REVERT: K 155 ARG cc_start: 0.6721 (mtp-110) cc_final: 0.6448 (mtp180) REVERT: K 182 SER cc_start: 0.8119 (t) cc_final: 0.7624 (m) REVERT: K 214 MET cc_start: 0.8936 (mtp) cc_final: 0.8639 (mtp) REVERT: K 239 GLN cc_start: 0.7460 (OUTLIER) cc_final: 0.7008 (mt0) outliers start: 32 outliers final: 7 residues processed: 237 average time/residue: 0.6931 time to fit residues: 180.9776 Evaluate side-chains 207 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 192 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 131 GLU Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 128 MET Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 141 LEU 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 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: 5.9990 chunk 41 optimal weight: 2.9990 chunk 183 optimal weight: 20.0000 chunk 55 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 166 optimal weight: 40.0000 chunk 174 optimal weight: 50.0000 chunk 117 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 63 ASN ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 HIS D 119 GLN F 58 GLN G 146 GLN G 242 GLN G 388 GLN K 297 ASN K 415 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.157616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.110554 restraints weight = 23688.539| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.49 r_work: 0.3202 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 18620 Z= 0.168 Angle : 0.585 21.923 26195 Z= 0.303 Chirality : 0.040 0.225 3072 Planarity : 0.005 0.072 2569 Dihedral : 19.932 102.721 5170 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.77 % Allowed : 14.75 % 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: -0.45 (0.20), residues: 1648 helix: 0.51 (0.26), residues: 386 sheet: -1.43 (0.24), residues: 351 loop : -0.03 (0.20), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 111 TYR 0.016 0.002 TYR K 244 PHE 0.015 0.002 PHE I 70 TRP 0.010 0.001 TRP K 395 HIS 0.005 0.001 HIS C 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (18620) covalent geometry : angle 0.58468 / 0.30 (26195) hydrogen bonds : bond 0.04661 / 3.20 ( 589) hydrogen bonds : angle 4.43384 / 3.06 ( 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 252 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 211 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 193 GLN cc_start: 0.7015 (mt0) cc_final: 0.6415 (tt0) REVERT: C 260 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8746 (ttp) REVERT: E 25 GLN cc_start: 0.7486 (tp40) cc_final: 0.6720 (tm130) REVERT: E 66 GLU cc_start: 0.7764 (tt0) cc_final: 0.7417 (tt0) REVERT: E 89 GLU cc_start: 0.8088 (mp0) cc_final: 0.7747 (mp0) REVERT: E 133 GLU cc_start: 0.7621 (pm20) cc_final: 0.6844 (mp0) REVERT: F 50 LYS cc_start: 0.7582 (mttt) cc_final: 0.7143 (mtmt) REVERT: G 254 MET cc_start: 0.8953 (mmm) cc_final: 0.8716 (mmm) REVERT: I 36 GLN cc_start: 0.8278 (mt0) cc_final: 0.7929 (mt0) REVERT: I 53 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7788 (mtpt) REVERT: I 57 GLN cc_start: 0.8312 (tp40) cc_final: 0.7931 (tp40) REVERT: I 62 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.8310 (mtt180) REVERT: J 40 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7930 (mmtp) REVERT: J 53 LYS cc_start: 0.8711 (mmmt) cc_final: 0.8459 (mmmt) REVERT: K 182 SER cc_start: 0.8287 (t) cc_final: 0.7756 (m) REVERT: K 214 MET cc_start: 0.8888 (mtp) cc_final: 0.8571 (mtp) REVERT: K 239 GLN cc_start: 0.7446 (OUTLIER) cc_final: 0.6948 (mt0) REVERT: K 452 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.7030 (pp20) outliers start: 41 outliers final: 13 residues processed: 236 average time/residue: 0.7165 time to fit residues: 186.0182 Evaluate side-chains 216 