Starting phenix.real_space_refine on Sun Jul 5 02:31:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lq8_63296/07_2026/9lq8_63296.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lq8_63296/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9lq8_63296/07_2026/9lq8_63296.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lq8_63296/07_2026/9lq8_63296.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lq8_63296/07_2026/9lq8_63296.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lq8_63296/07_2026/9lq8_63296.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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, 58 Ad-hoc single atom residues: {' MN': 1} Unusual residues: {'ATP': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain breaks: 1 Time building chain proxies: 5.46, per 1000 atoms: 0.22 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: 1.77 Conformation dependent library (CDL) restraints added in 956.5 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: 2.35 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: 4.29 Time building geometry restraints manager: 2.46 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 3.060 nonbonded pdb=" O2A ATP B 701 " pdb="MN MN B 703 " model vdw 2.117 3.060 nonbonded pdb=" OD2 ASP B 279 " pdb="MN MN B 703 " model vdw 2.123 3.060 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: 4.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.290 Find NCS groups from input model: 0.220 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:8.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8962 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= 0.165 Angle : 0.837 40.635 34366 Z= 0.438 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/Z covalent geometry : bond 0.00358 / 0.16 (25176) covalent geometry : angle 0.83708 / 0.44 (34366) hydrogen bonds : bond 0.15216 / 9.92 ( 1017) hydrogen bonds : angle 6.20416 / 4.22 ( 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 : 0.942 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: 0.6701 time to fit residues: 374.2661 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 : 0.993 ------------------------------------------------------------------------------- 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... ** A 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 GLN A 360 ASN ** 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 B 308 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.061605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.048660 restraints weight = 59481.529| |-----------------------------------------------------------------------------| r_work (start): 0.2577 rms_B_bonded: 1.86 r_work: 0.2488 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2386 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9020 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 25176 Z= 0.274 Angle : 0.853 40.064 34366 Z= 0.431 Chirality : 0.047 0.340 3869 Planarity : 0.006 0.117 4110 Dihedral : 15.054 175.893 4397 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.36 % Favored : 92.39 % Rotamer: Outliers : 7.72 % Allowed : 30.13 % Favored : 62.15 % 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: -0.44 (0.16), residues: 2800 helix: 0.94 (0.16), residues: 1072 sheet: 0.33 (0.24), residues: 425 loop : -1.60 (0.17), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 47 TYR 0.021 0.002 TYR A 349 PHE 0.025 0.003 PHE B 412 TRP 0.011 0.002 TRP F 219 HIS 0.006 0.001 HIS A 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00643 / 0.27 (25176) covalent geometry : angle 0.85294 / 0.43 (34366) hydrogen bonds : bond 0.05683 / 3.74 ( 1017) hydrogen bonds : angle 5.05889 / 3.49 ( 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 596 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 399 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 GLU cc_start: 0.8342 (tm-30) cc_final: 0.7915 (tm-30) REVERT: A 241 TYR cc_start: 0.8778 (t80) cc_final: 0.8537 (t80) REVERT: A 285 TRP cc_start: 0.6962 (OUTLIER) cc_final: 0.6161 (t60) REVERT: A 420 MET cc_start: 0.8669 (mmt) cc_final: 0.8384 (mmt) REVERT: C 119 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8625 (mtt) REVERT: D 47 LYS cc_start: 0.9060 (ttpp) cc_final: 0.8724 (ttpt) REVERT: E 73 LYS cc_start: 0.9167 (ptpp) cc_final: 0.8714 (ptmt) REVERT: E 100 MET cc_start: 0.9086 (mmt) cc_final: 0.8707 (mmm) REVERT: F 1 MET cc_start: 0.6990 (tpp) cc_final: 0.6445 (tpp) REVERT: F 108 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8164 (mm-40) REVERT: F 121 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.7154 (mp0) REVERT: G 13 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8695 (tt0) REVERT: G 117 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8914 (tttp) REVERT: H 13 GLU cc_start: 0.9016 (OUTLIER) cc_final: 0.7831 (tm-30) REVERT: H 87 ASP cc_start: 0.8353 (m-30) cc_final: 0.8132 (m-30) REVERT: I 256 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8461 (mptm) REVERT: I 311 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.8925 (mp) REVERT: B 83 LEU cc_start: 0.8886 (mt) cc_final: 0.8663 (tp) REVERT: B 90 GLN cc_start: 0.8806 (mm-40) cc_final: 0.8409 (tp-100) REVERT: B 113 GLN cc_start: 0.8441 (tm-30) cc_final: 0.8238 (tm-30) REVERT: B 116 HIS cc_start: 0.8525 (m-70) cc_final: 0.8306 (m90) REVERT: B 119 LYS cc_start: 0.9242 (tppp) cc_final: 0.8903 (tmtt) REVERT: B 128 GLU cc_start: 0.7891 (pp20) cc_final: 0.7527 (pp20) REVERT: B 132 GLU cc_start: 0.8711 (tm-30) cc_final: 0.8453 (tm-30) REVERT: B 176 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8082 (tp) REVERT: B 200 THR cc_start: 0.9045 (m) cc_final: 0.8733 (p) REVERT: B 259 LEU cc_start: 0.8856 (mp) cc_final: 0.8550 (mm) REVERT: B 262 ASN cc_start: 0.8635 (m110) cc_final: 0.8238 (m-40) REVERT: B 316 VAL cc_start: 0.8793 (t) cc_final: 0.8551 (m) outliers start: 197 outliers final: 91 residues processed: 547 average time/residue: 0.6485 time to fit residues: 407.1719 Evaluate side-chains 489 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 388 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 109 SER 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 334 ILE Chi-restraints excluded: chain A residue 349 TYR 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 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 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 