Starting phenix.real_space_refine on Sun Aug 24 06:16:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wzb_37949/08_2025/8wzb_37949.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wzb_37949/08_2025/8wzb_37949.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wzb_37949/08_2025/8wzb_37949.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wzb_37949/08_2025/8wzb_37949.map" model { file = "/net/cci-nas-00/data/ceres_data/8wzb_37949/08_2025/8wzb_37949.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wzb_37949/08_2025/8wzb_37949.cif" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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: 4 Type Number sf(0) Gaussians S 67 5.16 5 C 11274 2.51 5 N 2975 2.21 5 O 3278 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17594 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 369 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "B" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1489 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 164} Chain: "C" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 633 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 69} Chain breaks: 1 Chain: "D" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 387 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "E" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1612 Classifications: {'peptide': 201} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 182} Chain: "F" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1514 Classifications: {'peptide': 185} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 179} Chain: "G" Number of atoms: 3099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3099 Classifications: {'peptide': 387} Link IDs: {'CIS': 2, 'PTRANS': 31, 'TRANS': 353} Chain breaks: 5 Chain: "H" Number of atoms: 1912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1912 Classifications: {'peptide': 239} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 225} Chain breaks: 2 Chain: "S" Number of atoms: 3139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3139 Classifications: {'peptide': 392} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 360} Chain breaks: 5 Chain: "c" Number of atoms: 1926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1926 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Link IDs: {'CIS': 5, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 223} Chain breaks: 2 Chain: "I" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1514 Classifications: {'peptide': 185} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 179} Time building chain proxies: 3.59, per 1000 atoms: 0.20 Number of scatterers: 17594 At special positions: 0 Unit cell: (130.662, 228.872, 133.224, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 67 16.00 O 3278 8.00 N 2975 7.00 C 11274 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: 1.19 Conformation dependent library (CDL) restraints added in 470.3 milliseconds Enol-peptide restraints added in 1.2 microseconds 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4030 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 23 sheets defined 29.3% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 1 through 10 removed outlier: 3.847A pdb=" N PHE A 10 " --> pdb=" O LEU A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 24 Processing helix chain 'A' and resid 28 through 46 removed outlier: 3.618A pdb=" N ALA A 46 " --> pdb=" O SER A 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 154 Processing helix chain 'B' and resid 238 through 242 removed outlier: 3.987A pdb=" N LEU B 242 " --> pdb=" O LEU B 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 238 through 242' Processing helix chain 'B' and resid 303 through 315 removed outlier: 3.663A pdb=" N LYS B 307 " --> pdb=" O THR B 303 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN B 312 " --> pdb=" O GLN B 308 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU B 315 " --> pdb=" O ARG B 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 315 Processing helix chain 'D' and resid 286 through 290 Processing helix chain 'D' and resid 290 through 329 removed outlier: 3.520A pdb=" N TRP D 294 " --> pdb=" O GLY D 290 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU D 329 " --> pdb=" O ILE D 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 25 No H-bonds generated for 'chain 'E' and resid 23 through 25' Processing helix chain 'E' and resid 26 through 38 removed outlier: 3.810A pdb=" N ILE E 30 " --> pdb=" O LYS E 26 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY E 38 " --> pdb=" O ILE E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 58 removed outlier: 3.850A pdb=" N SER E 55 " --> pdb=" O PRO E 51 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASN E 56 " --> pdb=" O GLU E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 75 removed outlier: 4.021A pdb=" N THR E 71 " --> pdb=" O PHE E 67 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER E 75 " --> pdb=" O THR E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 98 Processing helix chain 'E' and resid 101 through 109 removed outlier: 4.268A pdb=" N GLU E 107 " --> pdb=" O LEU E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 118 removed outlier: 3.794A pdb=" N ILE E 116 " --> pdb=" O SER E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 143 Processing helix chain 'E' and resid 154 through 165 removed outlier: 3.981A pdb=" N LYS E 158 " --> pdb=" O GLY E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 178 removed outlier: 3.570A pdb=" N GLU E 175 " --> pdb=" O GLN E 171 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N CYS E 177 " --> pdb=" O LEU E 173 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS E 178 " --> pdb=" O THR E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 195 removed outlier: 4.385A pdb=" N TRP E 187 " --> pdb=" O ASP E 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 218 Processing helix chain 'G' and resid 227 through 241 removed outlier: 4.044A pdb=" N ASP G 241 " --> pdb=" O THR G 237 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 261 removed outlier: 3.502A pdb=" N SER G 255 " --> pdb=" O ILE G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 276 through 287 removed outlier: 3.758A pdb=" N TYR G 280 " --> pdb=" O MET G 276 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS G 287 " --> pdb=" O ALA G 283 " (cutoff:3.500A) Processing helix chain 'G' and resid 313 through 325 Processing helix chain 'G' and resid 329 through 347 Processing helix chain 'G' and resid 423 through 427 Processing helix chain 'G' and resid 478 through 495 removed outlier: 3.833A pdb=" N TYR G 482 " --> pdb=" O ASN G 478 " (cutoff:3.500A) Processing helix chain 'G' and resid 532 through 536 removed outlier: 3.668A pdb=" N VAL G 536 " --> pdb=" O ILE G 533 " (cutoff:3.500A) Processing helix chain 'G' and resid 617 through 621 removed outlier: 3.815A pdb=" N TYR G 620 " --> pdb=" O ILE G 617 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA G 621 " --> pdb=" O PRO G 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 617 through 621' Processing helix chain 'G' and resid 683 through 692 removed outlier: 3.602A pdb=" N MET G 692 " --> pdb=" O GLN G 688 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 9 Processing helix chain 'H' and resid 9 through 14 removed outlier: 4.028A pdb=" N ALA H 13 " --> pdb=" O SER H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 39 Processing helix chain 'H' and resid 89 through 94 Processing helix chain 'H' and resid 95 through 99 removed outlier: 3.765A pdb=" N VAL H 98 " --> pdb=" O GLN H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 151 Processing helix chain 'H' and resid 216 through 220 removed outlier: 3.924A pdb=" N TYR H 219 " --> pdb=" O SER H 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 271 through 276 Processing helix chain 'S' and resid 206 through 218 Processing helix chain 'S' and resid 227 through 242 Processing helix chain 'S' and resid 250 through 259 Processing helix chain 'S' and resid 277 through 286 removed outlier: 3.641A pdb=" N GLU S 281 " --> pdb=" O LEU S 277 " (cutoff:3.500A) Processing helix chain 'S' and resid 313 through 323 removed outlier: 3.770A pdb=" N SER S 317 " --> pdb=" O ASN S 313 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN S 323 " --> pdb=" O TYR S 319 " (cutoff:3.500A) Processing helix chain 'S' and resid 330 through 347 Processing helix chain 'S' and resid 447 through 452 Processing helix chain 'S' and resid 453 through 457 removed outlier: 4.221A pdb=" N LYS S 456 " --> pdb=" O THR S 453 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE S 457 " --> pdb=" O ALA S 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 453 through 457' Processing helix chain 'S' and resid 478 through 495 removed outlier: 3.589A pdb=" N HIS S 495 " --> pdb=" O SER S 491 " (cutoff:3.500A) Processing helix chain 'S' and resid 531 through 538 removed outlier: 3.605A pdb=" N SER S 538 " --> pdb=" O ASP S 534 " (cutoff:3.500A) Processing helix chain 'S' and resid 595 through 599 removed outlier: 3.728A pdb=" N GLU S 598 " --> pdb=" O PRO S 595 " (cutoff:3.500A) Processing helix chain 'S' and resid 683 through 693 Processing helix chain 'c' and resid 2 through 6 removed outlier: 4.045A pdb=" N LEU c 6 " --> pdb=" O ALA c 3 " (cutoff:3.500A) Processing helix chain 'c' and resid 11 through 15 removed outlier: 4.024A pdb=" N GLY c 15 " --> pdb=" O LEU c 12 " (cutoff:3.500A) Processing helix chain 'c' and resid 21 through 39 removed outlier: 3.502A pdb=" N TYR c 39 " --> pdb=" O VAL c 35 " (cutoff:3.500A) Processing helix chain 'c' and resid 89 through 95 removed outlier: 3.843A pdb=" N GLN c 95 " --> pdb=" O GLU c 91 " (cutoff:3.500A) Processing helix chain 'c' and resid 96 through 99 removed outlier: 3.503A pdb=" N VAL c 99 " --> pdb=" O ILE c 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 96 through 99' Processing helix chain 'c' and resid 136 through 151 Processing helix chain 'c' and resid 177 through 181 removed outlier: 3.573A pdb=" N VAL c 181 " --> pdb=" O LEU c 178 " (cutoff:3.500A) Processing helix chain 'c' and resid 232 through 235 Processing helix chain 'c' and resid 271 through 276 removed outlier: 3.533A pdb=" N MET c 275 " --> pdb=" O ASP c 271 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 140 through 146 removed outlier: 10.124A pdb=" N ILE B 140 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ILE B 214 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ARG B 142 " --> pdb=" O ILE B 214 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LYS B 216 " --> pdb=" O ARG B 142 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LEU B 144 " --> pdb=" O LYS B 216 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP B 210 " --> pdb=" O PHE B 196 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ILE B 194 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR B 195 " --> pdb=" O LYS E 201 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS E 201 " --> pdb=" O THR B 195 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 223 through 226 Processing sheet with id=AA3, first strand: chain 'B' and resid 247 through 250 Processing sheet with id=AA4, first strand: chain 'C' and resid 231 through 237 removed outlier: 6.470A pdb=" N PHE C 232 " --> pdb=" O PHE C 293 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ASP C 295 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N TYR C 234 " --> pdb=" O ASP C 295 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N GLN C 297 " --> pdb=" O TYR C 234 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ILE C 236 " --> pdb=" O GLN C 297 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU C 290 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL C 273 " --> pdb=" O LEU C 290 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ILE C 292 " --> pdb=" O LYS C 271 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS C 271 " --> pdb=" O ILE C 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 40 through 47 removed outlier: 6.360A pdb=" N ILE E 41 " --> pdb=" O ALA E 85 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ALA E 85 " --> pdb=" O ILE E 41 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLN E 43 " --> pdb=" O ILE E 83 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE E 83 " --> pdb=" O GLN E 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 19 through 21 removed outlier: 4.022A pdb=" N LYS F 35 " --> pdb=" O GLU F 21 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP F 70 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N GLN F 79 " --> pdb=" O ASP F 70 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N GLN F 102 " --> pdb=" O GLU F 93 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA F 95 " --> pdb=" O HIS F 100 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N HIS F 100 " --> pdb=" O ALA F 95 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY F 139 " --> pdb=" O GLY F 126 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ALA F 149 " --> pdb=" O THR F 140 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LYS F 162 " --> pdb=" O PRO F 171 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N CYS F 180 " --> pdb=" O PHE F 176 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 32 through 33 Processing sheet with id=AA8, first strand: chain 'G' and resid 441 through 442 removed outlier: 6.728A pdb=" N TYR G 365 " --> pdb=" O LYS G 357 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LYS G 357 " --> pdb=" O TYR G 365 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL G 367 " --> pdb=" O TRP G 355 " (cutoff:3.500A) removed outlier: 9.435A pdb=" N ASN G 644 " --> pdb=" O ARG G 353 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N TRP G 355 " --> pdb=" O ASN G 644 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR G 646 " --> pdb=" O TRP G 355 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY G 648 " --> pdb=" O LYS G 357 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 496 