Starting phenix.real_space_refine on Fri Feb 6 11:01:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lq8_63296/02_2026/9lq8_63296.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lq8_63296/02_2026/9lq8_63296.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lq8_63296/02_2026/9lq8_63296.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lq8_63296/02_2026/9lq8_63296.map" model { file = "/net/cci-nas-00/data/ceres_data/9lq8_63296/02_2026/9lq8_63296.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lq8_63296/02_2026/9lq8_63296.cif" } resolution = 2.85 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= -0.006 sd= 0.572 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: 6 Type Number sf(0) Gaussians Mn 1 7.51 5 P 78 5.49 5 S 106 5.16 5 C 15388 2.51 5 N 4095 2.21 5 O 4843 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24511 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3904 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 17, 'TRANS': 451} Chain: "C" Number of atoms: 3043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 3043 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 13, 'TRANS': 356} Chain breaks: 1 Chain: "D" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2214 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 13, 'TRANS': 265} Chain: "E" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2214 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 13, 'TRANS': 265} Chain: "F" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2214 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 13, 'TRANS': 265} Chain: "G" Number of atoms: 1071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1071 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 3, 'TRANS': 132} Chain: "H" Number of atoms: 1071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1071 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 3, 'TRANS': 132} Chain: "I" Number of atoms: 2534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2534 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 16, 'TRANS': 297} Chain: "K" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 721 Classifications: {'RNA': 34} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 14, 'rna3p_pyr': 14} Link IDs: {'rna2p': 6, 'rna3p': 27} Chain: "J" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 873 Classifications: {'RNA': 41} Modifications used: {'p5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 8, 'rna3p_pur': 12, 'rna3p_pyr': 12} Link IDs: {'rna2p': 17, 'rna3p': 23} Chain: "B" Number of atoms: 4593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4593 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 19, 'TRANS': 546} Chain breaks: 4 Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MN': 1, 'ATP': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Time building chain proxies: 5.86, per 1000 atoms: 0.24 Number of scatterers: 24511 At special positions: 0 Unit cell: (97.86, 114.636, 198.516, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 1 24.99 S 106 16.00 P 78 15.00 O 4843 8.00 N 4095 7.00 C 15388 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: 2.13 Conformation dependent library (CDL) restraints added in 960.9 milliseconds 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5390 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 31 sheets defined 41.8% alpha, 15.0% beta 24 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 2.85 Creating SS restraints... Processing helix chain 'A' and resid 27 through 44 removed outlier: 3.511A pdb=" N VAL A 31 " --> pdb=" O ARG A 27 " (cutoff:3.500A) Proline residue: A 33 - end of helix Processing helix chain 'A' and resid 47 through 58 Processing helix chain 'A' and resid 114 through 119 removed outlier: 3.634A pdb=" N CYS A 117 " --> pdb=" O GLN A 114 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL A 118 " --> pdb=" O GLU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 149 Processing helix chain 'A' and resid 168 through 186 Proline residue: A 180 - end of helix Processing helix chain 'A' and resid 191 through 195 Processing helix chain 'A' and resid 212 through 221 Processing helix chain 'A' and resid 238 through 259 removed outlier: 3.503A pdb=" N LYS A 258 " --> pdb=" O TYR A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.575A pdb=" N PHE A 276 " --> pdb=" O LEU A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 295 removed outlier: 4.179A pdb=" N LEU A 293 " --> pdb=" O LYS A 289 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE A 294 " --> pdb=" O MET A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 334 removed outlier: 3.774A pdb=" N ILE A 334 " --> pdb=" O ILE A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 443 through 452 removed outlier: 3.983A pdb=" N MET A 452 " --> pdb=" O MET A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 459 removed outlier: 3.831A pdb=" N GLY A 458 " --> pdb=" O LYS A 455 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS A 459 " --> pdb=" O LYS A 456 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 455 through 459' Processing helix chain 'C' and resid 84 through 101 Processing helix chain 'C' and resid 114 through 123 Processing helix chain 'C' and resid 129 through 133 Processing helix chain 'C' and resid 216 through 220 removed outlier: 3.717A pdb=" N TYR C 220 " --> pdb=" O HIS C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 223 No H-bonds generated for 'chain 'C' and resid 221 through 223' Processing helix chain 'C' and resid 239 through 242 No H-bonds generated for 'chain 'C' and resid 239 through 242' Processing helix chain 'C' and resid 317 through 327 removed outlier: 3.825A pdb=" N LYS C 321 " --> pdb=" O ASP C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 330 No H-bonds generated for 'chain 'C' and resid 328 through 330' Processing helix chain 'C' and resid 345 through 352 removed outlier: 3.752A pdb=" N LEU C 349 " --> pdb=" O ASN C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 410 Processing helix chain 'C' and resid 411 through 418 Processing helix chain 'D' and resid 42 through 54 Processing helix chain 'D' and resid 57 through 65 Processing helix chain 'D' and resid 104 through 118 Processing helix chain 'D' and resid 121 through 141 removed outlier: 4.414A pdb=" N TYR D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 182 Processing helix chain 'D' and resid 189 through 197 removed outlier: 3.602A pdb=" N ILE D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 253 Processing helix chain 'E' and resid 42 through 54 Processing helix chain 'E' and resid 57 through 65 Processing helix chain 'E' and resid 104 through 118 Processing helix chain 'E' and resid 121 through 141 removed outlier: 3.780A pdb=" N TYR E 125 " --> pdb=" O GLU E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 154 Processing helix chain 'E' and resid 174 through 182 Processing helix chain 'E' and resid 189 through 197 Processing helix chain 'E' and resid 240 through 253 Processing helix chain 'E' and resid 263 through 267 Processing helix chain 'F' and resid 42 through 54 Processing helix chain 'F' and resid 57 through 65 Processing helix chain 'F' and resid 104 through 118 Processing helix chain 'F' and resid 121 through 141 removed outlier: 3.953A pdb=" N TYR F 125 " --> pdb=" O GLU F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 182 Processing helix chain 'F' and resid 189 through 197 Processing helix chain 'F' and resid 240 through 252 Processing helix chain 'F' and resid 263 through 267 Processing helix chain 'G' and resid 4 through 18 Processing helix chain 'G' and resid 29 through 46 removed outlier: 4.314A pdb=" N GLY G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY G 39 " --> pdb=" O ILE G 35 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA G 40 " --> pdb=" O SER G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 56 Processing helix chain 'G' and resid 66 through 81 Processing helix chain 'G' and resid 101 through 109 Processing helix chain 'G' and resid 111 through 130 removed outlier: 3.831A pdb=" N LEU G 115 " --> pdb=" O ASN G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 133 No H-bonds generated for 'chain 'G' and resid 131 through 133' Processing helix chain 'H' and resid 4 through 18 Processing helix chain 'H' and resid 29 through 45 removed outlier: 4.276A pdb=" N GLY H 33 " --> pdb=" O LYS H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 56 removed outlier: 3.624A pdb=" N ASN H 56 " --> pdb=" O ILE H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 82 removed outlier: 3.624A pdb=" N GLN H 82 " --> pdb=" O ALA H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 91 removed outlier: 3.504A pdb=" N THR H 89 " --> pdb=" O VAL H 85 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE H 90 " --> pdb=" O THR H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 109 Processing helix chain 'H' and resid 112 through 132 removed outlier: 3.561A pdb=" N LEU H 116 " --> pdb=" O THR H 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 19 Processing helix chain 'I' and resid 32 through 38 removed outlier: 3.712A pdb=" N GLU I 37 " --> pdb=" O THR I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 53 Processing helix chain 'I' and resid 61 through 72 Processing helix chain 'I' and resid 116 through 127 removed outlier: 4.058A pdb=" N MET I 127 " --> pdb=" O THR I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 128 through 132 removed outlier: 4.385A pdb=" N LEU I 132 " --> pdb=" O PRO I 129 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 161 Processing helix chain 'I' and resid 167 through 179 Processing helix chain 'I' and resid 261 through 271 removed outlier: 3.556A pdb=" N GLU I 267 " --> pdb=" O LYS I 263 " (cutoff:3.500A) Processing helix chain 'I' and resid 283 through 299 Processing helix chain 'B' and resid 10 through 17 Processing helix chain 'B' and resid 20 through 45 removed outlier: 3.547A pdb=" N SER B 28 " --> pdb=" O LEU B 24 " (cutoff:3.500A) Proline residue: B 41 - end of helix Processing helix chain 'B' and resid 80 through 100 Processing helix chain 'B' and resid 111 through 122 Processing helix chain 'B' and resid 135 through 151 Proline residue: B 141 - end of helix removed outlier: 3.824A pdb=" N TYR B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE B 149 " --> pdb=" O LYS