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 197 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 148 SER 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 F residue 7 LEU Chi-restraints excluded: chain F residue 23 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 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 Chi-restraints excluded: chain K residue 452 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 105 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.157481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.110412 restraints weight = 23539.724| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.50 r_work: 0.3202 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18620 Z= 0.146 Angle : 0.549 21.210 26195 Z= 0.286 Chirality : 0.039 0.183 3072 Planarity : 0.005 0.065 2569 Dihedral : 19.916 102.805 5170 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.77 % Allowed : 15.36 % Favored : 81.87 % 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: -0.35 (0.20), residues: 1648 helix: 0.59 (0.26), residues: 386 sheet: -1.37 (0.25), residues: 341 loop : 0.01 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 298 TYR 0.026 0.001 TYR K 244 PHE 0.014 0.002 PHE I 70 TRP 0.010 0.001 TRP C 380 HIS 0.005 0.001 HIS G 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (18620) covalent geometry : angle 0.54948 / 0.29 (26195) hydrogen bonds : bond 0.04306 / 2.91 ( 589) hydrogen bonds : angle 4.35085 / 3.01 ( 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 244 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 203 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 118 THR cc_start: 0.8494 (OUTLIER) cc_final: 0.8228 (t) REVERT: C 193 GLN cc_start: 0.6927 (mt0) cc_final: 0.6271 (tt0) REVERT: C 258 ASP cc_start: 0.6632 (t70) cc_final: 0.6320 (t0) REVERT: C 260 MET cc_start: 0.9033 (OUTLIER) cc_final: 0.8765 (ttp) REVERT: D 115 GLU cc_start: 0.8318 (tp30) cc_final: 0.8093 (tp30) REVERT: E 25 GLN cc_start: 0.7612 (tp40) cc_final: 0.6802 (tm130) REVERT: E 66 GLU cc_start: 0.7825 (tt0) cc_final: 0.7429 (tt0) REVERT: E 89 GLU cc_start: 0.8062 (mp0) cc_final: 0.7631 (mp0) REVERT: E 128 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7761 (ttm) REVERT: F 10 GLN cc_start: 0.6746 (mp10) cc_final: 0.6462 (mt0) REVERT: F 18 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8098 (mmmt) REVERT: F 50 LYS cc_start: 0.7588 (mttt) cc_final: 0.7247 (mtmt) REVERT: G 254 MET cc_start: 0.8959 (mmm) cc_final: 0.8657 (mmm) REVERT: I 36 GLN cc_start: 0.8303 (mt0) cc_final: 0.8025 (mt0) REVERT: I 53 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7712 (mtpt) REVERT: I 57 GLN cc_start: 0.8289 (tp40) cc_final: 0.7895 (tp40) REVERT: I 62 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8309 (mtt180) REVERT: J 40 LYS cc_start: 0.8160 (mttm) cc_final: 0.7950 (mmtp) REVERT: J 53 LYS cc_start: 0.8673 (mmmt) cc_final: 0.8453 (mmmt) REVERT: K 182 SER cc_start: 0.8346 (t) cc_final: 0.7792 (m) REVERT: K 214 MET cc_start: 0.8899 (mtp) cc_final: 0.8552 (mtp) REVERT: K 239 GLN cc_start: 0.7454 (OUTLIER) cc_final: 0.6956 (mt0) outliers start: 41 outliers final: 16 residues processed: 227 average time/residue: 0.7789 time to fit residues: 194.0493 Evaluate side-chains 214 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 191 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 63 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 147 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 166 optimal weight: 40.0000 chunk 97 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 19 optimal weight: 0.0020 chunk 141 optimal weight: 0.9990 chunk 173 optimal weight: 50.0000 chunk 82 optimal weight: 5.9990 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 