through 498 Processing sheet with id=AB1, first strand: chain 'G' and resid 502 through 503 removed outlier: 3.836A pdb=" N GLU G 522 " --> pdb=" O GLN G 503 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 609 through 613 removed outlier: 3.703A pdb=" N SER G 613 " --> pdb=" O ILE G 622 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE G 622 " --> pdb=" O SER G 613 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 83 through 84 removed outlier: 3.533A pdb=" N GLY H 62 " --> pdb=" O LYS H 72 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N GLN H 61 " --> pdb=" O PHE H 46 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N PHE H 46 " --> pdb=" O GLN H 61 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N LEU H 63 " --> pdb=" O VAL H 44 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N VAL H 44 " --> pdb=" O LEU H 63 " (cutoff:3.500A) removed outlier: 14.131A pdb=" N TYR H 258 " --> pdb=" O ARG H 43 " (cutoff:3.500A) removed outlier: 9.858A pdb=" N LEU H 45 " --> pdb=" O TYR H 258 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N TYR H 260 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N TRP H 47 " --> pdb=" O TYR H 260 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY H 264 " --> pdb=" O ARG H 49 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ASN H 257 " --> pdb=" O ALA H 252 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY H 259 " --> pdb=" O TYR H 250 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR H 250 " --> pdb=" O GLY H 259 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N LEU H 247 " --> pdb=" O SER H 241 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 110 through 111 removed outlier: 3.574A pdb=" N ILE H 134 " --> pdb=" O TYR H 111 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 154 through 155 Processing sheet with id=AB6, first strand: chain 'H' and resid 159 through 161 Processing sheet with id=AB7, first strand: chain 'S' and resid 441 through 442 removed outlier: 7.055A pdb=" N TYR S 365 " --> pdb=" O GLY S 356 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLY S 356 " --> pdb=" O TYR S 365 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL S 367 " --> pdb=" O PHE S 354 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N PHE S 354 " --> pdb=" O VAL S 367 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLU S 369 " --> pdb=" O CYS S 352 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N CYS S 352 " --> pdb=" O GLU S 369 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLU S 371 " --> pdb=" O GLN S 350 " (cutoff:3.500A) removed outlier: 15.844A pdb=" N PHE S 642 " --> pdb=" O ARG S 351 " (cutoff:3.500A) removed outlier: 11.067A pdb=" N ARG S 353 " --> pdb=" O PHE S 642 " (cutoff:3.500A) removed outlier: 9.566A pdb=" N ASN S 644 " --> pdb=" O ARG S 353 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N TRP S 355 " --> pdb=" O ASN S 644 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR S 646 " --> pdb=" O TRP S 355 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY S 648 " --> pdb=" O LYS S 357 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ALA S 633 " --> pdb=" O SER S 627 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER S 637 " --> pdb=" O ALA S 623 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'S' and resid 496 through 498 Processing sheet with id=AB9, first strand: chain 'c' and resid 83 through 84 removed outlier: 3.564A pdb=" N SER c 83 " --> pdb=" O TYR c 75 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS c 72 " --> pdb=" O GLY c 62 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY c 62 " --> pdb=" O LYS c 72 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLN c 61 " --> pdb=" O PHE c 46 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N PHE c 46 " --> pdb=" O GLN c 61 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N LEU c 63 " --> pdb=" O VAL c 44 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N VAL c 44 " --> pdb=" O LEU c 63 " (cutoff:3.500A) removed outlier: 12.628A pdb=" N TYR c 260 " --> pdb=" O ARG c 43 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N LEU c 45 " --> pdb=" O TYR c 260 " (cutoff:3.500A) removed outlier: 9.703A pdb=" N TYR c 262 " --> pdb=" O LEU c 45 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N TRP c 47 " --> pdb=" O TYR c 262 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N GLY c 264 " --> pdb=" O TRP c 47 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ARG c 49 " --> pdb=" O GLY c 264 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'c' and resid 110 through 112 Processing sheet with id=AC2, first strand: chain 'c' and resid 153 through 155 Processing sheet with id=AC3, first strand: chain 'c' and resid 159 through 160 removed outlier: 4.026A pdb=" N PHE c 160 " --> pdb=" O HIS c 168 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N HIS c 168 " --> pdb=" O PHE c 160 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'c' and resid 226 through 231 Processing sheet with id=AC5, first strand: chain 'I' and resid 19 through 24 removed outlier: 3.714A pdb=" N GLU I 19 " --> pdb=" O ARG I 37 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS I 35 " --> pdb=" O GLU I 21 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLU I 23 " --> pdb=" O HIS I 33 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N HIS I 33 " --> pdb=" O GLU I 23 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER I 47 " --> pdb=" O GLN I 56 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLN I 56 " --> pdb=" O SER I 47 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLU I 49 " --> pdb=" O HIS I 54 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N HIS I 54 " --> pdb=" O GLU I 49 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLN I 79 " --> pdb=" O ASP I 70 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N GLN I 102 " --> pdb=" O GLU I 93 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N GLN I 125 " --> pdb=" O GLU I 116 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR I 140 " --> pdb=" O ALA I 149 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ALA I 149 " --> pdb=" O THR I 140 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY I 161 " --> pdb=" O ALA I 150 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS I 162 " --> pdb=" O PRO I 171 " (cutoff:3.500A) 633 hydrogen bonds defined for protein. 