B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 178 removed outlier: 3.504A pdb=" N ASN B 178 " --> pdb=" O PHE B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 204 Processing helix chain 'B' and resid 217 through 221 removed outlier: 3.672A pdb=" N ALA B 221 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 237 removed outlier: 3.569A pdb=" N LYS B 231 " --> pdb=" O ASN B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 261 Processing helix chain 'B' and resid 262 through 266 removed outlier: 3.664A pdb=" N GLN B 265 " --> pdb=" O ASN B 262 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU B 266 " --> pdb=" O LYS B 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 262 through 266' Processing helix chain 'B' and resid 267 through 270 Processing helix chain 'B' and resid 282 through 293 removed outlier: 3.666A pdb=" N TYR B 293 " --> pdb=" O SER B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 319 Processing helix chain 'B' and resid 343 through 362 Processing helix chain 'B' and resid 362 through 369 Processing helix chain 'B' and resid 391 through 406 removed outlier: 3.501A pdb=" N ALA B 395 " --> pdb=" O PRO B 391 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL B 406 " --> pdb=" O LEU B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 419 removed outlier: 3.606A pdb=" N LYS B 413 " --> pdb=" O ASP B 409 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS B 419 " --> pdb=" O THR B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 428 removed outlier: 3.875A pdb=" N MET B 426 " --> pdb=" O LEU B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 469 removed outlier: 4.406A pdb=" N VAL B 459 " --> pdb=" O GLY B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 495 removed outlier: 4.211A pdb=" N GLN B 490 " --> pdb=" O SER B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 505 Processing helix chain 'B' and resid 508 through 520 Processing helix chain 'B' and resid 523 through 528 removed outlier: 3.783A pdb=" N GLY B 528 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 561 removed outlier: 5.731A pdb=" N ASN B 553 " --> pdb=" O GLN B 549 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ARG B 554 " --> pdb=" O ASP B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 573 Processing helix chain 'B' and resid 575 through 596 removed outlier: 3.517A pdb=" N ALA B 580 " --> pdb=" O PRO B 576 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 77 removed outlier: 3.615A pdb=" N PHE A 160 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE A 7 " --> pdb=" O GLU A 202 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 16 removed outlier: 8.425A pdb=" N PHE A 104 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLU A 85 " --> pdb=" O PHE A 104 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ILE A 106 " --> pdb=" O GLU A 85 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU A 87 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 126 through 129 Processing sheet with id=AA4, first strand: chain 'A' and resid 371 through 375 removed outlier: 3.667A pdb=" N ILE A 379 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL A 224 " --> pdb=" O LEU A 467 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 283 through 284 Processing sheet with id=AA6, first strand: chain 'A' and resid 340 through 343 Processing sheet with id=AA7, first strand: chain 'C' and resid 143 through 146 removed outlier: 6.364A pdb=" N THR C 284 " --> pdb=" O LYS C 144 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE C 146 " --> pdb=" O TYR C 282 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N TYR C 282 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU C 151 " --> pdb=" O TYR C 164 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 143 through 146 removed outlier: 6.364A pdb=" N THR C 284 " --> pdb=" O LYS C 144 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE C 146 " --> pdb=" O TYR C 282 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N TYR C 282 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE C 305 " --> pdb=" O ILE C 296 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 76 through 77 Processing sheet with id=AB1, first strand: chain 'C' and resid 173 through 175 Processing sheet with id=AB2, first strand: chain 'C' and resid 192 through 193 Processing sheet with id=AB3, first strand: chain 'C' and resid 355 through 357 Processing sheet with id=AB4, first strand: chain 'C' and resid 360 through 363 Processing sheet with id=AB5, first strand: chain 'D' and resid 40 through 41 removed outlier: 7.409A pdb=" N ALA D 84 " --> pdb=" O MET D 233 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N MET D 233 " --> pdb=" O ALA D 84 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N LEU D 86 " --> pdb=" O TYR D 231 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N TYR D 231 " --> pdb=" O LEU D 86 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 229 through 236 current: chain 'D' and resid 185 through 188 Processing sheet with id=AB6, first strand: chain 'D' and resid 79 through 81 removed outlier: 6.161A pdb=" N TYR D 231 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N LEU D 86 " --> pdb=" O TYR D 231 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N MET D 233 " --> pdb=" O ALA D 84 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ALA D 84 " --> pdb=" O MET D 233 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 84 through 92 current: chain 'D' and resid 274 through 275 Processing sheet with id=AB7, first strand: chain 'D' and resid 156 through 158 removed outlier: 3.806A pdb=" N ALA D 156 " --> pdb=" O ALA D 165 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE D 163 " --> pdb=" O ILE D 158 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 204 through 211 removed outlier: 6.415A pdb=" N GLU D 211 " --> pdb=" O SER D 215 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N SER D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 258 through 259 Processing sheet with id=AC1, first strand: chain 'E' and resid 40 through 41 removed outlier: 6.715A pdb=" N ARG E 229 " --> pdb=" O LEU E 87 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 229 through 236 current: chain 'E' and resid 185 through 188 Processing sheet with id=AC2, first strand: chain 'E' and resid 79 through 81 removed outlier: 6.715A pdb=" N ARG E 229 " --> pdb=" O LEU E 87 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 84 through 92 current: chain 'E' and resid 270 through 275 Processing sheet with id=AC3, first strand: chain 'E' and resid 157 through 158 removed outlier: 3.916A pdb=" N ILE E 163 " --> pdb=" O ILE E 158 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 204 through 211 removed outlier: 6.192A pdb=" N LEU E 205 " --> pdb=" O TYR E 220 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TYR E 220 " --> pdb=" O LEU E 205 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ARG E 207 " --> pdb=" O LEU E 218 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LEU E 218 " --> pdb=" O ARG E 207 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ASN E 209 " --> pdb=" O ALA E 216 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 40 through 41 removed outlier: 6.565A pdb=" N ARG F 229 " --> pdb=" O LEU F 87 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 229 through 235 current: chain 'F' and resid 185 through 188 Processing sheet with id=AC6, first strand: chain 'F' and resid 80 through 81 removed outlier: 6.565A pdb=" N ARG F 229 " --> pdb=" O LEU F 87 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 84 through 92 current: chain 'F' and resid 270 through 275 Processing sheet with id=AC7, first strand: chain 'F' and resid 204 through 211 removed outlier: 6.289A pdb=" N LEU F 205 " --> pdb=" O TYR F 220 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N TYR F 220 " --> pdb=" O LEU F 205 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ARG F 207 " --> pdb=" O LEU F 218 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU F 218 " --> pdb=" O ARG F 207 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ASN F 209 " --> pdb=" O ALA F 216 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 114 through 115 removed outlier: 6.416A pdb=" N THR I 242 " --> pdb=" O ALA I 205 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N VAL I 241 " --> pdb=" O THR I 79 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 198 through 199 Processing sheet with id=AD1, first strand: chain 'I' and resid 213 through 218 Processing sheet with id=AD2, first strand: chain 'I' and resid 258 through 260 removed outlier: 3.820A pdb=" N HIS I 253 " --> pdb=" O CYS I 260 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 321 through 322 removed outlier: 4.261A pdb=" N SER B 378 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N LYS B 434 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TYR B 387 " --> pdb=" O GLN B 440 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 337 through 338 967 hydrogen bonds defined for protein. 2724 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 59 hydrogen bonds 118 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 4.53 Time building geometry restraints manager: 2.