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 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 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 F residue 2 THR 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 89 MET 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 121 GLU 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 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 57 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 G residue 117 LYS 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 28 VAL Chi-restraints excluded: chain I residue 41 THR 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 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 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 130 THR Chi-restraints excluded: chain B residue 149 ILE 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 224 LEU Chi-restraints excluded: chain B residue 358 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 562 THR 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: 0.0870 chunk 210 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 177 optimal weight: 0.7980 chunk 215 optimal weight: 2.9990 chunk 141 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 ASN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 259 GLN B 86 GLN B 87 HIS B 361 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.063113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.050276 restraints weight = 59377.428| |-----------------------------------------------------------------------------| r_work (start): 0.2624 rms_B_bonded: 1.85 r_work: 0.2533 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2430 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8994 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 25176 Z= 0.179 Angle : 0.785 40.464 34366 Z= 0.393 Chirality : 0.044 0.296 3869 Planarity : 0.005 0.114 4110 Dihedral : 14.819 175.687 4339 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.18 % Favored : 92.57 % Rotamer: Outliers : 6.94 % Allowed : 30.37 % 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: -0.35 (0.16), residues: 2800 helix: 1.07 (0.16), residues: 1077 sheet: 0.19 (0.24), residues: 446 loop : -1.57 (0.17), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 70 TYR 0.019 0.002 TYR B 117 PHE 0.031 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/Z covalent geometry : bond 0.00417 / 0.18 (25176) covalent geometry : angle 0.78533 / 0.39 (34366) hydrogen bonds : bond 0.04811 / 3.18 ( 1017) hydrogen bonds : angle 4.83475 / 3.34 ( 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 577 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 400 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7931 (tm-30) REVERT: A 241 TYR cc_start: 0.8747 (t80) cc_final: 0.8516 (t80) REVERT: A 245 GLN cc_start: 0.8433 (mm-40) cc_final: 0.8233 (mm110) REVERT: A 285 TRP cc_start: 0.6919 (OUTLIER) cc_final: 0.6164 (t60) REVERT: C 119 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.8586 (mtt) REVERT: D 47 LYS cc_start: 0.9064 (ttpp) cc_final: 0.8746 (ttpt) REVERT: D 152 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8995 (mt) REVERT: D 202 LEU cc_start: 0.8582 (pp) cc_final: 0.8345 (pt) REVERT: E 73 LYS cc_start: 0.9161 (ptpp) cc_final: 0.8713 (ptmt) REVERT: E 100 MET cc_start: 0.9044 (mmt) cc_final: 0.8750 (mmm) REVERT: F 1 MET cc_start: 0.6888 (tpp) cc_final: 0.6395 (tpp) REVERT: F 14 MET cc_start: 0.9132 (ttp) cc_final: 0.8768 (ttp) REVERT: F 108 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.8141 (mm-40) REVERT: F 178 LYS cc_start: 0.9163 (OUTLIER) cc_final: 0.8672 (mtpp) REVERT: G 13 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8701 (tt0) REVERT: G 80 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.5732 (mmt-90) REVERT: H 13 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.7816 (tm-30) REVERT: H 87 ASP cc_start: 0.8382 (m-30) cc_final: 0.8181 (m-30) REVERT: I 256 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8479 (mptm) REVERT: B 80 ASP cc_start: 0.8238 (p0) cc_final: 0.7910 (p0) REVERT: B 90 GLN cc_start: 0.8813 (mm-40) cc_final: 0.8444 (tp-100) REVERT: B 119 LYS cc_start: 0.9231 (tppp) cc_final: 0.8936 (tmtt) REVERT: B 132 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8468 (tm-30) REVERT: B 176 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8044 (tp) REVERT: B 200 THR cc_start: 0.9038 (m) cc_final: 0.8727 (p) REVERT: B 252 TRP cc_start: 0.5624 (OUTLIER) cc_final: 0.4647 (t-100) REVERT: B 259 LEU cc_start: 0.8895 (mp) cc_final: 0.8639 (tt) REVERT: B 316 VAL cc_start: 0.8745 (t) cc_final: 0.8446 (m) outliers start: 177 outliers final: 87 residues processed: 524 average time/residue: 0.6741 time to fit residues: 405.2976 Evaluate side-chains 482 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 383 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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 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 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 119 MET Chi-restraints excluded: chain C residue 127 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 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 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 170 HIS Chi-restraints excluded: chain D residue 235 MET Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 245 LYS 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 211 GLU Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 255 SER 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 89 MET 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 80 ARG 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 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 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 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 74 PHE Chi-restraints excluded: chain B residue 86 GLN Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 252 TRP 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 435 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 145 optimal weight: 3.9990 chunk 232 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 208 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 225 optimal weight: 7.9990 chunk 267 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 253 optimal weight: 1.9990 chunk 264 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 212 ASN A 316 