1761 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.27 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5446 1.34 - 1.46: 4398 1.46 - 1.59: 8092 1.59 - 1.71: 2 1.71 - 1.83: 113 Bond restraints: 18051 Sorted by residual: bond pdb=" CG PRO G 448 " pdb=" CD PRO G 448 " ideal model delta sigma weight residual 1.503 1.272 0.231 3.40e-02 8.65e+02 4.63e+01 bond pdb=" C ASP H 106 " pdb=" N PRO H 107 " ideal model delta sigma weight residual 1.334 1.403 -0.069 2.34e-02 1.83e+03 8.73e+00 bond pdb=" C LEU C 302 " pdb=" N THR C 303 " ideal model delta sigma weight residual 1.331 1.388 -0.057 2.07e-02 2.33e+03 7.68e+00 bond pdb=" CB PRO G 606 " pdb=" CG PRO G 606 " ideal model delta sigma weight residual 1.492 1.624 -0.132 5.00e-02 4.00e+02 6.98e+00 bond pdb=" CA ARG B 225 " pdb=" C ARG B 225 " ideal model delta sigma weight residual 1.528 1.493 0.035 1.37e-02 5.33e+03 6.35e+00 ... (remaining 18046 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.97: 24335 5.97 - 11.95: 115 11.95 - 17.92: 11 17.92 - 23.90: 4 23.90 - 29.87: 4 Bond angle restraints: 24469 Sorted by residual: angle pdb=" CA PRO G 448 " pdb=" N PRO G 448 " pdb=" CD PRO G 448 " ideal model delta sigma weight residual 112.00 84.11 27.89 1.40e+00 5.10e-01 3.97e+02 angle pdb=" C THR c 255 " pdb=" N LYS c 256 " pdb=" CA LYS c 256 " ideal model delta sigma weight residual 121.70 151.57 -29.87 1.80e+00 3.09e-01 2.75e+02 angle pdb=" C HIS c 251 " pdb=" N ALA c 252 " pdb=" CA ALA c 252 " ideal model delta sigma weight residual 121.70 150.29 -28.59 1.80e+00 3.09e-01 2.52e+02 angle pdb=" C SER G 637 " pdb=" N ASN G 638 " pdb=" CA ASN G 638 " ideal model delta sigma weight residual 121.70 148.46 -26.76 1.80e+00 3.09e-01 2.21e+02 angle pdb=" C LYS H 183 " pdb=" N LEU H 184 " pdb=" CA LEU H 184 " ideal model delta sigma weight residual 121.70 142.09 -20.39 1.80e+00 3.09e-01 1.28e+02 ... (remaining 24464 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.11: 9122 18.11 - 36.22: 1203 36.22 - 54.32: 335 54.32 - 72.43: 52 72.43 - 90.54: 25 Dihedral angle restraints: 10737 sinusoidal: 4430 harmonic: 6307 Sorted by residual: dihedral pdb=" CA LYS c 256 " pdb=" C LYS c 256 " pdb=" N ASN c 257 " pdb=" CA ASN c 257 " ideal model delta harmonic sigma weight residual 180.00 152.16 27.84 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA PHE B 213 " pdb=" C PHE B 213 " pdb=" N ILE B 214 " pdb=" CA ILE B 214 " ideal model delta harmonic sigma weight residual 180.00 154.73 25.27 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA TYR G 472 " pdb=" C TYR G 472 " pdb=" N PRO G 473 " pdb=" CA PRO G 473 " ideal model delta harmonic sigma weight residual 180.00 155.83 24.17 0 5.00e+00 4.00e-02 2.34e+01 ... (remaining 10734 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 2202 0.072 - 0.145: 341 0.145 - 0.217: 35 0.217 - 0.290: 5 0.290 - 0.362: 2 Chirality restraints: 2585 Sorted by residual: chirality pdb=" CG LEU c 29 " pdb=" CB LEU c 29 " pdb=" CD1 LEU c 29 " pdb=" CD2 LEU c 29 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" CB ILE G 676 " pdb=" CA ILE G 676 " pdb=" CG1 ILE G 676 " pdb=" CG2 ILE G 676 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CA PRO G 606 " pdb=" N PRO G 606 " pdb=" C PRO G 606 " pdb=" CB PRO G 606 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 2582 not shown) Planarity restraints: 3186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR G 447 " 0.161 5.00e-02 4.00e+02 2.08e-01 6.91e+01 pdb=" N PRO G 448 " -0.357 5.00e-02 4.00e+02 pdb=" CA PRO G 448 " 0.108 5.00e-02 4.00e+02 pdb=" CD PRO G 448 " 0.088 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 283 " 0.092 5.00e-02 4.00e+02 1.37e-01 2.99e+01 pdb=" N PRO B 284 " -0.236 5.00e-02 4.00e+02 pdb=" CA PRO B 284 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO B 284 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 166 " -0.069 5.00e-02 4.00e+02 1.03e-01 1.69e+01 pdb=" N PRO E 167 " 0.178 5.00e-02 4.00e+02 pdb=" CA PRO E 167 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO E 167 " -0.057 5.00e-02 4.00e+02 ... (remaining 3183 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4779 2.81 - 3.33: 14187 3.33 - 3.86: 30074 3.86 - 4.38: 33436 4.38 - 4.90: 58224 Nonbonded interactions: 140700 Sorted by model distance: nonbonded pdb=" OG1 THR B 246 " pdb=" OE2 GLU H 81 " model vdw 2.290 3.040 nonbonded pdb=" OH TYR F 44 " pdb=" O SER F 47 " model vdw 2.293 3.040 nonbonded pdb=" O ALA G 449 " pdb=" OG1 THR G 453 " model vdw 2.300 3.040 nonbonded pdb=" O ASP G 241 " pdb=" OH TYR S 216 " model vdw 2.317 3.040 nonbonded pdb=" OG SER G 683 " pdb=" OE1 GLU G 685 " model vdw 2.320 3.040 ... (remaining 140695 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 'F' selection = chain 'I' } ncs_group { reference = chain 'G' selection = (chain 'S' and (resid 206 through 261 or resid 273 through 377 or resid 413 thro \ ugh 693)) } ncs_group { reference = chain 'H' selection = (chain 'c' and (resid 1 through 113 or resid 133 through 276)) } 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: 15.190 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: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 13.490 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 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 : 0.005 0.231 18051 Z= 0.230 Angle : 1.119 29.869 24469 Z= 0.595 Chirality : 0.054 0.362 2585 Planarity : 0.010 0.208 3186 Dihedral : 17.825 90.538 6707 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.23 % Favored : 95.73 % Rotamer: Outliers : 0.74 % Allowed : 28.51 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.59 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.34 (0.16), residues: 2129 helix: -2.11 (0.17), residues: 526 sheet: -1.22 (0.26), residues: 380 loop : -1.37 (0.16), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG c 37 TYR 0.045 0.002 TYR F 44 PHE 0.035 0.002 PHE c 213 TRP 0.013 0.002 TRP A 36 HIS 0.019 0.001 HIS F 77 Details of bonding type rmsd covalent geometry : bond 0.00518 (18051) covalent geometry : angle 1.11902 (24469) hydrogen bonds : bond 0.21088 ( 633) hydrogen bonds : angle 8.69453 ( 1761) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 498 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.7571 (ttt180) cc_final: 0.7354 (ttt180) REVERT: E 97 MET cc_start: 0.6297 (tpp) cc_final: 0.5870 (ttm) REVERT: G 256 GLN cc_start: 0.8195 (mp10) cc_final: 0.7942 (mp-120) REVERT: G 341 LYS cc_start: 0.8343 (tttp) cc_final: 0.7684 (tttp) REVERT: G 675 GLU cc_start: 0.7317 (tm-30) cc_final: 0.7052 (tp30) REVERT: S 211 GLN cc_start: 0.8466 (mt0) cc_final: 0.8218 (mt0) REVERT: S 212 ASN cc_start: 0.8338 (m-40) cc_final: 0.8136 (m-40) REVERT: S 345 ASP cc_start: 0.7873 (m-30) cc_final: 0.7525 (m-30) REVERT: S 466 ASP cc_start: 0.7466 (t0) cc_final: 0.7123 (t0) REVERT: I 66 ARG cc_start: 0.7253 (ttm170) cc_final: 0.7002 (ttm-80) REVERT: I 75 LYS cc_start: 0.8197 (mtmm) cc_final: 0.7894 (mtmm) outliers start: 14 outliers final: 11 residues processed: 503 average time/residue: 0.1311 time to fit residues: 94.8575 Evaluate side-chains 490 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 479 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 225 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 269 TYR Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain G residue 470 ILE Chi-restraints excluded: chain H residue 271 ASP Chi-restraints excluded: chain c residue 23 ASP Chi-restraints excluded: chain c residue 214 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.0980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.0060 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 0.9980 chunk 212 