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7472 1.34 - 1.46: 5262 1.46 - 1.58: 12110 1.58 - 1.70: 153 1.70 - 1.82: 179 Bond restraints: 25176 Sorted by residual: bond pdb=" CA GLU B 151 " pdb=" C GLU B 151 " ideal model delta sigma weight residual 1.523 1.559 -0.036 1.34e-02 5.57e+03 7.03e+00 bond pdb=" CB PRO I 2 " pdb=" CG PRO I 2 " ideal model delta sigma weight residual 1.492 1.583 -0.091 5.00e-02 4.00e+02 3.28e+00 bond pdb=" CA ILE G 48 " pdb=" CB ILE G 48 " ideal model delta sigma weight residual 1.539 1.531 0.008 5.40e-03 3.43e+04 2.16e+00 bond pdb=" CB LYS C 112 " pdb=" CG LYS C 112 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.13e+00 bond pdb=" CB LYS C 136 " pdb=" CG LYS C 136 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.10e+00 ... (remaining 25171 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.13: 34347 8.13 - 16.25: 14 16.25 - 24.38: 1 24.38 - 32.51: 2 32.51 - 40.63: 2 Bond angle restraints: 34366 Sorted by residual: angle pdb=" OP1 A J 9 " pdb=" P A J 9 " pdb=" OP2 A J 9 " ideal model delta sigma weight residual 119.60 78.97 40.63 3.00e+00 1.11e-01 1.83e+02 angle pdb=" O3' C J 8 " pdb=" P A J 9 " pdb=" OP2 A J 9 " ideal model delta sigma weight residual 108.00 71.38 36.62 3.00e+00 1.11e-01 1.49e+02 angle pdb=" OP1 A J 9 " pdb=" P A J 9 " pdb=" O5' A J 9 " ideal model delta sigma weight residual 108.00 77.96 30.04 3.00e+00 1.11e-01 1.00e+02 angle pdb=" O3' C J 8 " pdb=" P A J 9 " pdb=" OP1 A J 9 " ideal model delta sigma weight residual 108.00 136.08 -28.08 3.00e+00 1.11e-01 8.76e+01 angle pdb=" OP2 A J 9 " pdb=" P A J 9 " pdb=" O5' A J 9 " ideal model delta sigma weight residual 108.00 129.98 -21.98 3.00e+00 1.11e-01 5.37e+01 ... (remaining 34361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.99: 14484 34.99 - 69.98: 843 69.98 - 104.96: 51 104.96 - 139.95: 0 139.95 - 174.94: 1 Dihedral angle restraints: 15379 sinusoidal: 7027 harmonic: 8352 Sorted by residual: dihedral pdb=" CA TYR I 81 " pdb=" C TYR I 81 " pdb=" N PRO I 82 " pdb=" CA PRO I 82 " ideal model delta harmonic sigma weight residual 180.00 126.33 53.67 0 5.00e+00 4.00e-02 1.15e+02 dihedral pdb=" O4' U K 30 " pdb=" C1' U K 30 " pdb=" N1 U K 30 " pdb=" C2 U K 30 " ideal model delta sinusoidal sigma weight residual 232.00 57.06 174.94 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" CA GLN C 105 " pdb=" C GLN C 105 " pdb=" N PHE C 106 " pdb=" CA PHE C 106 " ideal model delta harmonic sigma weight residual 180.00 151.81 28.19 0 5.00e+00 4.00e-02 3.18e+01 ... (remaining 15376 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2915 0.043 - 0.087: 706 0.087 - 0.130: 224 0.130 - 0.174: 16 0.174 - 0.217: 8 Chirality restraints: 3869 Sorted by residual: chirality pdb=" CA PRO I 2 " pdb=" N PRO I 2 " pdb=" C PRO I 2 " pdb=" CB PRO I 2 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CB ILE B 176 " pdb=" CA ILE B 176 " pdb=" CG1 ILE B 176 " pdb=" CG2 ILE B 176 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA MET A 408 " pdb=" N MET A 408 " pdb=" C MET A 408 " pdb=" CB MET A 408 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 3866 not shown) Planarity restraints: 4110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET I 1 " -0.077 5.00e-02 4.00e+02 1.17e-01 2.18e+01 pdb=" N PRO I 2 " 0.202 5.00e-02 4.00e+02 pdb=" CA PRO I 2 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO I 2 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR I 81 " 0.077 5.00e-02 4.00e+02 1.16e-01 2.17e+01 pdb=" N PRO I 82 " -0.202 5.00e-02 4.00e+02 pdb=" CA PRO I 82 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO I 82 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR I 81 " -0.016 2.00e-02 2.50e+03 3.15e-02 9.94e+00 pdb=" C TYR I 81 " 0.055 2.00e-02 2.50e+03 pdb=" O TYR I 81 " -0.020 2.00e-02 2.50e+03 pdb=" N PRO I 82 " -0.018 2.00e-02 2.50e+03 ... (remaining 4107 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 589 2.66 - 3.22: 22914 3.22 - 3.78: 40110 3.78 - 4.34: 55448 4.34 - 4.90: 89432 Nonbonded interactions: 208493 Sorted by model distance: nonbonded pdb=" O LYS B 173 " pdb=" OG1 THR B 177 " model vdw 2.102 3.040 nonbonded pdb=" O3' SAM B 702 " pdb="MN MN B 703 " model vdw 2.109 2.320 nonbonded pdb=" O2A ATP B 701 " pdb="MN MN B 703 " model vdw 2.117 2.320 nonbonded pdb=" OD2 ASP B 279 " pdb="MN MN B 703 " model vdw 2.123 2.320 nonbonded pdb=" N GLU C 259 " pdb=" OE1 GLU C 259 " model vdw 2.157 3.120 ... (remaining 208488 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 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 24.460 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 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 : 0.004 0.091 25176 Z= 0.158 Angle : 0.837 40.635 34366 Z= 0.421 Chirality : 0.042 0.217 3869 Planarity : 0.006 0.117 4110 Dihedral : 19.641 174.939 9989 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.39 % Favored : 92.18 % Rotamer: Outliers : 3.72 % Allowed : 36.52 % Favored : 59.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % 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: -0.41 (0.16), residues: 2800 helix: 0.96 (0.16), residues: 1060 sheet: 0.27 (0.24), residues: 437 loop : -1.54 (0.17), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 70 TYR 0.022 0.001 TYR I 81 PHE 0.029 0.002 PHE B 198 TRP 0.014 0.001 TRP A 157 HIS 0.007 0.001 HIS A 436 Details of bonding type rmsd covalent geometry : bond 0.00357 (25176) covalent geometry : angle 0.83707 (34366) hydrogen bonds : bond 0.15216 ( 1017) hydrogen bonds : angle 6.20416 ( 2842) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 418 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 GLU cc_start: 0.8305 (tm-30) cc_final: 0.7951 (tm-30) REVERT: A 241 TYR cc_start: 0.8670 (t80) cc_final: 0.8418 (t80) REVERT: A 285 TRP cc_start: 0.7091 (OUTLIER) cc_final: 0.6093 (t60) REVERT: D 57 ASN cc_start: 0.8692 (OUTLIER) cc_final: 0.7916 (t0) REVERT: D 152 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8881 (mt) REVERT: D 202 LEU cc_start: 0.8466 (pp) cc_final: 0.8259 (pt) REVERT: E 73 LYS cc_start: 0.9135 (ptpp) cc_final: 0.8716 (ptmt) REVERT: E 100 MET cc_start: 0.8839 (mmt) cc_final: 0.8596 (mmm) REVERT: F 1 MET cc_start: 0.6693 (tpp) cc_final: 0.6246 (tpp) REVERT: F 14 MET cc_start: 0.9170 (OUTLIER) cc_final: 0.8580 (ttp) REVERT: F 108 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.8094 (mm-40) REVERT: F 207 ARG cc_start: 0.9197 (OUTLIER) cc_final: 0.8594 (mtp180) REVERT: G 80 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.6933 (mmt-90) REVERT: G 81 GLN cc_start: 0.8385 (mt0) cc_final: 0.8116 (mt0) REVERT: G 115 LEU cc_start: 0.8975 (mm) cc_final: 0.8765 (mt) REVERT: I 256 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8302 (mptm) REVERT: B 55 ASN cc_start: 0.7940 (p0) cc_final: 0.7722 (p0) REVERT: B 90 GLN cc_start: 0.8763 (mm-40) cc_final: 0.8356 (tp-100) REVERT: B 113 GLN cc_start: 0.8275 (tm-30) cc_final: 0.8010 (tm-30) REVERT: B 116 HIS cc_start: 0.8581 (m-70) cc_final: 0.8363 (m90) REVERT: B 132 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8461 (tm-30) REVERT: B 259 LEU cc_start: 0.8763 (mp) cc_final: 0.8502 (mm) REVERT: B 262 ASN cc_start: 0.8548 (m110) cc_final: 0.8209 (m-40) outliers start: 95 outliers final: 65 residues processed: 488 average time/residue: 0.6664 time to fit residues: 370.9068 Evaluate side-chains 472 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 399 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 GLN Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain A residue 285 TRP Chi-restraints excluded: chain A residue 318 TRP Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 193 CYS Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 248 GLN Chi-restraints excluded: chain C residue 421 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 57 ASN Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 170 HIS Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 245 LYS Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain F residue 14 MET Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 89 MET Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 108 GLN Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 207 ARG Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain G residue 43 ILE Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 80 ARG Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 100 TYR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 193 LEU Chi-restraints excluded: chain I residue 240 ASP Chi-restraints excluded: chain I residue 256 LYS Chi-restraints excluded: chain I residue 273 ASP Chi-restraints excluded: chain I residue 275 SER Chi-restraints excluded: chain I residue 304 THR Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 507 ASP Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 594 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 GLN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 259 GLN G 44 GLN G 59 ASN I 272 ASN ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.060791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2564 r_free = 0.2564 target = 0.047902 restraints weight = 59737.514| |-----------------------------------------------------------------------------| r_work (start): 0.2560 rms_B_bonded: 1.89 r_work: 0.2467 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2363 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.107 25176 Z= 0.284 Angle : 0.862 40.119 34366 Z= 0.432 Chirality : 0.047 0.299 3869 Planarity : 0.006 0.116 4110 Dihedral : 15.036 173.931 4397 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.71 % Favored : 92.00 % Rotamer: Outliers : 7.60 % Allowed : 29.90 % Favored : 62.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.04 % 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: -0.51 (0.16), residues: 2800 helix: 0.88 (0.16), residues: 1074 sheet: 0.39 (0.25), residues: 404 loop : -1.64 (0.17), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 136 TYR 0.023 0.002 TYR A 464 PHE 0.028 0.002 PHE C 106 TRP 0.012 0.002 TRP F 219 HIS 0.006 0.001 HIS I 92 Details of bonding type rmsd covalent geometry : bond 0.00666 (25176) covalent geometry : angle 0.86150 (34366) hydrogen bonds : bond 0.05486 ( 1017) hydrogen bonds : angle 4.98984 ( 2842) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 404 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8000 (tm-30) REVERT: A 285 TRP cc_start: 0.6949 (OUTLIER) cc_final: 0.6088 (t60) REVERT: A 342 GLU cc_start: 0.8044 (mp0) cc_final: 0.7832 (mp0) REVERT: A 420 MET cc_start: 0.8783 (mmt) cc_final: 0.8439 (mmt) REVERT: C 119 MET cc_start: 0.9152 (OUTLIER) cc_final: 0.8459 (mtt) REVERT: D 47 LYS cc_start: 0.9077 (ttpp) cc_final: 0.8746 (ttpt) REVERT: E 73 LYS cc_start: 0.9185 (ptpp) cc_final: 0.8802 (ptmt) REVERT: E 100 MET cc_start: 0.9103 (mmt) cc_final: 0.8789 (mmm) REVERT: F 1 MET cc_start: 0.6965 (tpp) cc_final: 0.6474 (tpp) REVERT: F 108 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.8172 (mm-40) REVERT: G 13 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8742 (tt0) REVERT: G 81 GLN cc_start: 0.8469 (mt0) cc_final: 0.8169 (mt0) REVERT: H 1 MET cc_start: 0.7934 (OUTLIER) cc_final: 0.7034 (tpt) REVERT: H 13 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.7792 (tm-30) REVERT: H 121 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7785 (mm-30) REVERT: I 256 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8518 (mptm) REVERT: I 311 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.8928 (mp) REVERT: B 80 ASP cc_start: 0.8213 (p0) cc_final: 0.7911 (p0) REVERT: B 90 GLN cc_start: 0.8843 (mm-40) cc_final: 0.8449 (tp-100) REVERT: B 119 LYS cc_start: 0.9265 (tppp) cc_final: 0.8938 (tmtt) REVERT: B 128 GLU cc_start: 0.7954 (pp20) cc_final: 0.7584 (pp20) REVERT: B 132 GLU cc_start: 0.8780 (tm-30) cc_final: 0.8499 (tm-30) REVERT: B 176 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.7895 (tp) REVERT: B 200 THR cc_start: 0.9059 (m) cc_final: 0.8740 (p) REVERT: B 214 GLU cc_start: 0.6384 (OUTLIER) cc_final: 0.5795 (pt0) REVERT: B 259 LEU cc_start: 0.8870 (mp) cc_final: 0.8601 (tt) REVERT: B 316 VAL cc_start: 0.8854 (t) cc_final: 0.8573 (m) outliers start: 194 outliers final: 83 residues processed: 549 average time/residue: 0.6795 time to fit residues: 426.9929 Evaluate side-chains 478 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 384 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain A residue 285 TRP Chi-restraints excluded: chain A residue 318 TRP Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 349 TYR Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain A residue 454 TYR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 193 CYS Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 389 LYS Chi-restraints excluded: chain C residue 415 ARG Chi-restraints excluded: chain C residue 421 ILE Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 119 CYS Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 170 HIS Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 235 MET Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 245 LYS Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 108 GLN Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 187 ILE Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 100 TYR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 5 LYS Chi-restraints excluded: chain H residue 13 GLU Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain I residue 114 TYR Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 192 SER Chi-restraints excluded: chain I residue 193 LEU Chi-restraints excluded: chain I residue 256 LYS Chi-restraints excluded: chain I residue 297 CYS Chi-restraints excluded: chain I residue 304 THR Chi-restraints excluded: chain I residue 311 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 420 ASN Chi-restraints excluded: chain B residue 553 ASN Chi-restraints excluded: chain B residue 563 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 10 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 210 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 177 optimal weight: 0.9980 chunk 215 optimal weight: 2.9990 chunk 141 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 GLN A 421 HIS ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 ASN ** D 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 259 GLN ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 GLN B 308 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.062722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.049859 restraints weight = 59416.470| |-----------------------------------------------------------------------------| r_work (start): 0.2612 rms_B_bonded: 1.88 r_work: 0.2521 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2417 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 25176 Z= 0.186 Angle : 0.786 40.312 34366 Z= 0.389 Chirality : 0.044 0.287 3869 Planarity : 0.005 0.114 4110 Dihedral : 14.712 173.944 4328 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.04 % Favored : 92.75 % Rotamer: Outliers : 7.09 % Allowed : 30.21 % Favored : 62.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.16), residues: 2800 helix: 1.03 (0.16), residues: 1078 sheet: 0.24 (0.24), residues: 443 loop : -1.59 (0.17), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 70 TYR 0.017 0.002 TYR B 117 PHE 0.033 0.002 PHE C 106 TRP 0.008 0.001 TRP F 219 HIS 0.007 0.001 HIS A 436 Details of bonding type rmsd covalent geometry : bond 0.00433 (25176) covalent geometry : angle 0.78629 (34366) hydrogen bonds : bond 0.04605 ( 1017) hydrogen bonds : angle 4.76416 ( 2842) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 408 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 GLU cc_start: 0.8366 (tm-30) cc_final: 0.7971 (tm-30) REVERT: A 241 TYR cc_start: 0.8754 (t80) cc_final: 0.8465 (t80) REVERT: A 285 TRP cc_start: 0.6923 (OUTLIER) cc_final: 0.6364 (t60) REVERT: D 47 LYS cc_start: 0.9061 (ttpp) cc_final: 0.8740 (ttpt) REVERT: D 152 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.9019 (mt) REVERT: D 202 LEU cc_start: 0.8542 (pp) cc_final: 0.8331 (pt) REVERT: E 73 LYS cc_start: 0.9163 (ptpp) cc_final: 0.8791 (ptmt) REVERT: E 100 MET cc_start: 0.9048 (mmt) cc_final: 0.8679 (mmm) REVERT: F 1 MET cc_start: 0.6904 (tpp) cc_final: 0.6458 (tpp) REVERT: F 108 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.8123 (mm-40) REVERT: F 178 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8660 (mtpp) REVERT: G 13 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8702 (tt0) REVERT: H 13 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.7804 (tm-30) REVERT: H 58 ASP cc_start: 0.8262 (t0) cc_final: 0.8056 (t0) REVERT: H 87 ASP cc_start: 0.8431 (m-30) cc_final: 0.8211 (m-30) REVERT: I 256 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8420 (mptm) REVERT: B 55 ASN cc_start: 0.8388 (OUTLIER) cc_final: 0.8182 (OUTLIER) REVERT: B 90 GLN cc_start: 0.8834 (mm-40) cc_final: 0.8457 (tp-100) REVERT: B 119 LYS cc_start: 0.9241 (tppp) cc_final: 0.8885 (tmtt) REVERT: B 132 GLU cc_start: 0.8812 (tm-30) cc_final: 0.8500 (tm-30) REVERT: B 176 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8064 (tp) REVERT: B 200 THR cc_start: 0.9053 (m) cc_final: 0.8739 (p) REVERT: B 252 TRP cc_start: 0.5693 (OUTLIER) cc_final: 0.4729 (t-100) REVERT: B 259 LEU cc_start: 0.8886 (mp) cc_final: 0.8668 (tt) REVERT: B 316 VAL cc_start: 0.8686 (t) cc_final: 0.8403 (m) outliers start: 181 outliers final: 92 residues processed: 540 average time/residue: 0.7017 time to fit residues: 432.4119 Evaluate side-chains 495 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 394 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 107 GLN Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain A residue 285 TRP Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 318 TRP Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 349 TYR Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain A residue 454 TYR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 193 CYS Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 415 ARG Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 119 CYS Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 170 HIS Chi-restraints excluded: chain D residue 235 MET Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain F residue 4 ARG Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 108 GLN Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 178 LYS Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain G residue 43 ILE Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 100 TYR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 13 GLU Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 134 LYS Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 192 SER Chi-restraints excluded: chain I residue 228 ASP Chi-restraints excluded: chain I residue 240 ASP Chi-restraints excluded: chain I residue 256 LYS Chi-restraints excluded: chain I residue 275 SER Chi-restraints excluded: chain I residue 297 CYS Chi-restraints excluded: chain I residue 304 THR Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 55 ASN Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 553 ASN Chi-restraints excluded: chain B residue 563 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 145 optimal weight: 0.9990 chunk 232 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 244 optimal weight: 4.9990 chunk 208 optimal weight: 0.4980 chunk 1 optimal weight: 0.5980 chunk 225 optimal weight: 4.9990 chunk 267 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 253 optimal weight: 2.9990 chunk 264 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 212 ASN A 245 GLN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 ASN C 84 GLN C 354 ASN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN B 87 HIS ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.063938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.051059 restraints weight = 59403.594| |-----------------------------------------------------------------------------| r_work (start): 0.2641 rms_B_bonded: 1.89 r_work: 0.2552 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2449 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 25176 Z= 0.154 Angle : 0.763 40.461 34366 Z= 0.374 Chirality : 0.043 0.237 3869 Planarity : 0.005 0.112 4110 Dihedral : 14.520 174.366 4316 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.29 % Favored : 92.54 % Rotamer: Outliers : 6.66 % Allowed : 31.07 % Favored : 62.