ASN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 259 GLN G 59 ASN ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.060871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.048045 restraints weight = 59590.793| |-----------------------------------------------------------------------------| r_work (start): 0.2562 rms_B_bonded: 1.88 r_work: 0.2473 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2370 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9031 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.119 25176 Z= 0.282 Angle : 0.849 40.101 34366 Z= 0.428 Chirality : 0.047 0.340 3869 Planarity : 0.006 0.113 4110 Dihedral : 14.786 175.738 4325 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.57 % Favored : 92.21 % Rotamer: Outliers : 7.76 % Allowed : 30.02 % Favored : 62.23 % 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: -0.48 (0.16), residues: 2800 helix: 0.93 (0.16), residues: 1076 sheet: 0.17 (0.24), residues: 446 loop : -1.63 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 70 TYR 0.024 0.002 TYR B 387 PHE 0.026 0.002 PHE C 106 TRP 0.011 0.002 TRP F 219 HIS 0.008 0.001 HIS B 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00666 / 0.28 (25176) covalent geometry : angle 0.84881 / 0.43 (34366) hydrogen bonds : bond 0.05302 / 3.49 ( 1017) hydrogen bonds : angle 4.86541 / 3.36 ( 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 591 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 393 time to evaluate : 0.984 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: 0.8026 (tm-30) REVERT: A 285 TRP cc_start: 0.6947 (OUTLIER) cc_final: 0.6171 (t60) REVERT: A 328 TYR cc_start: 0.8645 (m-80) cc_final: 0.8255 (m-80) REVERT: C 119 MET cc_start: 0.9152 (OUTLIER) cc_final: 0.8619 (mtt) REVERT: D 47 LYS cc_start: 0.9068 (ttpp) cc_final: 0.8741 (ttpt) REVERT: D 152 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.9010 (mt) REVERT: E 73 LYS cc_start: 0.9183 (ptpp) cc_final: 0.8710 (ptmt) REVERT: F 1 MET cc_start: 0.6977 (tpp) cc_final: 0.6502 (tpp) REVERT: F 108 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8140 (mm-40) REVERT: F 121 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.7205 (mp0) REVERT: F 178 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8686 (mtpp) REVERT: G 13 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8699 (tt0) REVERT: G 80 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.7117 (mmt-90) REVERT: H 13 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.7806 (tm-30) REVERT: H 87 ASP cc_start: 0.8365 (m-30) cc_final: 0.8141 (m-30) REVERT: I 256 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8369 (mptm) REVERT: I 311 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.8877 (mp) REVERT: B 55 ASN cc_start: 0.8475 (OUTLIER) cc_final: 0.8145 (p0) REVERT: B 56 GLU cc_start: 0.7509 (mp0) cc_final: 0.7262 (mp0) REVERT: B 83 LEU cc_start: 0.9007 (tp) cc_final: 0.8803 (tm) REVERT: B 90 GLN cc_start: 0.8817 (mm-40) cc_final: 0.8480 (tp-100) REVERT: B 119 LYS cc_start: 0.9256 (tppp) cc_final: 0.8942 (tmtt) REVERT: B 132 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8493 (tm-30) REVERT: B 176 ILE cc_start: 0.8512 (OUTLIER) cc_final: 0.8109 (tp) REVERT: B 200 THR cc_start: 0.9051 (m) cc_final: 0.8759 (p) REVERT: B 252 TRP cc_start: 0.5790 (OUTLIER) cc_final: 0.4717 (t-100) REVERT: B 259 LEU cc_start: 0.8900 (mp) cc_final: 0.8677 (tt) REVERT: B 316 VAL cc_start: 0.8784 (t) cc_final: 0.8485 (m) REVERT: B 466 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8182 (tp40) outliers start: 198 outliers final: 110 residues processed: 540 average time/residue: 0.6773 time to fit residues: 420.2431 Evaluate side-chains 509 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 383 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 107 GLN 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 285 TRP Chi-restraints excluded: chain A residue 318 TRP Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 335 LEU 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 119 MET 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 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 10 THR 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 152 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 236 ASP Chi-restraints excluded: chain D residue 245 LYS Chi-restraints excluded: chain D residue 251 LEU 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 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 245 LYS Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 74 THR 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 112 THR Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 178 LYS Chi-restraints excluded: chain F residue 187 ILE 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 57 GLU 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 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 47 LEU 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 61 SER 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 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 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 55 ASN 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 149 ILE 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 219 ILE Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 358 ILE 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 563 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 222 optimal weight: 5.9990 chunk 180 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 234 optimal weight: 0.7980 chunk 12 optimal weight: 0.0970 chunk 193 optimal weight: 1.9990 chunk 205 optimal weight: 0.8980 chunk 101 optimal weight: 0.0670 chunk 36 optimal weight: 1.9990 chunk 248 optimal weight: 4.9990 chunk 121 optimal weight: 0.5980 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 ASN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN C 367 GLN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.063827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.050914 restraints weight = 59177.329| |-----------------------------------------------------------------------------| r_work (start): 0.2639 rms_B_bonded: 1.90 r_work: 0.2550 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2447 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8983 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 25176 Z= 0.149 Angle : 0.774 40.807 34366 Z= 0.384 Chirality : 