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 297 GLN E 87 HIS F 77 HIS G 347 HIS H 133 GLN H 257 ASN S 211 GLN S 481 ASN S 651 HIS c 61 GLN c 67 GLN c 109 HIS c 269 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.139144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.120470 restraints weight = 31855.614| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.59 r_work: 0.3487 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 18051 Z= 0.181 Angle : 0.673 13.549 24469 Z= 0.347 Chirality : 0.044 0.177 2585 Planarity : 0.007 0.120 3186 Dihedral : 5.685 55.882 2423 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.80 % Favored : 96.10 % Rotamer: Outliers : 4.28 % Allowed : 25.55 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.59 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.17), residues: 2129 helix: -0.57 (0.21), residues: 549 sheet: -0.93 (0.25), residues: 388 loop : -1.07 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 224 TYR 0.014 0.002 TYR H 262 PHE 0.014 0.001 PHE c 213 TRP 0.018 0.001 TRP A 36 HIS 0.006 0.001 HIS c 109 Details of bonding type rmsd covalent geometry : bond 0.00408 (18051) covalent geometry : angle 0.67267 (24469) hydrogen bonds : bond 0.04262 ( 633) hydrogen bonds : angle 5.86723 ( 1761) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 517 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 44 TYR cc_start: 0.8245 (t80) cc_final: 0.7946 (t80) REVERT: F 193 ARG cc_start: 0.8086 (ttt180) cc_final: 0.7840 (ttt180) REVERT: G 233 SER cc_start: 0.7865 (t) cc_final: 0.7520 (p) REVERT: G 252 GLU cc_start: 0.7257 (tp30) cc_final: 0.6628 (tp30) REVERT: G 256 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7596 (mm-40) REVERT: G 281 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7394 (mt-10) REVERT: G 341 LYS cc_start: 0.8349 (tttp) cc_final: 0.8076 (tttp) REVERT: G 619 GLN cc_start: 0.7707 (pm20) cc_final: 0.7476 (pm20) REVERT: G 626 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7680 (mtm-85) REVERT: G 688 GLN cc_start: 0.7757 (pp30) cc_final: 0.7555 (pp30) REVERT: H 6 LEU cc_start: 0.7892 (mt) cc_final: 0.7525 (mp) REVERT: H 68 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8498 (mm) REVERT: H 216 SER cc_start: 0.8324 (t) cc_final: 0.7905 (p) REVERT: H 258 TYR cc_start: 0.8304 (p90) cc_final: 0.8057 (p90) REVERT: S 211 GLN cc_start: 0.8631 (mt0) cc_final: 0.8417 (mt0) REVERT: S 284 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7165 (mm-30) REVERT: S 332 GLU cc_start: 0.7718 (tp30) cc_final: 0.7375 (tp30) REVERT: S 336 VAL cc_start: 0.8701 (OUTLIER) cc_final: 0.8500 (t) REVERT: S 345 ASP cc_start: 0.7817 (m-30) cc_final: 0.7507 (m-30) REVERT: S 419 GLU cc_start: 0.4510 (mt-10) cc_final: 0.3972 (mt-10) REVERT: S 466 ASP cc_start: 0.7455 (t0) cc_final: 0.7116 (t0) REVERT: S 622 ILE cc_start: 0.8014 (mm) cc_final: 0.7756 (tp) REVERT: S 687 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7218 (mt-10) REVERT: c 24 ARG cc_start: 0.8163 (mmt180) cc_final: 0.7932 (mmt-90) REVERT: c 29 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7919 (mm) REVERT: I 75 LYS cc_start: 0.8319 (mtmm) cc_final: 0.8069 (mtmm) REVERT: I 79 GLN cc_start: 0.8504 (tp40) cc_final: 0.8278 (mm-40) REVERT: I 193 ARG cc_start: 0.8046 (ttt-90) cc_final: 0.7675 (mtt-85) outliers start: 81 outliers final: 52 residues processed: 549 average time/residue: 0.1325 time to fit residues: 104.4285 Evaluate side-chains 553 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 496 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 297 GLN Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 323 ARG Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain E residue 5 MET Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 256 GLN Chi-restraints excluded: chain G residue 286 GLN Chi-restraints excluded: chain G residue 290 PHE Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 357 LYS Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 523 GLU Chi-restraints excluded: chain G residue 546 VAL Chi-restraints excluded: chain G residue 626 ARG Chi-restraints excluded: chain G residue 638 ASN Chi-restraints excluded: chain G residue 655 VAL Chi-restraints excluded: chain G residue 683 SER Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 79 CYS Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 271 ASP Chi-restraints excluded: chain H residue 276 LEU Chi-restraints excluded: chain S residue 205 MET Chi-restraints excluded: chain S residue 251 ILE Chi-restraints excluded: chain S residue 336 VAL Chi-restraints excluded: chain S residue 350 GLN Chi-restraints excluded: chain S residue 470 ILE Chi-restraints excluded: chain S residue 692 MET Chi-restraints excluded: chain c residue 29 LEU Chi-restraints excluded: chain c residue 68 LEU Chi-restraints excluded: chain c residue 94 MET Chi-restraints excluded: chain c residue 178 LEU Chi-restraints excluded: chain c residue 214 LEU Chi-restraints excluded: chain c residue 220 ASP Chi-restraints excluded: chain c residue 261 ILE Chi-restraints excluded: chain c residue 267 GLU Chi-restraints excluded: chain I residue 62 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 170 optimal weight: 0.9990 chunk 166 optimal weight: 0.5980 chunk 33 optimal weight: 0.0770 chunk 159 optimal weight: 0.9990 chunk 178 optimal weight: 0.9980 chunk 185 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 43 GLN E 155 GLN E 162 ASN G 256 GLN H 61 GLN S 531 GLN S 651 HIS c 18 GLN I 56 GLN I 183 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.133222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.114087 restraints weight = 31851.061| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.58 r_work: 0.3366 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 18051 Z= 0.225 Angle : 0.681 14.354 24469 Z= 0.351 Chirality : 0.045 0.182 2585 Planarity : 0.006 0.084 3186 Dihedral : 5.252 55.292 2405 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.85 % Favored : 96.10 % Rotamer: Outliers : 5.49 % Allowed : 24.08 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.54 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 aren not related in a simple way. whole: -1.12 (0.18), residues: 2129 helix: -0.05 (0.22), residues: 555 sheet: -1.28 (0.24), residues: 435 loop : -0.79 (0.18), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 49 TYR 0.023 0.002 TYR F 20 PHE 0.016 0.002 PHE c 213 TRP 0.022 0.001 TRP A 36 HIS 0.008 0.001 HIS F 154 Details of bonding type rmsd covalent geometry : bond 0.00512 (18051) covalent geometry : angle 0.68101 (24469) hydrogen bonds : bond 0.04074 ( 633) hydrogen bonds : angle 5.47634 ( 1761) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 527 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 ILE cc_start: 0.7358 (mm) cc_final: 0.6986 (tp) REVERT: B 271 LYS cc_start: 0.8325 (ptmm) cc_final: 0.8102 (ttmm) REVERT: F 20 TYR cc_start: 0.8278 (t80) cc_final: 0.7817 (t80) REVERT: F 89 ARG cc_start: 0.8303 (ttp80) cc_final: 0.7946 (ttp-110) REVERT: F 106 TYR cc_start: 0.8445 (m-80) cc_final: 