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.04 % 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: -0.24 (0.16), residues: 2800 helix: 1.20 (0.16), residues: 1072 sheet: 0.32 (0.24), residues: 449 loop : -1.56 (0.17), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 70 TYR 0.023 0.001 TYR B 117 PHE 0.030 0.002 PHE C 106 TRP 0.008 0.001 TRP F 219 HIS 0.006 0.001 HIS A 436 Details of bonding type rmsd covalent geometry : bond 0.00357 (25176) covalent geometry : angle 0.76278 (34366) hydrogen bonds : bond 0.04197 ( 1017) hydrogen bonds : angle 4.60519 ( 2842) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 415 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8765 (mtpt) REVERT: A 141 GLU cc_start: 0.8325 (tm-30) cc_final: 0.7785 (tm-30) REVERT: A 143 LYS cc_start: 0.9081 (mmpt) cc_final: 0.8837 (mmpt) REVERT: A 241 TYR cc_start: 0.8760 (t80) cc_final: 0.8509 (t80) REVERT: A 285 TRP cc_start: 0.6807 (OUTLIER) cc_final: 0.6404 (t60) REVERT: A 328 TYR cc_start: 0.8537 (m-80) cc_final: 0.8177 (m-80) REVERT: A 452 MET cc_start: 0.5682 (OUTLIER) cc_final: 0.4923 (ppp) REVERT: C 68 ASP cc_start: 0.7494 (OUTLIER) cc_final: 0.7196 (m-30) REVERT: D 47 LYS cc_start: 0.9035 (ttpp) cc_final: 0.8718 (ttpt) REVERT: D 152 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8977 (mt) REVERT: D 249 ASP cc_start: 0.8603 (m-30) cc_final: 0.8360 (m-30) REVERT: E 73 LYS cc_start: 0.9152 (ptpp) cc_final: 0.8704 (ptmt) REVERT: E 100 MET cc_start: 0.9041 (mmt) cc_final: 0.8715 (mmm) REVERT: F 1 MET cc_start: 0.6912 (tpp) cc_final: 0.6472 (tpp) REVERT: F 108 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.8110 (mm-40) REVERT: F 178 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8671 (mtpp) REVERT: G 13 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8653 (tt0) REVERT: H 13 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.7711 (tm-30) REVERT: H 58 ASP cc_start: 0.8240 (t0) cc_final: 0.8031 (t0) REVERT: H 87 ASP cc_start: 0.8413 (m-30) cc_final: 0.8169 (m-30) REVERT: I 256 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8472 (mptm) REVERT: I 311 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8825 (mp) REVERT: B 94 GLU cc_start: 0.8459 (mt-10) cc_final: 0.7824 (mt-10) REVERT: B 119 LYS cc_start: 0.9222 (tppp) cc_final: 0.8940 (tmtt) REVERT: B 132 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8484 (tm-30) REVERT: B 176 ILE cc_start: 0.8542 (OUTLIER) cc_final: 0.8077 (tp) REVERT: B 200 THR cc_start: 0.9025 (m) cc_final: 0.8708 (p) REVERT: B 259 LEU cc_start: 0.8908 (mp) cc_final: 0.8672 (tt) REVERT: B 316 VAL cc_start: 0.8602 (t) cc_final: 0.8391 (m) REVERT: B 394 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8195 (mt-10) REVERT: B 504 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.8499 (mt0) outliers start: 170 outliers final: 84 residues processed: 539 average time/residue: 0.6319 time to fit residues: 391.2934 Evaluate side-chains 495 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 397 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 107 GLN Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain A residue 285 TRP Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 318 TRP Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 454 TYR Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 248 GLN Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 415 ARG Chi-restraints excluded: chain C residue 421 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 119 CYS Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 170 HIS Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 235 MET Chi-restraints excluded: chain D residue 245 LYS Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain F residue 4 ARG Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 108 GLN Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 178 LYS Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain G residue 43 ILE Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 100 TYR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 13 GLU Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 165 GLU Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 192 SER Chi-restraints excluded: chain I residue 193 LEU Chi-restraints excluded: chain I residue 240 ASP Chi-restraints excluded: chain I residue 256 LYS Chi-restraints excluded: chain I residue 275 SER Chi-restraints excluded: chain I residue 304 THR Chi-restraints excluded: chain I residue 311 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 55 ASN Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 394 GLU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 504 GLN Chi-restraints excluded: chain B residue 553 ASN Chi-restraints excluded: chain B residue 563 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 222 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 234 optimal weight: 5.9990 chunk 12 optimal weight: 0.0770 chunk 193 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 248 optimal weight: 7.9990 chunk 121 optimal weight: 0.8980 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 GLN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 ASN C 367 GLN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 GLN B 113 GLN B 167 GLN B 504 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.062918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.050031 restraints weight = 58775.318| |-----------------------------------------------------------------------------| r_work (start): 0.2613 rms_B_bonded: 1.89 r_work: 0.2523 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2420 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 25176 Z= 0.196 Angle : 0.794 40.349 34366 Z= 0.391 Chirality : 0.044 0.250 3869 Planarity : 0.005 0.111 4110 Dihedral : 14.464 174.091 4310 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.68 % Favored : 92.14 % Rotamer: Outliers : 6.62 % Allowed : 31.94 % Favored : 61.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.04 % 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: -0.25 (0.16), residues: 2800 helix: 1.16 (0.16), residues: 1073 sheet: 0.29 (0.24), residues: 457 loop : -1.53 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 70 TYR 0.022 0.002 TYR B 72 PHE 0.026 0.002 PHE C 106 TRP 0.009 0.001 TRP F 219 HIS 0.005 0.001 HIS A 436 Details of bonding type rmsd covalent geometry : bond 0.00461 (25176) covalent geometry : angle 0.79351 (34366) hydrogen bonds : bond 0.04490 ( 1017) hydrogen bonds : angle 4.62532 ( 2842) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 409 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LYS cc_start: 0.9234 (OUTLIER) cc_final: 0.8785 (mtpt) REVERT: A 141 GLU cc_start: 0.8326 (tm-30) cc_final: 0.7750 (tm-30) REVERT: A 143 LYS cc_start: 0.9037 (mmpt) cc_final: 0.8772 (mmpt) REVERT: A 241 TYR cc_start: 0.8756 (t80) cc_final: 0.8539 (t80) REVERT: A 245 GLN cc_start: 0.8368 (mm-40) cc_final: 0.8167 (mm110) REVERT: A 285 TRP cc_start: 0.6713 (OUTLIER) cc_final: 0.6422 (t60) REVERT: C 68 ASP cc_start: 0.7545 (OUTLIER) cc_final: 0.7316 (m-30) REVERT: D 47 LYS cc_start: 0.9043 (ttpp) cc_final: 0.8745 (ttpt) REVERT: D 152 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8987 (mt) REVERT: E 73 LYS cc_start: 0.9147 (ptpp) cc_final: 0.8720 (ptmt) REVERT: E 100 MET cc_start: 0.9064 (mmt) cc_final: 0.8725 (mmm) REVERT: F 1 MET cc_start: 0.6944 (tpp) cc_final: 0.6547 (tpp) REVERT: F 14 MET cc_start: 0.9179 (OUTLIER) cc_final: 0.8877 (ttp) REVERT: F 108 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8141 (mm-40) REVERT: F 178 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8655 (mtpp) REVERT: G 13 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8692 (tt0) REVERT: H 13 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.7787 (tm-30) REVERT: H 87 ASP cc_start: 0.8363 (m-30) cc_final: 0.8139 (m-30) REVERT: I 23 ARG cc_start: 0.9062 (ptp90) cc_final: 0.8785 (ptp90) REVERT: I 256 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8464 (mptm) REVERT: I 311 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.8839 (mp) REVERT: B 83 LEU cc_start: 0.9040 (tm) cc_final: 0.8775 (tp) REVERT: B 90 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8354 (tp-100) REVERT: B 132 GLU cc_start: 0.8750 (tm-30) cc_final: 0.8411 (tm-30) REVERT: B 167 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.8091 (pm20) REVERT: B 176 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8089 (tp) REVERT: B 200 THR cc_start: 0.9037 (m) cc_final: 0.8720 (p) REVERT: B 263 LYS cc_start: 0.9030 (tppt) cc_final: 0.8616 (mmpt) REVERT: B 316 VAL cc_start: 0.8636 (t) cc_final: 0.8431 (m) REVERT: B 387 TYR cc_start: 0.7554 (OUTLIER) cc_final: 0.7281 (t80) REVERT: B 420 ASN cc_start: 0.9073 (OUTLIER) cc_final: 0.8835 (t0) REVERT: B 466 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8112 (tp40) REVERT: B 504 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8763 (mt0) outliers start: 169 outliers final: 93 residues processed: 524 average time/residue: 0.6796 time to fit residues: 407.8382 Evaluate side-chains 498 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 387 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 107 GLN Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain A residue 285 TRP Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 318 TRP Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 454 TYR Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 193 CYS Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 248 GLN Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 415 ARG Chi-restraints excluded: chain C residue 421 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 119 CYS Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 170 HIS Chi-restraints excluded: chain D residue 235 MET Chi-restraints excluded: chain D residue 245 LYS Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 245 LYS Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain F residue 4 ARG Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 14 MET Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 108 GLN Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 178 LYS Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain G residue 43 ILE Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 100 TYR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 13 GLU Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 61 SER Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 192 SER Chi-restraints excluded: chain I residue 193 LEU Chi-restraints excluded: chain I residue 240 ASP Chi-restraints excluded: chain I residue 256 LYS Chi-restraints excluded: chain I residue 275 SER Chi-restraints excluded: chain I residue 297 CYS Chi-restraints excluded: chain I residue 304 THR Chi-restraints excluded: chain I residue 311 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 387 TYR Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 420 ASN Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain B residue 504 GLN Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 553 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 210 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 204 optimal weight: 0.7980 chunk 243 optimal weight: 0.3980 chunk 283 optimal weight: 0.6980 chunk 257 optimal weight: 0.5980 chunk 233 optimal weight: 0.0570 chunk 49 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 279 optimal weight: 1.