0.043 0.283 3869 Planarity : 0.005 0.111 4110 Dihedral : 14.721 175.952 4322 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.36 % Favored : 92.46 % Rotamer: Outliers : 6.54 % Allowed : 31.74 % Favored : 61.72 % 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: -0.31 (0.16), residues: 2800 helix: 1.15 (0.16), residues: 1063 sheet: 0.18 (0.24), residues: 454 loop : -1.56 (0.17), residues: 1283 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 0.028 0.002 PHE C 106 TRP 0.008 0.001 TRP A 157 HIS 0.008 0.001 HIS A 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (25176) covalent geometry : angle 0.77386 / 0.38 (34366) hydrogen bonds : bond 0.04328 / 2.85 ( 1017) hydrogen bonds : angle 4.69059 / 3.25 ( 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 566 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 399 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8783 (mtpt) REVERT: A 141 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7967 (tm-30) REVERT: A 241 TYR cc_start: 0.8753 (t80) cc_final: 0.8484 (t80) REVERT: A 263 PHE cc_start: 0.6998 (t80) cc_final: 0.6673 (t80) REVERT: A 285 TRP cc_start: 0.6791 (OUTLIER) cc_final: 0.6152 (t60) REVERT: C 68 ASP cc_start: 0.7525 (OUTLIER) cc_final: 0.7243 (m-30) REVERT: D 47 LYS cc_start: 0.9038 (ttpp) cc_final: 0.8714 (ttpt) REVERT: D 152 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8976 (mt) REVERT: D 202 LEU cc_start: 0.8495 (pp) cc_final: 0.8276 (pt) REVERT: E 73 LYS cc_start: 0.9164 (ptpp) cc_final: 0.8717 (ptmt) REVERT: E 100 MET cc_start: 0.8914 (mmt) cc_final: 0.8627 (mmm) REVERT: E 273 ILE cc_start: 0.9397 (OUTLIER) cc_final: 0.8974 (mm) REVERT: F 1 MET cc_start: 0.6930 (tpp) cc_final: 0.6435 (tpp) REVERT: F 108 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.8137 (mm-40) REVERT: F 178 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8669 (mtpp) REVERT: G 13 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8675 (tt0) REVERT: H 13 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.7789 (tm-30) REVERT: H 87 ASP cc_start: 0.8382 (m-30) cc_final: 0.8168 (m-30) REVERT: I 256 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8392 (mptm) REVERT: I 311 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8777 (mt) REVERT: B 94 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7771 (mt-10) REVERT: B 119 LYS cc_start: 0.9223 (tppp) cc_final: 0.8861 (tmtt) REVERT: B 132 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8452 (tm-30) REVERT: B 176 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8177 (tt) REVERT: B 200 THR cc_start: 0.9027 (m) cc_final: 0.8721 (p) REVERT: B 202 ASP cc_start: 0.8858 (t0) cc_final: 0.8619 (t0) REVERT: B 252 TRP cc_start: 0.5734 (OUTLIER) cc_final: 0.4767 (t-100) REVERT: B 316 VAL cc_start: 0.8638 (t) cc_final: 0.8371 (m) REVERT: B 387 TYR cc_start: 0.7779 (OUTLIER) cc_final: 0.7477 (t80) REVERT: B 466 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8118 (tp40) REVERT: B 504 GLN cc_start: 0.9016 (OUTLIER) cc_final: 0.8573 (mt0) outliers start: 167 outliers final: 81 residues processed: 516 average time/residue: 0.6834 time to fit residues: 404.3833 Evaluate side-chains 485 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 386 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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 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 371 LEU Chi-restraints excluded: chain A residue 409 ARG 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 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 255 VAL Chi-restraints excluded: chain C residue 415 ARG Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 10 THR 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 188 LEU Chi-restraints excluded: chain D residue 235 MET Chi-restraints excluded: chain D residue 245 LYS Chi-restraints excluded: chain D residue 251 LEU 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 255 SER Chi-restraints excluded: chain E residue 273 ILE Chi-restraints excluded: chain F residue 7 VAL 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 89 MET 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 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 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 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 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 80 ASP 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 176 ILE Chi-restraints excluded: chain B residue 252 TRP Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 387 TYR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 210 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 204 optimal weight: 0.6980 chunk 243 optimal weight: 0.9990 chunk 283 optimal weight: 0.8980 chunk 257 optimal weight: 0.6980 chunk 233 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 279 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 GLN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 ASN ** 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 90 GLN B 410 ASN B 504 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.063559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.050648 restraints weight = 59216.627| |-----------------------------------------------------------------------------| r_work (start): 0.2632 rms_B_bonded: 1.90 r_work: 0.2541 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2439 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8987 moved from start: 0.1365 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= 0.170 Angle : 0.792 40.489 34366 Z= 0.392 Chirality : 0.044 0.296 3869 Planarity : 0.005 0.109 4110 Dihedral : 14.581 176.463 4313 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.36 % Favored : 92.46 % Rotamer: Outliers : 6.03 % Allowed : 32.21 % Favored : 61.76 % 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: -0.28 (0.16), residues: 2800 helix: 1.18 (0.16), residues: 1070 sheet: 0.23 (0.24), residues: 449 loop : -1.57 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 70 TYR 0.021 0.002 TYR B 72 PHE 0.028 0.002 PHE C 106 TRP 0.008 0.001 TRP F 219 HIS 0.007 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (25176) covalent geometry : angle 0.79175 / 0.39 (34366) hydrogen bonds : bond 0.04424 / 2.91 ( 1017) hydrogen bonds : angle 4.64984 / 3.23 ( 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 546 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 