275 ASN F 58 GLN G 242 GLN G 388 GLN J 10 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.158514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.111612 restraints weight = 23392.367| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.48 r_work: 0.3220 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 18620 Z= 0.109 Angle : 0.525 20.106 26195 Z= 0.272 Chirality : 0.037 0.162 3072 Planarity : 0.004 0.042 2569 Dihedral : 19.891 100.467 5170 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.64 % Allowed : 16.31 % Favored : 81.06 % 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: -0.28 (0.20), residues: 1648 helix: 0.74 (0.27), residues: 385 sheet: -1.34 (0.25), residues: 350 loop : 0.04 (0.20), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 298 TYR 0.017 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 0.00250 / 0.11 (18620) covalent geometry : angle 0.52452 / 0.27 (26195) hydrogen bonds : bond 0.03896 / 2.59 ( 589) hydrogen bonds : angle 4.18071 / 2.90 ( 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 241 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 202 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: C 118 THR cc_start: 0.8450 (m) cc_final: 0.8223 (t) REVERT: C 212 ARG cc_start: 0.7738 (mpp80) cc_final: 0.7141 (mtp85) REVERT: C 258 ASP cc_start: 0.6606 (t70) cc_final: 0.6326 (t0) REVERT: C 260 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8751 (ttp) REVERT: E 25 GLN cc_start: 0.7652 (tp40) cc_final: 0.6652 (tm-30) REVERT: E 66 GLU cc_start: 0.7780 (tt0) cc_final: 0.7429 (tt0) REVERT: E 89 GLU cc_start: 0.8106 (mp0) cc_final: 0.7657 (mp0) REVERT: E 128 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.7665 (ttm) REVERT: E 133 GLU cc_start: 0.7382 (pm20) cc_final: 0.6991 (pm20) REVERT: F 10 GLN cc_start: 0.6584 (mp10) cc_final: 0.6288 (mt0) REVERT: F 18 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.8072 (mmmt) REVERT: F 50 LYS cc_start: 0.7563 (mttt) cc_final: 0.7244 (mtmt) REVERT: G 254 MET cc_start: 0.8914 (mmm) cc_final: 0.8645 (mmm) REVERT: I 36 GLN cc_start: 0.8300 (mt0) cc_final: 0.8024 (mt0) REVERT: I 53 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7718 (mtpt) REVERT: I 57 GLN cc_start: 0.8228 (tp40) cc_final: 0.7839 (tp40) REVERT: I 62 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8280 (mtt180) REVERT: J 40 LYS cc_start: 0.8182 (mttm) cc_final: 0.7957 (mmtp) REVERT: J 53 LYS cc_start: 0.8613 (mmmt) cc_final: 0.8386 (mmmt) REVERT: K 182 SER cc_start: 0.8362 (t) cc_final: 0.7806 (m) REVERT: K 214 MET cc_start: 0.8890 (mtp) cc_final: 0.8465 (mtp) REVERT: K 239 GLN cc_start: 0.7443 (OUTLIER) cc_final: 0.6947 (mt0) outliers start: 39 outliers final: 15 residues processed: 224 average time/residue: 0.7336 time to fit residues: 181.0951 Evaluate side-chains 215 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 194 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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 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 258 ASP 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 J residue 63 VAL Chi-restraints excluded: chain K residue 239 GLN Chi-restraints excluded: chain K residue 394 CYS 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: 5.9990 chunk 96 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 76 optimal weight: 0.0870 chunk 174 optimal weight: 50.0000 overall best weight: 1.3162 ------------------------------------------------------------------------------- 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 G 388 GLN H 93 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.157414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.110568 restraints weight = 