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 ASN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 GLN ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 HIS ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN B 504 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.064987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.052005 restraints weight = 58725.532| |-----------------------------------------------------------------------------| r_work (start): 0.2668 rms_B_bonded: 1.90 r_work: 0.2578 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2475 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 25176 Z= 0.140 Angle : 0.771 40.631 34366 Z= 0.375 Chirality : 0.043 0.227 3869 Planarity : 0.005 0.119 4110 Dihedral : 14.386 174.506 4308 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.21 % Favored : 92.61 % Rotamer: Outliers : 6.07 % Allowed : 32.68 % Favored : 61.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % 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: -0.14 (0.16), residues: 2800 helix: 1.30 (0.16), residues: 1070 sheet: 0.25 (0.23), residues: 467 loop : -1.49 (0.17), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 136 TYR 0.024 0.001 TYR B 117 PHE 0.027 0.002 PHE B 198 TRP 0.007 0.001 TRP F 219 HIS 0.005 0.001 HIS A 436 Details of bonding type rmsd covalent geometry : bond 0.00325 (25176) covalent geometry : angle 0.77087 (34366) hydrogen bonds : bond 0.03964 ( 1017) hydrogen bonds : angle 4.51808 ( 2842) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 408 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8778 (mtpt) REVERT: A 129 LYS cc_start: 0.8932 (ttmm) cc_final: 0.8608 (mtpp) REVERT: A 138 LYS cc_start: 0.8880 (mmmm) cc_final: 0.8655 (mmmt) REVERT: A 141 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7711 (tm-30) REVERT: A 142 PHE cc_start: 0.9016 (t80) cc_final: 0.8799 (t80) REVERT: A 241 TYR cc_start: 0.8747 (t80) cc_final: 0.8504 (t80) REVERT: A 245 GLN cc_start: 0.8412 (mm-40) cc_final: 0.8185 (mm110) REVERT: A 452 MET cc_start: 0.5592 (OUTLIER) cc_final: 0.4890 (ppp) REVERT: C 68 ASP cc_start: 0.7388 (OUTLIER) cc_final: 0.7138 (m-30) REVERT: C 111 ASN cc_start: 0.8467 (m-40) cc_final: 0.8146 (p0) REVERT: C 187 PHE cc_start: 0.7968 (m-10) cc_final: 0.7700 (m-80) REVERT: D 47 LYS cc_start: 0.9032 (ttpp) cc_final: 0.8737 (ttpt) REVERT: D 152 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8939 (mt) REVERT: E 73 LYS cc_start: 0.9146 (ptpp) cc_final: 0.8840 (ptmt) REVERT: E 100 MET cc_start: 0.9014 (mmt) cc_final: 0.8639 (mmm) REVERT: F 1 MET cc_start: 0.6816 (tpp) cc_final: 0.6461 (tpp) REVERT: F 108 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.8112 (mm-40) REVERT: F 178 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8660 (mtpp) REVERT: G 13 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8624 (tt0) REVERT: H 13 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.7739 (tm-30) REVERT: H 57 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8502 (mt-10) REVERT: H 87 ASP cc_start: 0.8388 (m-30) cc_final: 0.8181 (m-30) REVERT: H 100 TYR cc_start: 0.8488 (OUTLIER) cc_final: 0.8086 (t80) REVERT: I 187 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8393 (ptmm) REVERT: I 256 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8466 (mptm) REVERT: I 311 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8817 (mp) REVERT: B 22 LYS cc_start: 0.8448 (mptt) cc_final: 0.8219 (mttt) REVERT: B 83 LEU cc_start: 0.9022 (tm) cc_final: 0.8789 (tp) REVERT: B 90 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8158 (tp-100) REVERT: B 132 GLU cc_start: 0.8772 (tm-30) cc_final: 0.8403 (tm-30) REVERT: B 176 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8214 (tt) REVERT: B 200 THR cc_start: 0.8972 (m) cc_final: 0.8657 (p) REVERT: B 466 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8082 (tp40) REVERT: B 504 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.8679 (mt0) outliers start: 155 outliers final: 79 residues processed: 514 average time/residue: 0.6724 time to fit residues: 394.3739 Evaluate side-chains 492 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 396 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 107 GLN Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 318 TRP Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 454 TYR Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 193 CYS Chi-restraints excluded: chain C residue 248 GLN Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 415 ARG Chi-restraints excluded: chain C residue 421 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 119 CYS Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 170 HIS Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 235 MET Chi-restraints excluded: chain D residue 245 LYS Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain F residue 4 ARG Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 108 GLN Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 178 LYS Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain G residue 43 ILE Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 100 TYR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 13 GLU Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 165 GLU Chi-restraints excluded: chain I residue 187 LYS Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 192 SER Chi-restraints excluded: chain I residue 193 LEU Chi-restraints excluded: chain I residue 240 ASP Chi-restraints excluded: chain I residue 256 LYS Chi-restraints excluded: chain I residue 275 SER Chi-restraints excluded: chain I residue 297 CYS Chi-restraints excluded: chain I residue 311 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain B residue 504 GLN Chi-restraints excluded: chain B residue 563 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 121 optimal weight: 0.6980 chunk 161 optimal weight: 1.9990 chunk 261 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 chunk 27 optimal weight: 0.9990 chunk 239 optimal weight: 0.8980 chunk 195 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 436 HIS ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 GLN G 95 GLN G 104 GLN ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.064304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.051289 restraints weight = 58679.650| |-----------------------------------------------------------------------------| r_work (start): 0.2649 rms_B_bonded: 1.90 r_work: 0.2559 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2456 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 25176 Z= 0.166 Angle : 0.796 40.473 34366 Z= 0.389 Chirality : 0.043 0.239 3869 Planarity : 0.005 0.107 4110 Dihedral : 14.278 174.703 4300 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.36 % Favored : 92.46 % Rotamer: Outliers : 5.76 % Allowed : 33.54 % Favored : 60.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % 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 (0.16), residues: 2800 helix: 1.29 (0.16), residues: 1072 sheet: 0.29 (0.23), residues: 475 loop : -1.47 (0.17), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 136 TYR 0.024 0.002 TYR B 72 PHE 0.024 0.002 PHE C 106 TRP 0.011 0.001 TRP A 285 HIS 0.004 0.001 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00392 (25176) covalent geometry : angle 0.79629 (34366) hydrogen bonds : bond 0.04163 ( 1017) hydrogen bonds : angle 4.52968 ( 2842) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 406 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LYS cc_start: 0.9215 (OUTLIER) cc_final: 0.8781 (mtpt) REVERT: A 129 LYS cc_start: 0.8929 (ttmm) cc_final: 0.8114 (mtpp) REVERT: A 139 GLU cc_start: 0.8727 (tt0) cc_final: 0.8051 (pt0) REVERT: A 141 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7916 (tm-30) REVERT: A 279 LYS cc_start: 0.8964 (ttmt) cc_final: 0.8750 (ptpp) REVERT: A 452 MET cc_start: 0.5739 (OUTLIER) cc_final: 0.4906 (ppp) REVERT: A 454 TYR cc_start: 0.7574 (OUTLIER) cc_final: 0.6909 (m-80) REVERT: A 463 ASN cc_start: 0.8509 (OUTLIER) cc_final: 0.8168 (p0) REVERT: C 68 ASP cc_start: 0.7418 (OUTLIER) cc_final: 0.7135 (m-30) REVERT: C 111 ASN cc_start: 0.8378 (m-40) cc_final: 0.8105 (p0) REVERT: C 187 PHE cc_start: 0.7986 (m-10) cc_final: 0.7761 (m-80) REVERT: D 47 LYS cc_start: 0.9034 (ttpp) cc_final: 0.8736 (ttpt) REVERT: E 73 LYS cc_start: 0.9125 (ptpp) cc_final: 0.8824 (ptmt) REVERT: E 100 MET cc_start: 0.9071 (mmt) cc_final: 0.8794 (mmm) REVERT: F 1 MET cc_start: 0.6896 (tpp) cc_final: 0.6518 (tpp) REVERT: F 108 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.8125 (mm-40) REVERT: F 178 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8635 (mtpp) REVERT: G 13 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8630 (tt0) REVERT: H 13 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.7771 (tm-30) REVERT: H 57 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8497 (mt-10) REVERT: H 87 ASP cc_start: 0.8384 (m-30) cc_final: 0.8168 (m-30) REVERT: H 100 TYR cc_start: 0.8500 (OUTLIER) cc_final: 0.8107 (t80) REVERT: I 256 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8476 (mptm) REVERT: I 311 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8825 (mp) REVERT: B 22 LYS cc_start: 0.8412 (mptt) cc_final: 0.8180 (mttt) REVERT: B 83 LEU cc_start: 0.9041 (tm) cc_final: 0.8558 (tp) REVERT: B 90 GLN cc_start: 0.8649 (tp-100) cc_final: 0.8295 (tp-100) REVERT: B 94 GLU cc_start: 0.8291 (mp0) cc_final: 0.8075 (mp0) REVERT: B 132 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8379 (tm-30) REVERT: B 176 ILE cc_start: 0.8513 (OUTLIER) cc_final: 0.8312 (tt) REVERT: B 200 THR cc_start: 0.8979 (m) cc_final: 0.8666 (p) REVERT: B 394 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8240 (mt-10) REVERT: B 466 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8078 (tp40) REVERT: B 504 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8598 (mt0) outliers start: 147 outliers final: 84 residues processed: 510 average time/residue: 0.7098 time to fit residues: 412.9777 Evaluate side-chains 492 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 390 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 107 GLN Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 318 TRP Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 454 TYR Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 193 CYS Chi-restraints excluded: chain C residue 246 LYS Chi-restraints excluded: chain C residue 248 GLN Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 415 ARG Chi-restraints excluded: chain C residue 421 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 119 CYS Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 170 HIS Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 