392 time to evaluate : 0.992 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 141 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7783 (tm-30) REVERT: A 143 LYS cc_start: 0.9092 (mmpt) cc_final: 0.8819 (mmpt) REVERT: A 241 TYR cc_start: 0.8748 (t80) cc_final: 0.8478 (t80) REVERT: A 285 TRP cc_start: 0.6704 (OUTLIER) cc_final: 0.6107 (t60) REVERT: C 68 ASP cc_start: 0.7495 (OUTLIER) cc_final: 0.7267 (m-30) REVERT: C 187 PHE cc_start: 0.8142 (m-10) cc_final: 0.7743 (m-10) REVERT: D 47 LYS cc_start: 0.9032 (ttpp) cc_final: 0.8709 (ttpt) REVERT: D 152 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8973 (mt) REVERT: D 202 LEU cc_start: 0.8472 (pp) cc_final: 0.8263 (pt) REVERT: E 73 LYS cc_start: 0.9159 (ptpp) cc_final: 0.8728 (ptmt) REVERT: E 100 MET cc_start: 0.8953 (mmt) cc_final: 0.8733 (mmm) REVERT: E 273 ILE cc_start: 0.9410 (OUTLIER) cc_final: 0.8982 (mm) REVERT: F 1 MET cc_start: 0.6948 (tpp) cc_final: 0.6537 (tpp) REVERT: F 108 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8144 (mm-40) REVERT: F 178 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8673 (mtpp) REVERT: G 13 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8683 (tt0) REVERT: G 55 GLU cc_start: 0.9426 (OUTLIER) cc_final: 0.9222 (tt0) REVERT: H 13 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.7777 (tm-30) REVERT: H 87 ASP cc_start: 0.8393 (m-30) cc_final: 0.8158 (m-30) REVERT: I 256 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8404 (mptm) REVERT: I 311 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8815 (mt) REVERT: B 55 ASN cc_start: 0.8590 (OUTLIER) cc_final: 0.8210 (p0) REVERT: B 83 LEU cc_start: 0.9021 (tm) cc_final: 0.8735 (tp) REVERT: B 90 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.8330 (tp-100) REVERT: B 119 LYS cc_start: 0.9196 (tppp) cc_final: 0.8920 (tmtt) REVERT: B 132 GLU cc_start: 0.8748 (tm-30) cc_final: 0.8423 (tm-30) REVERT: B 176 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8346 (tt) REVERT: B 198 PHE cc_start: 0.7852 (p90) cc_final: 0.7644 (p90) REVERT: B 200 THR cc_start: 0.9011 (m) cc_final: 0.8715 (p) REVERT: B 202 ASP cc_start: 0.8868 (t0) cc_final: 0.8589 (t0) REVERT: B 252 TRP cc_start: 0.5734 (OUTLIER) cc_final: 0.4776 (t-100) REVERT: B 316 VAL cc_start: 0.8598 (t) cc_final: 0.8362 (m) REVERT: B 387 TYR cc_start: 0.7764 (OUTLIER) cc_final: 0.7531 (t80) REVERT: B 466 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.8124 (tp40) outliers start: 154 outliers final: 87 residues processed: 501 average time/residue: 0.6801 time to fit residues: 390.2652 Evaluate side-chains 490 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 384 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 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 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 371 LEU 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 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 246 LYS 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 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 188 LEU 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 20 GLU Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain E residue 273 ILE Chi-restraints excluded: chain F residue 7 VAL 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 89 MET 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 55 GLU Chi-restraints excluded: chain G residue 57 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 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 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 90 GLN Chi-restraints excluded: chain B residue 94 GLU 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 252 TRP Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 387 TYR 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 508 LYS Chi-restraints excluded: chain B residue 553 ASN 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: 0.9990 chunk 161 optimal weight: 1.9990 chunk 261 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 45 optimal weight: 0.0980 chunk 27 optimal weight: 0.9980 chunk 239 optimal weight: 0.6980 chunk 195 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 129 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 GLN A 314 ASN A 405 ASN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 HIS B 90 GLN B 504 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.063924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.051045 restraints weight = 59279.098| |-----------------------------------------------------------------------------| r_work (start): 0.2644 rms_B_bonded: 1.89 r_work: 0.2553 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2450 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8980 moved from start: 0.1400 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= 0.161 Angle : 0.795 40.583 34366 Z= 0.393 Chirality : 0.044 0.289 3869 Planarity : 0.005 0.108 4110 Dihedral : 14.519 176.603 4309 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.43 % Favored : 92.39 % Rotamer: Outliers : 5.72 % Allowed : 32.68 % Favored : 61.60 % 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: 1.22 (0.16), residues: 1072 sheet: 0.20 (0.24), residues: 459 loop : -1.54 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 136 TYR 0.024 0.002 TYR B 72 PHE 0.027 0.002 PHE C 106 TRP 0.007 0.001 TRP F 219 HIS 0.006 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (25176) covalent geometry : angle 0.79522 / 0.39 (34366) hydrogen bonds : bond 0.04341 / 2.86 ( 1017) hydrogen bonds : angle 4.61412 / 3.20 ( 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 538 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 392 time to evaluate : 0.966 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: 0.9213 (OUTLIER) cc_final: 0.8785 (mtpt) REVERT: A 141 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7770 (tm-30) REVERT: A 142 PHE cc_start: 0.9017 (t80) cc_final: 0.8796 (t80) REVERT: A 285 TRP cc_start: 0.6659 (OUTLIER) cc_final: 0.6084 (t60) REVERT: C 68 ASP cc_start: 0.7439 (OUTLIER) cc_final: 0.7140 (m-30) REVERT: C 187 PHE cc_start: 0.8003 (m-10) cc_final: 0.7784 (m-80) REVERT: D 47 LYS cc_start: 0.9031 (ttpp) cc_final: 0.8713 (ttpt) REVERT: D 152 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8958 (mt) REVERT: D 202 LEU cc_start: 0.8439 (pp) cc_final: 0.8220 (pt) REVERT: E 73 LYS cc_start: 0.9154 (ptpp) cc_final: 