23759.885| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.48 r_work: 0.3202 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 18620 Z= 0.132 Angle : 0.525 20.123 26195 Z= 0.272 Chirality : 0.038 0.201 3072 Planarity : 0.004 0.040 2569 Dihedral : 19.883 99.618 5168 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.57 % Allowed : 16.51 % Favored : 80.92 % 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: 0.77 (0.27), residues: 385 sheet: -1.25 (0.26), residues: 335 loop : 0.03 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 298 TYR 0.015 0.001 TYR E 135 PHE 0.011 0.002 PHE H 123 TRP 0.010 0.001 TRP K 231 HIS 0.004 0.001 HIS G 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (18620) covalent geometry : angle 0.52491 / 0.27 (26195) hydrogen bonds : bond 0.04009 / 2.66 ( 589) hydrogen bonds : angle 4.18875 / 2.91 ( 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 241 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 203 time to evaluate : 0.625 Fit side-chains revert: symmetry clash REVERT: C 118 THR cc_start: 0.8513 (OUTLIER) cc_final: 0.8266 (t) REVERT: C 212 ARG cc_start: 0.7833 (mpp80) cc_final: 0.7214 (mtp85) REVERT: C 260 MET cc_start: 0.9014 (OUTLIER) cc_final: 0.8772 (ttp) REVERT: E 25 GLN cc_start: 0.7727 (tp40) cc_final: 0.6920 (tm-30) REVERT: E 66 GLU cc_start: 0.7832 (tt0) cc_final: 0.7490 (tt0) REVERT: E 89 GLU cc_start: 0.8112 (mp0) cc_final: 0.7649 (mp0) REVERT: E 128 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.7645 (ttm) REVERT: F 10 GLN cc_start: 0.6687 (mp10) cc_final: 0.6402 (mt0) REVERT: F 18 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.8075 (mmmt) REVERT: F 50 LYS cc_start: 0.7594 (mttt) cc_final: 0.7260 (mtmt) REVERT: F 58 GLN cc_start: 0.7692 (OUTLIER) cc_final: 0.7490 (mt0) REVERT: G 254 MET cc_start: 0.8916 (mmm) cc_final: 0.8665 (mmm) REVERT: G 388 GLN cc_start: 0.7221 (mm-40) cc_final: 0.6973 (mm-40) REVERT: H 134 LYS cc_start: 0.8056 (mtmm) cc_final: 0.7394 (mmtm) REVERT: I 36 GLN cc_start: 0.8294 (mt0) cc_final: 0.8009 (mt0) REVERT: I 53 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7731 (mtpt) REVERT: I 57 GLN cc_start: 0.8237 (tp40) cc_final: 0.7869 (tp40) REVERT: I 62 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.8408 (mmt180) REVERT: J 40 LYS cc_start: 0.8166 (mttm) cc_final: 0.7946 (mmtp) REVERT: J 53 LYS cc_start: 0.8592 (mmmt) cc_final: 0.8363 (mmmt) REVERT: K 182 SER cc_start: 0.8536 (t) cc_final: 0.7922 (m) REVERT: K 214 MET cc_start: 0.8912 (mtp) cc_final: 0.8446 (mtp) REVERT: K 239 GLN cc_start: 0.7435 (OUTLIER) cc_final: 0.6947 (mt0) REVERT: K 400 SER cc_start: 0.7726 (OUTLIER) cc_final: 0.7521 (p) outliers start: 38 outliers final: 16 residues processed: 225 average time/residue: 0.7253 time to fit residues: 180.0260 Evaluate side-chains 214 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 189 time to evaluate : 0.706 ------------------------------------------------------------------------------- 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 F residue 58 GLN Chi-restraints excluded: chain G residue 85 ASP 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 J residue 63 VAL Chi-restraints excluded: chain K residue 239 GLN Chi-restraints excluded: chain K residue 394 CYS 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: 2.9990 chunk 18 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 162 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 137 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 169 optimal weight: 50.0000 chunk 159 optimal weight: 0.4980 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 = 0.4000 r_free = 0.4000 target = 0.156894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.110596 restraints weight = 