245 LYS Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain F residue 4 ARG Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 108 GLN Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 178 LYS Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain G residue 43 ILE Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 100 TYR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 13 GLU Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 134 LYS Chi-restraints excluded: chain I residue 61 SER Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 192 SER Chi-restraints excluded: chain I residue 193 LEU Chi-restraints excluded: chain I residue 240 ASP Chi-restraints excluded: chain I residue 256 LYS Chi-restraints excluded: chain I residue 275 SER Chi-restraints excluded: chain I residue 297 CYS Chi-restraints excluded: chain I residue 304 THR Chi-restraints excluded: chain I residue 311 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 394 GLU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain B residue 504 GLN Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 553 ASN Chi-restraints excluded: chain B residue 563 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 178 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 chunk 166 optimal weight: 0.9990 chunk 281 optimal weight: 3.9990 chunk 69 optimal weight: 0.0770 chunk 195 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 229 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 GLN ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.063873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.050842 restraints weight = 58502.060| |-----------------------------------------------------------------------------| r_work (start): 0.2638 rms_B_bonded: 1.90 r_work: 0.2548 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2447 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 25176 Z= 0.181 Angle : 0.818 40.460 34366 Z= 0.401 Chirality : 0.044 0.244 3869 Planarity : 0.005 0.127 4110 Dihedral : 14.279 174.102 4299 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.54 % Favored : 92.32 % Rotamer: Outliers : 5.33 % Allowed : 34.29 % Favored : 60.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % 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: -0.17 (0.16), residues: 2800 helix: 1.22 (0.16), residues: 1074 sheet: 0.35 (0.24), residues: 457 loop : -1.50 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 70 TYR 0.023 0.002 TYR B 72 PHE 0.034 0.002 PHE B 198 TRP 0.009 0.001 TRP A 285 HIS 0.006 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00427 (25176) covalent geometry : angle 0.81753 (34366) hydrogen bonds : bond 0.04290 ( 1017) hydrogen bonds : angle 4.57549 ( 2842) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 401 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LYS cc_start: 0.9218 (OUTLIER) cc_final: 0.8778 (mtpt) REVERT: A 129 LYS cc_start: 0.8877 (ttmm) cc_final: 0.7980 (mtpp) REVERT: A 136 ARG cc_start: 0.8221 (mtm110) cc_final: 0.7987 (mtm110) REVERT: A 139 GLU cc_start: 0.8722 (tt0) cc_final: 0.8036 (pt0) REVERT: A 141 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7892 (tm-30) REVERT: A 241 TYR cc_start: 0.8715 (t80) cc_final: 0.8422 (t80) REVERT: A 279 LYS cc_start: 0.8960 (ttmt) cc_final: 0.8751 (ptpp) REVERT: A 452 MET cc_start: 0.5802 (OUTLIER) cc_final: 0.4915 (ppp) REVERT: A 454 TYR cc_start: 0.7589 (OUTLIER) cc_final: 0.6995 (m-80) REVERT: C 68 ASP cc_start: 0.7419 (OUTLIER) cc_final: 0.7175 (m-30) REVERT: C 111 ASN cc_start: 0.8426 (m-40) cc_final: 0.8117 (p0) REVERT: C 187 PHE cc_start: 0.8029 (m-10) cc_final: 0.7780 (m-80) REVERT: D 14 MET cc_start: 0.9177 (mtm) cc_final: 0.8944 (ttp) REVERT: D 47 LYS cc_start: 0.9040 (ttpp) cc_final: 0.8740 (ttpt) REVERT: E 73 LYS cc_start: 0.9148 (ptpp) cc_final: 0.8835 (ptmt) REVERT: E 100 MET cc_start: 0.9102 (mmt) cc_final: 0.8793 (mmm) REVERT: E 273 ILE cc_start: 0.9400 (OUTLIER) cc_final: 0.8984 (mm) REVERT: F 1 MET cc_start: 0.6827 (tpp) cc_final: 0.6472 (tpp) REVERT: F 108 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8133 (mm-40) REVERT: F 178 LYS cc_start: 0.9133 (OUTLIER) cc_final: 0.8640 (mtpp) REVERT: G 13 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8637 (tt0) REVERT: H 13 GLU cc_start: 0.9010 (OUTLIER) cc_final: 0.7783 (tm-30) REVERT: H 87 ASP cc_start: 0.8373 (m-30) cc_final: 0.8139 (m-30) REVERT: H 100 TYR cc_start: 0.8499 (OUTLIER) cc_final: 0.8088 (t80) REVERT: I 256 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8448 (mptm) REVERT: I 311 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8832 (mp) REVERT: B 22 LYS cc_start: 0.8446 (mptt) cc_final: 0.8224 (mttt) REVERT: B 90 GLN cc_start: 0.8653 (tp-100) cc_final: 0.8190 (tp-100) REVERT: B 94 GLU cc_start: 0.8279 (mp0) cc_final: 0.7862 (mp0) REVERT: B 123 LYS cc_start: 0.7337 (pptt) cc_final: 0.6774 (pptt) REVERT: B 132 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8391 (tm-30) REVERT: B 176 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8281 (tt) REVERT: B 200 THR cc_start: 0.8945 (m) cc_final: 0.8628 (p) REVERT: B 263 LYS cc_start: 0.8977 (tppt) cc_final: 0.8549 (mmpt) REVERT: B 316 VAL cc_start: 0.8622 (t) cc_final: 0.8379 (m) REVERT: B 394 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8223 (mt-10) REVERT: B 420 ASN cc_start: 0.9101 (OUTLIER) cc_final: 0.8874 (t0) REVERT: B 466 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8109 (tp40) outliers start: 136 outliers final: 92 residues processed: 501 average time/residue: 0.6754 time to fit residues: 386.1605 Evaluate side-chains 505 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 397 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 107 GLN Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 318 TRP Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 454 TYR Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 193 CYS Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 415 ARG Chi-restraints excluded: chain C residue 421 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 119 CYS Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 170 HIS Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 245 LYS Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 245 LYS Chi-restraints excluded: chain E residue 273 ILE Chi-restraints excluded: chain F residue 4 ARG Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 108 GLN Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 178 LYS Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain G residue 43 ILE Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 100 TYR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 5 LYS Chi-restraints excluded: chain H residue 13 GLU Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 61 SER Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 192 SER Chi-restraints excluded: chain I residue 193 LEU Chi-restraints excluded: chain I residue 240 ASP Chi-restraints excluded: chain I residue 256 LYS Chi-restraints excluded: chain I residue 275 SER Chi-restraints excluded: chain I residue 297 CYS Chi-restraints excluded: chain I residue 304 THR Chi-restraints excluded: chain I residue 311 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 394 GLU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 420 ASN Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 553 ASN Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 563 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 110 optimal weight: 0.0470 chunk 90 optimal weight: 3.9990 chunk 34 optimal weight: 0.0870 chunk 197 optimal weight: 0.6980 chunk 196 optimal weight: 0.9980 chunk 246 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 239 optimal weight: 3.9990 overall best weight: 0.5656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 GLN A 405 ASN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 GLN G 104 GLN ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.065317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.052315 restraints weight = 58425.296| |-----------------------------------------------------------------------------| r_work (start): 0.2678 rms_B_bonded: 1.88 r_work: 0.2590 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2488 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 25176 Z= 0.149 Angle : 0.806 40.632 34366 Z= 0.393 Chirality : 0.043 0.227 3869 Planarity : 0.005 0.104 4110 Dihedral : 14.234 174.598 4299 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.54 % Favored : 92.32 % Rotamer: Outliers : 4.47 % Allowed : 34.95 % Favored : 60.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % 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: -0.12 (0.16), residues: 2800 helix: 1.28 (0.16), residues: 1073 sheet: 0.24 (0.23), residues: 474 loop : -1.45 (0.18), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 70 TYR 0.024 0.001 TYR B 117 PHE 0.027 0.002 PHE B 198 TRP 0.006 0.001 TRP F 219 HIS 0.004 0.001 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00350 (25176) covalent geometry : angle 0.80633 (34366) hydrogen bonds : bond 0.03975 ( 1017) hydrogen bonds : angle 4.51774 ( 2842) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 404 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LYS cc_start: 0.9211 (OUTLIER) cc_final: 0.8780 (mtpt) REVERT: A 129 LYS cc_start: 0.8876 (ttmm) cc_final: 0.8143 (mtpp) REVERT: A 139 GLU cc_start: 0.8750 (tt0) cc_final: 0.8065 (pt0) REVERT: A 141 GLU cc_start: 0.8266 (tm-30) cc_final: 0.7684 (tm-30) REVERT: A 225 TYR cc_start: 0.8041 (m-10) cc_final: 0.7710 (m-10) REVERT: A 452 MET cc_start: 0.5749 (OUTLIER) cc_final: 0.4961 (ppp) REVERT: A 454 TYR cc_start: 0.7529 (OUTLIER) cc_final: 0.6885 (m-80) REVERT: C 68 ASP cc_start: 0.7321 (OUTLIER) cc_final: 0.7048 (m-30) REVERT: C 111 ASN cc_start: 0.8425 (m-40) cc_final: 0.8137 (p0) REVERT: C 185 LYS cc_start: 0.8316 (mmtt) cc_final: 0.7989 (mmtt) REVERT: D 14 MET cc_start: 0.9175 (mtm) cc_final: 0.8967 (ttp) REVERT: D 47 LYS cc_start: 0.9012 (ttpp) cc_final: 0.8713 (ttpt) REVERT: D 218 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8525 (tp) REVERT: E 73 LYS cc_start: 0.9127 (ptpp) cc_final: 0.8902 (ptmt) REVERT: E 100 MET cc_start: 0.9039 (mmt) cc_final: 0.8764 (mmm) REVERT: F 1 MET cc_start: 0.6835 (tpp) cc_final: 0.6487 (tpp) REVERT: F 108 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.8091 (mm-40) REVERT: F 178 