0.8727 (ptmt) REVERT: E 273 ILE cc_start: 0.9403 (OUTLIER) cc_final: 0.8981 (mm) REVERT: F 1 MET cc_start: 0.6973 (tpp) cc_final: 0.6581 (tpp) REVERT: F 108 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.8127 (mm-40) REVERT: F 178 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8673 (mtpp) REVERT: G 13 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.8669 (tt0) REVERT: G 55 GLU cc_start: 0.9423 (OUTLIER) cc_final: 0.9150 (tt0) REVERT: H 13 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.7753 (tm-30) REVERT: H 87 ASP cc_start: 0.8401 (m-30) cc_final: 0.8168 (m-30) REVERT: I 256 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8458 (mptm) REVERT: I 311 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8783 (mp) REVERT: B 90 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8339 (tp-100) REVERT: B 132 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8415 (tm-30) REVERT: B 176 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8274 (tt) REVERT: B 200 THR cc_start: 0.8981 (m) cc_final: 0.8684 (p) REVERT: B 316 VAL cc_start: 0.8624 (t) cc_final: 0.8407 (m) REVERT: B 466 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.8136 (tp40) outliers start: 146 outliers final: 85 residues processed: 495 average time/residue: 0.6825 time to fit residues: 386.5227 Evaluate side-chains 484 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 383 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LYS 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 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 371 LEU Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 415 ILE 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 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 246 LYS 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 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 148 VAL 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 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 83 GLU Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain E residue 273 ILE Chi-restraints excluded: chain F residue 7 VAL 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 89 MET 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 55 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 H residue 5 LYS 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 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 90 GLN Chi-restraints excluded: chain B residue 94 GLU 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 219 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 508 LYS Chi-restraints excluded: chain B residue 553 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 178 optimal weight: 0.0980 chunk 120 optimal weight: 0.6980 chunk 39 optimal weight: 0.0570 chunk 158 optimal weight: 3.9990 chunk 166 optimal weight: 0.7980 chunk 281 optimal weight: 3.9990 chunk 69 optimal weight: 0.0970 chunk 195 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 229 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 GLN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 GLN B 86 GLN B 504 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.065807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.052792 restraints weight = 58387.403| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 1.91 r_work: 0.2600 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2498 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.1521 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= 0.136 Angle : 0.786 40.864 34366 Z= 0.385 Chirality : 0.043 0.273 3869 Planarity : 0.005 0.106 4110 Dihedral : 14.435 177.621 4306 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.07 % Favored : 92.75 % Rotamer: Outliers : 5.02 % Allowed : 33.35 % Favored : 61.64 % 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: -0.18 (0.16), residues: 2800 helix: 1.31 (0.16), residues: 1069 sheet: 0.22 (0.24), residues: 456 loop : -1.54 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 70 TYR 0.022 0.001 TYR B 72 PHE 0.033 0.002 PHE B 198 TRP 0.009 0.001 TRP B 252 HIS 0.009 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (25176) covalent geometry : angle 0.78603 / 0.38 (34366) hydrogen bonds : bond 0.03978 / 2.61 ( 1017) hydrogen bonds : angle 4.54473 / 3.16 ( 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 533 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 405 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8821 (mtpt) REVERT: A 141 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7852 (tm-30) REVERT: A 241 TYR cc_start: 0.8693 (t80) cc_final: 0.8450 (t80) REVERT: A 285 TRP cc_start: 0.6612 (OUTLIER) cc_final: 0.6376 (t60) REVERT: A 454 TYR cc_start: 0.7402 (OUTLIER) cc_final: 0.6769 (m-80) REVERT: C 68 ASP cc_start: 0.7430 (OUTLIER) cc_final: 0.7145 (m-30) REVERT: C 421 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8975 (mp) REVERT: D 47 LYS cc_start: 0.9013 (ttpp) cc_final: 0.8715 (ttpt) REVERT: D 218 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8569 (tp) REVERT: E 73 LYS cc_start: 0.9139 (ptpp) cc_final: 0.8754 (ptmt) REVERT: E 273 ILE cc_start: 0.9385 (OUTLIER) cc_final: 0.8950 (mm) REVERT: F 1 MET cc_start: 0.6904 (tpp) cc_final: 0.6531 (tpp) REVERT: F 108 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.8117 (mm-40) REVERT: F 178 LYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8656 (mtpp) REVERT: G 13 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8626 (tt0) REVERT: G 55 GLU cc_start: 0.9422 (OUTLIER) cc_final: 0.9127 (tt0) REVERT: H 13 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.7747 (tm-30) REVERT: H 100 TYR cc_start: 0.8521 (OUTLIER) cc_final: 0.8156 (t80) REVERT: I 256 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8452 (mptm) REVERT: B 94 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7948 (mt-10) REVERT: B 132 GLU cc_start: 0.8748 (tm-30) cc_final: 0.8371 (tm-30) REVERT: B 200 THR cc_start: 0.8945 (m) cc_final: 0.8632 (p) REVERT: B 202 ASP cc_start: 0.8821 (t0) cc_final: 0.8579 (t0) REVERT: B 263 LYS cc_start: 0.8974 (tppt) cc_final: 0.8750 (mmpt) REVERT: B 466 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8080 (tp40) REVERT: B 504 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8352 (mt0) outliers start: 128 outliers final: 70 residues processed: 491 average time/residue: 0.6821 time to fit residues: 383.8734 Evaluate side-chains 477 