23421.051| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.39 r_work: 0.3196 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 18620 Z= 0.139 Angle : 0.536 20.449 26195 Z= 0.277 Chirality : 0.038 0.162 3072 Planarity : 0.004 0.043 2569 Dihedral : 19.895 99.128 5168 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.44 % Allowed : 16.91 % 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: -0.22 (0.20), residues: 1648 helix: 0.81 (0.27), residues: 383 sheet: -1.30 (0.26), residues: 341 loop : 0.04 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 298 TYR 0.018 0.001 TYR K 244 PHE 0.012 0.002 PHE K 485 TRP 0.010 0.001 TRP K 231 HIS 0.004 0.001 HIS G 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (18620) covalent geometry : angle 0.53644 / 0.28 (26195) hydrogen bonds : bond 0.04067 / 2.69 ( 589) hydrogen bonds : angle 4.19840 / 2.92 ( 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 232 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 196 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: C 118 THR cc_start: 0.8513 (OUTLIER) cc_final: 0.8257 (t) REVERT: C 212 ARG cc_start: 0.7892 (mpp80) cc_final: 0.7287 (mtp85) REVERT: C 258 ASP cc_start: 0.6595 (t70) cc_final: 0.6349 (t0) REVERT: C 260 MET cc_start: 0.9019 (OUTLIER) cc_final: 0.8756 (ttp) REVERT: E 25 GLN cc_start: 0.7876 (tp40) cc_final: 0.6922 (tm-30) REVERT: E 66 GLU cc_start: 0.7820 (tt0) cc_final: 0.7523 (tt0) REVERT: E 89 GLU cc_start: 0.8122 (mp0) cc_final: 0.7767 (mp0) REVERT: E 128 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7639 (ttm) REVERT: E 135 TYR cc_start: 0.7090 (p90) cc_final: 0.6849 (p90) REVERT: F 1 MET cc_start: 0.7803 (mmt) cc_final: 0.7597 (mmt) REVERT: F 18 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.8091 (mmmt) REVERT: G 254 MET cc_start: 0.8906 (mmm) cc_final: 0.8628 (mmm) REVERT: G 388 GLN cc_start: 0.7254 (mm-40) cc_final: 0.7008 (mm-40) REVERT: H 134 LYS cc_start: 0.8063 (mtmm) cc_final: 0.7414 (mmtm) REVERT: I 53 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7768 (mtpt) REVERT: I 57 GLN cc_start: 0.8249 (tp40) cc_final: 0.7902 (tp40) REVERT: J 40 LYS cc_start: 0.8223 (mttm) cc_final: 0.8003 (mmtp) REVERT: J 53 LYS cc_start: 0.8573 (mmmt) cc_final: 0.8336 (mmmt) REVERT: K 182 SER cc_start: 0.8524 (t) cc_final: 0.7917 (m) REVERT: K 214 MET cc_start: 0.8919 (mtp) cc_final: 0.8522 (mtp) REVERT: K 239 GLN cc_start: 0.7362 (OUTLIER) cc_final: 0.6867 (mt0) outliers start: 36 outliers final: 20 residues processed: 218 average time/residue: 0.7380 time to fit residues: 177.1945 Evaluate side-chains 216 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 190 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 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 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 85 ASP Chi-restraints excluded: chain G residue 157 VAL 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 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 394 CYS Chi-restraints excluded: chain K residue 400 SER 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: 0.6980 chunk 42 optimal weight: 7.9990 chunk 114 optimal weight: 6.9990 chunk 135 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** K 152 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.157786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.110714 restraints weight = 23571.144| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.48 r_work: 0.3211 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18620 Z= 0.112 Angle : 0.521 19.955 26195 Z= 0.270 Chirality : 0.036 0.151 3072 Planarity : 0.004 0.047 2569 Dihedral : 19.878 97.286 5168 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.30 % Allowed : 17.46 % Favored : 80.24 % 