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8629 (mtpp) REVERT: G 13 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8612 (tt0) REVERT: H 13 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.7734 (tm-30) REVERT: H 100 TYR cc_start: 0.8483 (OUTLIER) cc_final: 0.8161 (t80) REVERT: I 23 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.7675 (ptp90) REVERT: I 256 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8461 (mptm) REVERT: I 311 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8827 (mp) REVERT: B 22 LYS cc_start: 0.8486 (mptt) cc_final: 0.8259 (mttt) REVERT: B 90 GLN cc_start: 0.8665 (tp-100) cc_final: 0.8295 (tp-100) REVERT: B 123 LYS cc_start: 0.7208 (pptt) cc_final: 0.6798 (pptt) REVERT: B 128 GLU cc_start: 0.7707 (pp20) cc_final: 0.7262 (pp20) REVERT: B 132 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8340 (tm-30) REVERT: B 200 THR cc_start: 0.8901 (m) cc_final: 0.8576 (p) REVERT: B 263 LYS cc_start: 0.8969 (tppt) cc_final: 0.8571 (mmpt) REVERT: B 420 ASN cc_start: 0.9086 (OUTLIER) cc_final: 0.8849 (t0) REVERT: B 466 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8076 (tp40) outliers start: 114 outliers final: 79 residues processed: 486 average time/residue: 0.7184 time to fit residues: 398.3487 Evaluate side-chains 478 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 384 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 107 GLN Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 318 TRP Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 454 TYR Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 193 CYS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 415 ARG Chi-restraints excluded: chain C residue 421 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 119 CYS Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 170 HIS Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain F residue 4 ARG Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 108 GLN Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 178 LYS Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain G residue 43 ILE Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 100 TYR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 13 GLU Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 134 LYS Chi-restraints excluded: chain I residue 23 ARG Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 192 SER Chi-restraints excluded: chain I residue 193 LEU Chi-restraints excluded: chain I residue 240 ASP Chi-restraints excluded: chain I residue 256 LYS Chi-restraints excluded: chain I residue 275 SER Chi-restraints excluded: chain I residue 297 CYS Chi-restraints excluded: chain I residue 304 THR Chi-restraints excluded: chain I residue 311 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 117 TYR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 420 ASN Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 553 ASN Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 563 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 156 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 254 optimal weight: 4.9990 chunk 237 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 192 optimal weight: 0.0970 chunk 142 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 246 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 GLN A 405 ASN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 259 GLN G 44 GLN G 104 GLN ** B 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.063429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.050439 restraints weight = 58798.575| |-----------------------------------------------------------------------------| r_work (start): 0.2627 rms_B_bonded: 1.90 r_work: 0.2537 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2433 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 25176 Z= 0.205 Angle : 0.851 40.395 34366 Z= 0.418 Chirality : 0.045 0.253 3869 Planarity : 0.006 0.135 4110 Dihedral : 14.262 173.865 4299 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.68 % Favored : 92.18 % Rotamer: Outliers : 4.35 % Allowed : 35.15 % Favored : 60.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % 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 (0.16), residues: 2800 helix: 1.16 (0.16), residues: 1071 sheet: 0.31 (0.24), residues: 459 loop : -1.49 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 70 TYR 0.025 0.002 TYR B 33 PHE 0.038 0.002 PHE B 198 TRP 0.012 0.002 TRP A 285 HIS 0.029 0.001 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00487 (25176) covalent geometry : angle 0.85120 (34366) hydrogen bonds : bond 0.04455 ( 1017) hydrogen bonds : angle 4.62956 ( 2842) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 393 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.8781 (mtpt) REVERT: A 129 LYS cc_start: 0.8884 (ttmm) cc_final: 0.8201 (mtpp) REVERT: A 139 GLU cc_start: 0.8718 (tt0) cc_final: 0.8074 (pt0) REVERT: A 141 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7785 (tm-30) REVERT: A 454 TYR cc_start: 0.7611 (OUTLIER) cc_final: 0.7060 (m-80) REVERT: C 68 ASP cc_start: 0.7407 (OUTLIER) cc_final: 0.7161 (m-30) REVERT: C 111 ASN cc_start: 0.8500 (m-40) cc_final: 0.8181 (p0) REVERT: C 185 LYS cc_start: 0.8386 (mmtt) cc_final: 0.8047 (mmtt) REVERT: D 14 MET cc_start: 0.9164 (mtm) cc_final: 0.8938 (ttp) REVERT: D 47 LYS cc_start: 0.9039 (ttpp) cc_final: 0.8741 (ttpt) REVERT: D 211 GLU cc_start: 0.8213 (tt0) cc_final: 0.7908 (tt0) REVERT: D 218 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8543 (tp) REVERT: E 73 LYS cc_start: 0.9129 (ptpp) cc_final: 0.8814 (ptmt) REVERT: E 100 MET cc_start: 0.9094 (mmt) cc_final: 0.8810 (mmm) REVERT: E 273 ILE cc_start: 0.9403 (OUTLIER) cc_final: 0.8993 (mm) REVERT: F 1 MET cc_start: 0.6981 (tpp) cc_final: 0.6591 (tpp) REVERT: F 108 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.8122 (mm-40) REVERT: F 178 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8619 (mtpp) REVERT: G 13 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8673 (tt0) REVERT: H 13 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.7761 (tm-30) REVERT: H 87 ASP cc_start: 0.8342 (m-30) cc_final: 0.8088 (m-30) REVERT: H 100 TYR cc_start: 0.8488 (OUTLIER) cc_final: 0.8064 (t80) REVERT: I 256 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8455 (mptm) REVERT: I 311 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8820 (mp) REVERT: B 90 GLN cc_start: 0.8680 (tp-100) cc_final: 0.8184 (tp-100) REVERT: B 94 GLU cc_start: 0.8309 (mp0) cc_final: 0.7796 (mp0) REVERT: B 123 LYS cc_start: 0.7208 (pptt) cc_final: 0.6805 (pptt) REVERT: B 128 GLU cc_start: 0.7893 (pp20) cc_final: 0.7424 (pp20) REVERT: B 132 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8331 (tm-30) REVERT: B 263 LYS cc_start: 0.8954 (tppt) cc_final: 0.8585 (mmpt) REVERT: B 466 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.8102 (tp40) outliers start: 111 outliers final: 84 residues processed: 477 average time/residue: 0.6824 time to fit residues: 372.1203 Evaluate side-chains 480 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 383 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 107 GLN Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 318 TRP Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 454 TYR Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 193 CYS Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 415 ARG Chi-restraints excluded: chain C residue 421 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 119 CYS Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 170 HIS Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 245 LYS Chi-restraints excluded: chain E residue 273 ILE Chi-restraints excluded: chain F residue 4 ARG Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 108 GLN Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 178 LYS Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain G residue 43 ILE Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 100 TYR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 5 LYS Chi-restraints excluded: chain H residue 13 GLU Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 192 SER Chi-restraints excluded: chain I residue 193 LEU Chi-restraints excluded: chain I residue 240 ASP Chi-restraints excluded: chain I residue 256 LYS Chi-restraints excluded: chain I residue 275 SER Chi-restraints excluded: chain I residue 297 CYS Chi-restraints excluded: chain I residue 304 THR Chi-restraints excluded: chain I residue 311 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 420 ASN Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain B residue 553 ASN Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 563 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 210 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 165 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 187 optimal weight: 0.4980 chunk 67 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 273 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 ASN A 421 HIS ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.063072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.050152 restraints weight = 58808.844| |-----------------------------------------------------------------------------| r_work (start): 0.2618 rms_B_bonded: 1.89 r_work: 0.2528 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2425 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 25176 Z= 0.211 Angle : 0.865 40.306 34366 Z= 0.427 Chirality : 0.045 0.256 3869 Planarity : 0.006 0.102 4110 Dihedral : 14.284 173.560 4297 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.82 % Favored : 92.04 % Rotamer: Outliers : 4.62 % Allowed : 35.11 % Favored : 60.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % 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: -0.24 (0.16), residues: 2800 helix: 1.14 (0.16), residues: 1069 sheet: 0.29 (0.24), residues: 448 loop : -1.48 (0.17), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 70 TYR 0.028 0.002 TYR A 241 PHE 0.034 0.002 PHE B 198 TRP 0.012 0.002 TRP A 285 HIS 0.024 0.001 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00501 (25176) covalent geometry : angle 0.86480 (34366) hydrogen bonds : bond 0.04511 ( 1017) hydrogen bonds : angle 4.64968 ( 2842) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9290.15 seconds wall clock time: 159 minutes 19.07 seconds (9559.07 seconds total)