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 389 time to evaluate : 0.934 ------------------------------------------------------------------------------- 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 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 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 371 LEU Chi-restraints excluded: chain A residue 415 ILE 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 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 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 148 VAL Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 170 HIS Chi-restraints excluded: chain D residue 218 LEU 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 273 ILE 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 89 MET Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 108 GLN Chi-restraints excluded: chain F residue 178 LYS Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain G residue 43 ILE Chi-restraints excluded: chain G residue 55 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 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 86 THR 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 156 LEU 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 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 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 94 GLU Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 149 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 110 optimal weight: 0.2980 chunk 90 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 197 optimal weight: 1.9990 chunk 196 optimal weight: 0.9980 chunk 246 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 239 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 GLN A 436 HIS ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 504 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.063679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.050617 restraints weight = 58647.116| |-----------------------------------------------------------------------------| r_work (start): 0.2631 rms_B_bonded: 1.90 r_work: 0.2541 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2439 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8987 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 25176 Z= 0.209 Angle : 0.835 40.434 34366 Z= 0.413 Chirality : 0.045 0.302 3869 Planarity : 0.005 0.105 4110 Dihedral : 14.393 176.865 4305 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.57 % Favored : 92.29 % Rotamer: Outliers : 4.43 % Allowed : 34.25 % Favored : 61.32 % 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: 1.18 (0.16), residues: 1070 sheet: 0.26 (0.24), residues: 461 loop : -1.53 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 70 TYR 0.027 0.002 TYR B 33 PHE 0.033 0.002 PHE B 198 TRP 0.009 0.001 TRP E 219 HIS 0.005 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.21 (25176) covalent geometry : angle 0.83501 / 0.41 (34366) hydrogen bonds : bond 0.04479 / 2.93 ( 1017) hydrogen bonds : angle 4.61400 / 3.20 ( 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 501 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 388 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.8800 (mtpt) REVERT: A 141 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7922 (tm-30) REVERT: A 279 LYS cc_start: 0.8988 (ttmt) cc_final: 0.8728 (ptpp) REVERT: A 285 TRP cc_start: 0.6688 (OUTLIER) cc_final: 0.6431 (t60) REVERT: A 454 TYR cc_start: 0.7486 (OUTLIER) cc_final: 0.6851 (m-80) REVERT: C 68 ASP cc_start: 0.7486 (OUTLIER) cc_final: 0.7239 (m-30) REVERT: D 47 LYS cc_start: 0.9039 (ttpp) cc_final: 0.8734 (ttpt) REVERT: D 202 LEU cc_start: 0.8474 (pp) cc_final: 0.8214 (pt) REVERT: E 73 LYS cc_start: 0.9140 (ptpp) cc_final: 0.8741 (ptmt) REVERT: E 273 ILE cc_start: 0.9415 (OUTLIER) cc_final: 0.8985 (mm) REVERT: F 1 MET cc_start: 0.6986 (tpp) cc_final: 0.6639 (tpp) REVERT: F 108 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8174 (mm-40) REVERT: F 178 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8664 (mtpp) REVERT: F 183 ASP cc_start: 0.8440 (t0) cc_final: 0.8011 (t0) REVERT: G 13 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8678 (tt0) REVERT: H 13 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.7774 (tm-30) REVERT: H 87 ASP cc_start: 0.8325 (m-30) cc_final: 0.8086 (m-30) REVERT: H 100 TYR cc_start: 0.8561 (OUTLIER) cc_final: 0.8140 (t80) REVERT: I 23 ARG cc_start: 0.9023 (ptp90) cc_final: 0.8714 (ptp90) REVERT: I 256 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8470 (mptm) REVERT: I 311 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8820 (mt) REVERT: B 90 GLN cc_start: 0.8601 (tp-100) cc_final: 0.7363 (tp40) REVERT: B 123 LYS cc_start: 0.7140 (pptt) cc_final: 0.6900 (pptt) REVERT: B 132 GLU cc_start: 0.8737 (tm-30) cc_final: 0.8361 (tm-30) REVERT: B 176 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8404 (tt) REVERT: B 466 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.8119 (tp40) outliers start: 113 outliers final: 75 residues processed: 470 average time/residue: 0.6904 time to fit residues: 371.8322 Evaluate side-chains 472 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 383 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 371 LEU 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 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 415 ARG Chi-restraints excluded: chain C residue 421 ILE Chi-restraints excluded: chain D residue 1 MET 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 148 VAL Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 170 HIS 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 20 GLU Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 273 ILE 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 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 126 MET 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 86 THR 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 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 95 ILE Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 305 LEU 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 563 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 156 optimal weight: 0.0570 chunk 168 optimal weight: 3.9990 chunk 254 optimal weight: 3.9990 chunk 237 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 192 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 139 optimal weight: 0.1980 chunk 