0.8052 (m-80) REVERT: F 158 ARG cc_start: 0.8156 (ptp-170) cc_final: 0.7818 (ptp90) REVERT: F 198 GLU cc_start: 0.6936 (mt-10) cc_final: 0.6195 (tt0) REVERT: G 281 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7424 (mt-10) REVERT: G 314 VAL cc_start: 0.7910 (OUTLIER) cc_final: 0.7609 (t) REVERT: G 341 LYS cc_start: 0.8328 (tttp) cc_final: 0.7990 (tttp) REVERT: G 619 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7763 (pm20) REVERT: G 675 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7402 (tp30) REVERT: G 688 GLN cc_start: 0.7911 (pp30) cc_final: 0.7481 (pp30) REVERT: H 6 LEU cc_start: 0.7903 (mt) cc_final: 0.7677 (mp) REVERT: H 98 VAL cc_start: 0.8236 (m) cc_final: 0.7952 (p) REVERT: H 216 SER cc_start: 0.8567 (t) cc_final: 0.8247 (p) REVERT: S 281 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7384 (mm-30) REVERT: S 284 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7517 (mm-30) REVERT: S 332 GLU cc_start: 0.7834 (tp30) cc_final: 0.7583 (tp30) REVERT: S 353 ARG cc_start: 0.8491 (ptt90) cc_final: 0.8089 (ptt90) REVERT: S 617 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8453 (mm) REVERT: S 622 ILE cc_start: 0.8073 (mm) cc_final: 0.7586 (pt) REVERT: S 640 LYS cc_start: 0.8166 (mttm) cc_final: 0.7773 (mttm) REVERT: S 687 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7332 (mt-10) REVERT: c 24 ARG cc_start: 0.8196 (mmt180) cc_final: 0.7928 (mmt-90) REVERT: c 29 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7993 (mm) REVERT: I 75 LYS cc_start: 0.8370 (mtmm) cc_final: 0.8120 (mtmm) REVERT: I 193 ARG cc_start: 0.8148 (ttt-90) cc_final: 0.7775 (mtt-85) outliers start: 104 outliers final: 65 residues processed: 576 average time/residue: 0.1476 time to fit residues: 120.7879 Evaluate side-chains 584 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 515 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 31 GLN Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 286 GLN Chi-restraints excluded: chain G residue 290 PHE Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 357 LYS Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain G residue 433 CYS Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 523 GLU Chi-restraints excluded: chain G residue 592 LEU Chi-restraints excluded: chain G residue 619 GLN Chi-restraints excluded: chain G residue 638 ASN Chi-restraints excluded: chain G residue 655 VAL Chi-restraints excluded: chain G residue 683 SER Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 261 ILE Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 271 ASP Chi-restraints excluded: chain H residue 276 LEU Chi-restraints excluded: chain S residue 216 TYR Chi-restraints excluded: chain S residue 251 ILE Chi-restraints excluded: chain S residue 457 ILE Chi-restraints excluded: chain S residue 526 ASP Chi-restraints excluded: chain S residue 617 ILE Chi-restraints excluded: chain S residue 692 MET Chi-restraints excluded: chain c residue 29 LEU Chi-restraints excluded: chain c residue 54 VAL Chi-restraints excluded: chain c residue 68 LEU Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain c residue 143 ILE Chi-restraints excluded: chain c residue 181 VAL Chi-restraints excluded: chain c residue 214 LEU Chi-restraints excluded: chain c residue 220 ASP Chi-restraints excluded: chain c residue 261 ILE Chi-restraints excluded: chain c residue 267 GLU Chi-restraints excluded: chain I residue 49 GLU Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain I residue 136 LYS Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain I residue 156 ASN Chi-restraints excluded: chain I residue 180 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 42 optimal weight: 0.0870 chunk 45 optimal weight: 0.9980 chunk 127 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 198 optimal weight: 0.0970 chunk 66 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 95 optimal weight: 0.0470 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 297 GLN E 43 GLN F 77 HIS F 157 HIS ** G 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 211 GLN S 350 GLN S 651 HIS c 109 HIS c 113 HIS c 229 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.132506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.113681 restraints weight = 31540.685| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.53 r_work: 0.3370 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 18051 Z= 0.187 Angle : 0.649 13.783 24469 Z= 0.332 Chirality : 0.044 0.195 2585 Planarity : 0.005 0.070 3186 Dihedral : 5.202 59.000 2405 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.71 % Favored : 96.20 % Rotamer: Outliers : 5.60 % Allowed : 25.24 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.54 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 aren not related in a simple way. whole: -0.92 (0.18), residues: 2129 helix: 0.24 (0.22), residues: 554 sheet: -1.25 (0.25), residues: 417 loop : -0.71 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG c 156 TYR 0.020 0.002 TYR B 234 PHE 0.021 0.001 PHE c 213 TRP 0.018 0.001 TRP A 36 HIS 0.005 0.001 HIS F 77 Details of bonding type rmsd covalent geometry : bond 0.00431 (18051) covalent geometry : angle 0.64872 (24469) hydrogen bonds : bond 0.03672 ( 633) hydrogen bonds : angle 5.27437 ( 1761) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 540 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 ILE cc_start: 0.7344 (mm) cc_final: 0.6977 (tp) REVERT: B 234 TYR cc_start: 0.8209 (t80) cc_final: 0.7948 (t80) REVERT: B 262 ASN cc_start: 0.8757 (m-40) cc_final: 0.8502 (m110) REVERT: E 142 MET cc_start: 0.8628 (tpp) cc_final: 0.8349 (tpp) REVERT: F 20 TYR cc_start: 0.8273 (t80) cc_final: 0.7933 (t80) REVERT: F 106 TYR cc_start: 0.8578 (m-80) cc_final: 0.7986 (m-80) REVERT: F 158 ARG cc_start: 0.8170 (ptp-170) cc_final: 0.7913 (ptp-170) REVERT: G 252 GLU cc_start: 0.7571 (tp30) cc_final: 0.7044 (tp30) REVERT: G 281 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7465 (mt-10) REVERT: G 314 VAL cc_start: 0.8009 (OUTLIER) cc_final: 0.7698 (t) REVERT: G 320 TYR cc_start: 0.8149 (m-10) cc_final: 0.7604 (m-10) REVERT: G 326 VAL cc_start: 0.8197 (OUTLIER) cc_final: 0.7859 (p) REVERT: G 341 LYS cc_start: 0.8325 (tttp) cc_final: 0.8042 (tttp) REVERT: G 451 ILE cc_start: 0.5506 (OUTLIER) cc_final: 0.4949 (mt) REVERT: G 466 ASP cc_start: 0.7537 (t0) cc_final: 0.7168 (t0) REVERT: G 626 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.7754 (mtm-85) REVERT: G 688 GLN cc_start: 0.7856 (pp30) cc_final: 0.7582 (pp30) REVERT: H 98 VAL cc_start: 0.8247 (m) cc_final: 0.7957 (p) REVERT: H 216 SER cc_start: 0.8557 (t) cc_final: 0.8270 (p) REVERT: S 238 LYS cc_start: 0.8122 (mtpp) cc_final: 0.7805 (ttpp) REVERT: S 282 ILE cc_start: 0.8218 (pt) cc_final: 0.7940 (pt) REVERT: S 284 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7434 (mm-30) REVERT: S 330 THR cc_start: 0.8011 (p) cc_final: 0.7635 (m) REVERT: S 332 GLU cc_start: 0.7834 (tp30) cc_final: 0.7536 (tp30) REVERT: S 345 ASP cc_start: 0.7867 (m-30) cc_final: 0.7548 (m-30) REVERT: S 419 GLU cc_start: 0.4824 (mt-10) cc_final: 0.4616 (mp0) REVERT: S 466 ASP cc_start: 0.7484 (t0) cc_final: 0.7174 (t0) REVERT: S 470 ILE cc_start: 0.7572 (OUTLIER) cc_final: 0.7328 (mm) REVERT: S 479 GLU cc_start: 0.7656 (tt0) cc_final: 0.7227 (tt0) REVERT: S 587 GLU cc_start: 0.7878 (pt0) cc_final: 0.7239 (pt0) REVERT: S 622 ILE cc_start: 0.8123 (mm) cc_final: 0.7701 (pt) REVERT: S 640 LYS cc_start: 0.8186 (mttm) cc_final: 0.7791 (mttm) REVERT: c 24 ARG cc_start: 0.8195 (mmt180) cc_final: 0.7955 (mmt-90) REVERT: c 29 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7970 (mm) REVERT: c 34 LEU cc_start: 0.7966 (mt) cc_final: 0.7631 (mt) REVERT: c 139 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7362 (ttt-90) REVERT: I 75 LYS cc_start: 0.8360 (mtmm) cc_final: 0.8112 (mtmm) REVERT: I 91 GLU cc_start: 0.7388 (mp0) cc_final: 0.7130 (mp0) REVERT: I 193 ARG cc_start: 0.8107 (ttt-90) cc_final: 0.7707 (mtt-85) outliers start: 106 outliers final: 66 residues processed: 586 average time/residue: 0.1377 time to fit residues: 115.1371 Evaluate side-chains 603 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 530 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 297 GLN Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 31 GLN Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 199 GLU Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 257 ASP Chi-restraints excluded: chain G residue 286 GLN Chi-restraints excluded: chain G residue 290 PHE Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 357 LYS Chi-restraints excluded: chain G residue 371 GLU Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 451 ILE Chi-restraints excluded: chain G residue 592 LEU Chi-restraints excluded: chain G residue 619 GLN Chi-restraints excluded: chain G residue 626 ARG Chi-restraints excluded: chain G residue 638 ASN Chi-restraints excluded: chain G residue 655 VAL Chi-restraints excluded: chain G residue 677 THR Chi-restraints excluded: chain G residue 683 SER Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 261 ILE Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 271 ASP Chi-restraints excluded: chain H residue 275 MET Chi-restraints excluded: chain H residue 276 LEU Chi-restraints excluded: chain S residue 205 MET Chi-restraints excluded: chain S residue 216 TYR Chi-restraints excluded: chain S residue 251 ILE Chi-restraints excluded: chain S residue 432 VAL Chi-restraints excluded: chain S residue 447 THR Chi-restraints excluded: chain S residue 470 ILE Chi-restraints excluded: chain S residue 614 SER Chi-restraints excluded: chain S residue 692 MET Chi-restraints excluded: chain c residue 23 ASP Chi-restraints excluded: chain c residue 29 LEU Chi-restraints excluded: chain c residue 110 GLU Chi-restraints excluded: chain c residue 138 THR Chi-restraints excluded: chain c residue 139 ARG Chi-restraints excluded: chain c residue 143 ILE Chi-restraints excluded: chain c residue 214 LEU Chi-restraints excluded: chain c residue 229 GLN Chi-restraints excluded: chain c residue 261 ILE Chi-restraints excluded: chain c residue 267 GLU Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 120 HIS Chi-restraints excluded: chain I residue 136 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 86 optimal weight: 0.6980 chunk 90 optimal weight: 0.7980 chunk 192 optimal weight: 0.8980 chunk 181 optimal weight: 0.9990 chunk 29 optimal weight: 0.0010 chunk 151 optimal weight: 0.6980 chunk 11 optimal weight: 0.1980 chunk 153 optimal weight: 0.5980 chunk 79 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 201 optimal weight: 1.9990 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 77 HIS ** G 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 GLN S 350 GLN S 651 HIS c 109 HIS c 229 GLN I 183 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.132050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.113361 restraints weight = 31332.592| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.49 r_work: 0.3364 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18051 Z= 0.186 Angle : 0.647 13.864 24469 Z= 0.330 Chirality : 0.044 0.202 2585 Planarity : 0.005 0.070 3186 Dihedral : 5.125 58.769 2404 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.04 % Favored : 95.87 % Rotamer: Outliers : 6.02 % Allowed : 25.50 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.54 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 aren not related in a simple way. whole: -0.83 (0.18), residues: 2129 helix: 0.37 (0.22), residues: 555 sheet: -1.26 (0.25), residues: 418 loop : -0.65 (0.18), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 66 TYR 0.015 0.002 TYR B 234 PHE 0.020 0.001 PHE c 213 TRP 0.018 0.001 TRP A 36 HIS 0.005 0.001 HIS F 77 Details of bonding type rmsd covalent geometry : bond 0.00426 (18051) covalent geometry : angle 0.64735 (24469) hydrogen bonds : bond 0.03659 ( 633) hydrogen bonds : angle 5.21507 ( 1761) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 541 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 ILE cc_start: 0.7425 (mm) cc_final: 0.7050 (tp) REVERT: B 231 PHE cc_start: 0.8798 (m-10) cc_final: 0.8461 (m-10) REVERT: B 242 LEU cc_start: 0.6248 (mt) cc_final: 0.5870 (mt) REVERT: C 311 ARG cc_start: 0.6695 (OUTLIER) cc_final: 0.5854 (mtt90) REVERT: D 300 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7239 (mp0) REVERT: F 20 TYR cc_start: 0.8271 (t80) cc_final: 0.7924 (t80) REVERT: F 89 ARG cc_start: 0.8331 (ttp80) cc_final: 0.7997 (ttp-110) REVERT: F 97 ASP cc_start: 0.7247 (OUTLIER) cc_final: 0.6871 (t70) REVERT: G 234 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7847 (tttp) REVERT: G 281 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7514 (mt-10) REVERT: G 284 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7440 (mm-30) REVERT: G 314 VAL cc_start: 0.8106 (OUTLIER) cc_final: 0.7803 (t) REVERT: G 320 TYR cc_start: 0.8248 (m-10) cc_final: 0.7576 (m-10) REVERT: G 326 VAL cc_start: 0.8234 (OUTLIER) cc_final: 0.7955 (p) REVERT: G 341 LYS cc_start: 0.8315 (tttp) cc_final: 0.8063 (tttp) REVERT: G 466 ASP cc_start: 0.7566 (t0) cc_final: 0.7189 (t0) REVERT: G 626 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.7705 (mtm-85) REVERT: G 685 GLU cc_start: 0.8067 (pp20) cc_final: 0.7695 (pp20) REVERT: G 688 GLN cc_start: 0.7841 (pp30) cc_final: 0.7582 (pp30) REVERT: H 98 VAL cc_start: 0.8244 (m) cc_final: 0.7963 (p) REVERT: H 216 SER cc_start: 0.8574 (t) cc_final: 0.8334 (p) REVERT: S 238 LYS cc_start: 0.8124 (mtpp) cc_final: 0.7816 (ttpp) REVERT: S 282 ILE cc_start: 0.8230 (pt) cc_final: 0.7977 (pt) REVERT: S 284 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7456 (mm-30) REVERT: S 330 THR cc_start: 0.8094 (p) cc_final: 0.7735 (m) REVERT: S 332 GLU cc_start: 0.7852 (tp30) cc_final: 0.7546 (tp30) REVERT: S 470 ILE cc_start: 0.7688 (OUTLIER) cc_final: 0.7453 (mm) REVERT: S 479 GLU cc_start: 0.7685 (tt0) cc_final: 0.7178 (tt0) REVERT: S 484 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.7654 (mmm160) REVERT: S 587 GLU cc_start: 