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: 0.90 (0.27), residues: 383 sheet: -1.28 (0.26), residues: 344 loop : 0.08 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 298 TYR 0.020 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 0.00258 / 0.11 (18620) covalent geometry : angle 0.52090 / 0.27 (26195) hydrogen bonds : bond 0.03807 / 2.48 ( 589) hydrogen bonds : angle 4.07907 / 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 230 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 196 time to evaluate : 0.611 Fit side-chains revert: symmetry clash REVERT: C 118 THR cc_start: 0.8443 (OUTLIER) cc_final: 0.8217 (t) REVERT: C 212 ARG cc_start: 0.7887 (mpp80) cc_final: 0.7228 (mtp85) REVERT: C 258 ASP cc_start: 0.6566 (t70) cc_final: 0.6329 (t0) REVERT: C 260 MET cc_start: 0.9001 (OUTLIER) cc_final: 0.8750 (ttp) REVERT: D 157 PHE cc_start: 0.7355 (m-80) cc_final: 0.6984 (m-80) REVERT: E 25 GLN cc_start: 0.7925 (tp40) cc_final: 0.6920 (tm-30) REVERT: E 89 GLU cc_start: 0.8129 (mp0) cc_final: 0.7752 (mp0) REVERT: E 128 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7636 (ttm) REVERT: F 10 GLN cc_start: 0.6685 (mp10) cc_final: 0.6369 (mt0) REVERT: F 18 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.8041 (mmmt) REVERT: F 49 LYS cc_start: 0.8535 (mttm) cc_final: 0.8241 (mttp) REVERT: G 254 MET cc_start: 0.8880 (mmm) cc_final: 0.8621 (mmm) REVERT: G 388 GLN cc_start: 0.7319 (mm-40) cc_final: 0.7084 (mm-40) REVERT: H 134 LYS cc_start: 0.8067 (mtmm) cc_final: 0.7417 (mmtm) REVERT: H 158 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7786 (mp) REVERT: I 53 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7725 (mtpt) REVERT: I 57 GLN cc_start: 0.8218 (tp40) cc_final: 0.7894 (tp40) REVERT: I 70 PHE cc_start: 0.7134 (m-10) cc_final: 0.6856 (m-10) REVERT: J 40 LYS cc_start: 0.8252 (mttm) cc_final: 0.8008 (mmtp) REVERT: K 182 SER cc_start: 0.8554 (t) cc_final: 0.7944 (m) REVERT: K 214 MET cc_start: 0.8951 (mtp) cc_final: 0.8467 (mtp) REVERT: K 239 GLN cc_start: 0.7355 (OUTLIER) cc_final: 0.6861 (mt0) REVERT: K 400 SER cc_start: 0.7792 (OUTLIER) cc_final: 0.7298 (m) outliers start: 34 outliers final: 16 residues processed: 217 average time/residue: 0.7028 time to fit residues: 168.2797 Evaluate side-chains 211 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 0.653 ------------------------------------------------------------------------------- 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 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 H residue 91 ASP 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 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 394 CYS Chi-restraints excluded: chain K residue 400 SER 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: 5.9990 chunk 53 optimal weight: 8.9990 chunk 88 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 70 optimal weight: 0.0970 chunk 111 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 415 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 = 0.158116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.110792 restraints weight = 23414.085| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.48 r_work: 0.3213 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18620 Z= 0.107 Angle : 0.526 19.865 26195 Z= 0.272 Chirality : 0.036 0.162 3072 Planarity : 0.004 0.057 2569 Dihedral : 19.869 96.277 5168 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.96 % Allowed : 18.34 % Favored : 79.70 % 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: -0.10 (0.20), residues: 1648 helix: 0.91 (0.27), residues: 383 sheet: -1.21 (0.25), residues: 351 loop : 0.13 (0.20), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 34 TYR 0.022 0.001 TYR K 244 PHE 0.013 