246 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.5700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 GLN A 421 HIS ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 GLN ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.065092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.052120 restraints weight = 58654.230| |-----------------------------------------------------------------------------| r_work (start): 0.2669 rms_B_bonded: 1.90 r_work: 0.2579 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2477 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8962 moved from start: 0.1600 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= 0.152 Angle : 0.824 40.716 34366 Z= 0.404 Chirality : 0.043 0.279 3869 Planarity : 0.005 0.103 4110 Dihedral : 14.383 176.926 4302 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.96 % Favored : 92.89 % Rotamer: Outliers : 3.72 % Allowed : 34.91 % Favored : 61.36 % 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: 1.22 (0.16), residues: 1070 sheet: 0.24 (0.24), residues: 456 loop : -1.53 (0.17), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 70 TYR 0.021 0.001 TYR B 72 PHE 0.026 0.002 PHE B 126 TRP 0.007 0.001 TRP A 157 HIS 0.004 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (25176) covalent geometry : angle 0.82356 / 0.40 (34366) hydrogen bonds : bond 0.04152 / 2.70 ( 1017) hydrogen bonds : angle 4.58524 / 3.20 ( 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 490 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 395 time to evaluate : 0.940 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: 0.9217 (OUTLIER) cc_final: 0.8796 (mtpt) REVERT: A 129 LYS cc_start: 0.8920 (ttmm) cc_final: 0.8591 (mtpp) REVERT: A 141 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7667 (tm-30) REVERT: A 279 LYS cc_start: 0.8962 (ttmt) cc_final: 0.8747 (ptpp) REVERT: A 328 TYR cc_start: 0.8411 (m-80) cc_final: 0.8117 (m-80) REVERT: A 454 TYR cc_start: 0.7436 (OUTLIER) cc_final: 0.6792 (m-80) REVERT: C 68 ASP cc_start: 0.7455 (OUTLIER) cc_final: 0.7196 (m-30) REVERT: D 47 LYS cc_start: 0.9024 (ttpp) cc_final: 0.8728 (ttpt) REVERT: D 202 LEU cc_start: 0.8426 (pp) cc_final: 0.8158 (pt) REVERT: D 218 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8559 (tp) REVERT: E 73 LYS cc_start: 0.9140 (ptpp) cc_final: 0.8750 (ptmt) REVERT: E 273 ILE cc_start: 0.9398 (OUTLIER) cc_final: 0.8987 (mm) REVERT: F 1 MET cc_start: 0.6955 (tpp) cc_final: 0.6613 (tpp) REVERT: F 108 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.8116 (mm-40) REVERT: F 178 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8644 (mtpp) REVERT: G 13 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8642 (tt0) REVERT: H 13 GLU cc_start: 0.8989 (OUTLIER) cc_final: 0.7733 (tm-30) REVERT: H 87 ASP cc_start: 0.8350 (m-30) cc_final: 0.8121 (m-30) REVERT: H 100 TYR cc_start: 0.8534 (OUTLIER) cc_final: 0.8132 (t80) REVERT: H 119 ILE cc_start: 0.8813 (mm) cc_final: 0.8594 (mp) REVERT: I 23 ARG cc_start: 0.9012 (ptp90) cc_final: 0.8700 (ptp90) REVERT: I 256 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8458 (mptm) REVERT: B 29 TYR cc_start: 0.8076 (t80) cc_final: 0.7790 (t80) REVERT: B 123 LYS cc_start: 0.7069 (pptt) cc_final: 0.6665 (pptt) REVERT: B 132 GLU cc_start: 0.8717 (tm-30) cc_final: 0.8324 (tm-30) REVERT: B 202 ASP cc_start: 0.8849 (t0) cc_final: 0.8566 (t0) REVERT: B 466 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8084 (tp40) REVERT: B 504 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8202 (mt0) outliers start: 95 outliers final: 68 residues processed: 468 average time/residue: 0.6960 time to fit residues: 372.7127 Evaluate side-chains 466 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 385 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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 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 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 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 148 VAL Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 170 HIS Chi-restraints excluded: chain D residue 218 LEU 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 273 ILE 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 178 LYS Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 258 ILE 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 126 MET Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 13 GLU Chi-restraints excluded: chain H residue 47 LEU 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 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 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 305 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 210 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 187 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 106 optimal weight: 0.2980 chunk 273 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 GLN A 421 HIS A 460 ASN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 ASN ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.062927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.049911 restraints weight = 58875.741| |-----------------------------------------------------------------------------| r_work (start): 0.2611 rms_B_bonded: 1.91 r_work: 0.2521 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2419 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9000 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 25176 Z= 0.232 Angle : 0.879 40.230 34366 Z= 0.435 Chirality : 0.046 0.313 3869 Planarity : 0.006 0.102 4110 Dihedral : 14.366 176.078 4300 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.64 % Favored : 92.21 % Rotamer: Outliers : 3.92 % Allowed : 34.76 % Favored : 61.32 % 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: -0.29 (0.16), residues: 2800 helix: 1.11 (0.16), residues: 1066 sheet: 0.26 (0.24), residues: 449 loop : -1.52 (0.17), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 70 TYR 0.026 0.002 TYR B 72 PHE 0.024 0.002 PHE C 106 TRP 0.013 0.002 TRP A 285 HIS 0.005 0.001 HIS I 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.23 (25176) covalent geometry : angle 0.87884 / 0.44 (34366) hydrogen bonds : bond 0.04727 / 3.08 ( 1017) hydrogen bonds : angle 4.68900 / 3.26 ( 2842) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9166.26 seconds wall clock time: 157 minutes 39.15 seconds (9459.15 seconds total)