0.001 PHE H 123 TRP 0.010 0.001 TRP K 231 HIS 0.007 0.001 HIS E 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (18620) covalent geometry : angle 0.52637 / 0.27 (26195) hydrogen bonds : bond 0.03755 / 2.44 ( 589) hydrogen bonds : angle 4.06913 / 2.83 ( 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 : 0.584 Fit side-chains revert: symmetry clash REVERT: C 118 THR cc_start: 0.8412 (OUTLIER) cc_final: 0.8197 (t) REVERT: C 195 ARG cc_start: 0.6845 (mtt-85) cc_final: 0.6540 (ttm-80) REVERT: C 212 ARG cc_start: 0.7898 (mpp80) cc_final: 0.7227 (mtp85) REVERT: C 258 ASP cc_start: 0.6574 (t70) cc_final: 0.6342 (t0) REVERT: C 260 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.8740 (ttp) REVERT: D 157 PHE cc_start: 0.7429 (m-80) cc_final: 0.7108 (m-80) REVERT: E 25 GLN cc_start: 0.7924 (tp40) cc_final: 0.6920 (tm-30) REVERT: E 89 GLU cc_start: 0.8114 (mp0) cc_final: 0.7749 (mp0) REVERT: E 128 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7639 (ttm) REVERT: F 18 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.8059 (mmmt) REVERT: F 49 LYS cc_start: 0.8505 (mttm) cc_final: 0.8229 (mttp) REVERT: G 254 MET cc_start: 0.8872 (mmm) cc_final: 0.8631 (mmm) REVERT: G 388 GLN cc_start: 0.7288 (mm-40) cc_final: 0.7053 (mm-40) REVERT: H 134 LYS cc_start: 0.8083 (mtmm) cc_final: 0.7421 (mmtm) REVERT: H 158 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7786 (mp) REVERT: I 53 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7724 (mtpt) REVERT: I 57 GLN cc_start: 0.8211 (tp40) cc_final: 0.7862 (tp40) REVERT: I 70 PHE cc_start: 0.7089 (m-10) cc_final: 0.6840 (m-10) REVERT: J 40 LYS cc_start: 0.8242 (mttm) cc_final: 0.8001 (mmtp) REVERT: K 182 SER cc_start: 0.8581 (t) cc_final: 0.7963 (m) REVERT: K 214 MET cc_start: 0.8945 (mtp) cc_final: 0.8455 (mtp) REVERT: K 239 GLN cc_start: 0.7348 (OUTLIER) cc_final: 0.6855 (mt0) REVERT: K 400 SER cc_start: 0.7757 (OUTLIER) cc_final: 0.7262 (m) outliers start: 29 outliers final: 14 residues processed: 213 average time/residue: 0.6640 time to fit residues: 156.4106 Evaluate side-chains 207 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 185 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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 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 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 H residue 158 LEU 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 394 CYS Chi-restraints excluded: chain K residue 400 SER 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: 2.9990 chunk 105 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.4012 r_free = 0.4012 target = 0.157967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.110558 restraints weight = 23574.902| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.49 r_work: 0.3210 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.259 18620 Z= 0.172 Angle : 0.700 59.200 26195 Z= 0.396 Chirality : 0.039 0.713 3072 Planarity : 0.004 0.057 2569 Dihedral : 19.870 96.289 5168 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.62 % Allowed : 18.81 % Favored : 79.57 % Cbeta Deviations : 0.06 % 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: 383 sheet: -1.21 (0.25), residues: 351 loop : 0.12 (0.20), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 111 TYR 0.019 0.001 TYR K 244 PHE 0.012 0.001 PHE H 123 TRP 0.010 0.001 TRP K 231 HIS 0.008 0.001 HIS E 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 (18620) covalent geometry : angle 0.69969 / 0.40 (26195) hydrogen bonds : bond 0.03844 / 2.48 ( 589) hydrogen bonds : angle 4.06870 / 2.83 ( 1410) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6719.89 seconds wall clock time: 115 minutes 4.41 seconds (6904.41 seconds total)