0.7972 (pt0) cc_final: 0.7343 (pt0) REVERT: S 622 ILE cc_start: 0.8157 (mm) cc_final: 0.7797 (pt) REVERT: S 640 LYS cc_start: 0.8185 (mttm) cc_final: 0.7794 (mttm) REVERT: S 641 LYS cc_start: 0.8413 (pttt) cc_final: 0.8066 (ptmm) REVERT: c 24 ARG cc_start: 0.8174 (mmt180) cc_final: 0.7883 (mmt-90) REVERT: c 29 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8031 (mm) REVERT: c 37 ARG cc_start: 0.8548 (ttp80) cc_final: 0.7989 (ttp-170) REVERT: c 43 ARG cc_start: 0.8426 (ptt-90) cc_final: 0.8121 (ptt-90) REVERT: c 49 ARG cc_start: 0.8382 (ttp-170) cc_final: 0.8048 (ttp-170) REVERT: I 75 LYS cc_start: 0.8372 (mtmm) cc_final: 0.8121 (mtmm) REVERT: I 167 ASN cc_start: 0.8128 (p0) cc_final: 0.7862 (p0) REVERT: I 191 THR cc_start: 0.8817 (m) cc_final: 0.8350 (p) REVERT: I 193 ARG cc_start: 0.8111 (ttt-90) cc_final: 0.7711 (mtt-85) outliers start: 114 outliers final: 76 residues processed: 593 average time/residue: 0.1446 time to fit residues: 122.3202 Evaluate side-chains 615 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 529 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 297 GLN Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain C residue 311 ARG Chi-restraints excluded: chain D residue 300 GLU Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 88 LYS Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 199 GLU Chi-restraints excluded: chain G residue 234 LYS Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 286 GLN Chi-restraints excluded: chain G residue 290 PHE Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 357 LYS Chi-restraints excluded: chain G residue 371 GLU Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain G residue 433 CYS Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 455 ARG Chi-restraints excluded: chain G residue 619 GLN Chi-restraints excluded: chain G residue 626 ARG Chi-restraints excluded: chain G residue 638 ASN Chi-restraints excluded: chain G residue 655 VAL Chi-restraints excluded: chain G residue 677 THR Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 261 ILE Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 271 ASP Chi-restraints excluded: chain H residue 275 MET Chi-restraints excluded: chain H residue 276 LEU Chi-restraints excluded: chain S residue 205 MET Chi-restraints excluded: chain S residue 216 TYR Chi-restraints excluded: chain S residue 248 VAL Chi-restraints excluded: chain S residue 251 ILE Chi-restraints excluded: chain S residue 275 GLU Chi-restraints excluded: chain S residue 432 VAL Chi-restraints excluded: chain S residue 447 THR Chi-restraints excluded: chain S residue 470 ILE Chi-restraints excluded: chain S residue 484 ARG Chi-restraints excluded: chain S residue 614 SER Chi-restraints excluded: chain S residue 692 MET Chi-restraints excluded: chain c residue 23 ASP Chi-restraints excluded: chain c residue 29 LEU Chi-restraints excluded: chain c residue 54 VAL Chi-restraints excluded: chain c residue 68 LEU Chi-restraints excluded: chain c residue 94 MET Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain c residue 110 GLU Chi-restraints excluded: chain c residue 138 THR Chi-restraints excluded: chain c residue 142 SER Chi-restraints excluded: chain c residue 178 LEU Chi-restraints excluded: chain c residue 181 VAL Chi-restraints excluded: chain c residue 214 LEU Chi-restraints excluded: chain c residue 223 ARG Chi-restraints excluded: chain c residue 251 HIS Chi-restraints excluded: chain c residue 261 ILE Chi-restraints excluded: chain c residue 267 GLU Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 120 HIS Chi-restraints excluded: chain I residue 136 LYS Chi-restraints excluded: chain I residue 180 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 124 optimal weight: 0.1980 chunk 118 optimal weight: 0.9980 chunk 123 optimal weight: 0.4980 chunk 162 optimal weight: 0.6980 chunk 145 optimal weight: 0.5980 chunk 26 optimal weight: 0.3980 chunk 155 optimal weight: 0.0980 chunk 10 optimal weight: 0.7980 chunk 108 optimal weight: 0.8980 chunk 207 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 297 GLN F 77 HIS S 350 GLN S 503 GLN S 651 HIS c 109 HIS c 229 GLN I 145 GLN I 183 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.132003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.113386 restraints weight = 31278.376| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.49 r_work: 0.3361 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18051 Z= 0.165 Angle : 0.649 13.615 24469 Z= 0.329 Chirality : 0.044 0.208 2585 Planarity : 0.005 0.069 3186 Dihedral : 5.089 59.492 2404 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.27 % Favored : 95.68 % Rotamer: Outliers : 5.86 % Allowed : 26.24 % Favored : 67.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.54 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 aren not related in a simple way. whole: -0.79 (0.18), residues: 2129 helix: 0.42 (0.22), residues: 556 sheet: -1.20 (0.26), residues: 416 loop : -0.65 (0.18), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 66 TYR 0.024 0.002 TYR F 44 PHE 0.025 0.001 PHE B 231 TRP 0.016 0.001 TRP A 36 HIS 0.005 0.001 HIS F 77 Details of bonding type rmsd covalent geometry : bond 0.00380 (18051) covalent geometry : angle 0.64925 (24469) hydrogen bonds : bond 0.03535 ( 633) hydrogen bonds : angle 5.16911 ( 1761) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 531 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 ILE cc_start: 0.7470 (mm) cc_final: 0.7090 (tp) REVERT: C 311 ARG cc_start: 0.6665 (OUTLIER) cc_final: 0.5831 (mtt90) REVERT: D 300 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7246 (mp0) REVERT: E 88 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7959 (mtmm) REVERT: E 95 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7235 (mt-10) REVERT: E 142 MET cc_start: 0.8585 (tpp) cc_final: 0.8341 (tpp) REVERT: E 161 ILE cc_start: 0.7916 (mt) cc_final: 0.7646 (mm) REVERT: E 188 LEU cc_start: 0.7974 (tp) cc_final: 0.7747 (tp) REVERT: F 20 TYR cc_start: 0.8259 (t80) cc_final: 0.7976 (t80) REVERT: F 60 LYS cc_start: 0.8589 (mttm) cc_final: 0.8377 (mttt) REVERT: F 89 ARG cc_start: 0.8330 (ttp80) cc_final: 0.7998 (ttp-110) REVERT: F 97 ASP cc_start: 0.7222 (OUTLIER) cc_final: 0.6861 (t70) REVERT: G 233 SER cc_start: 0.8025 (m) cc_final: 0.7696 (p) REVERT: G 281 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7532 (mt-10) REVERT: G 284 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7503 (mm-30) REVERT: G 314 VAL cc_start: 0.8100 (OUTLIER) cc_final: 0.7779 (t) REVERT: G 320 TYR cc_start: 0.8294 (m-10) cc_final: 0.7754 (m-10) REVERT: G 326 VAL cc_start: 0.8166 (OUTLIER) cc_final: 0.7937 (p) REVERT: G 341 LYS cc_start: 0.8306 (tttp) cc_final: 0.8074 (tttp) REVERT: G 466 ASP cc_start: 0.7527 (t0) cc_final: 0.7172 (t0) REVERT: G 626 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.7661 (mtm-85) REVERT: G 685 GLU cc_start: 0.8059 (pp20) cc_final: 0.7694 (pp20) REVERT: G 688 GLN cc_start: 0.7824 (pp30) cc_final: 0.7591 (pp30) REVERT: H 98 VAL cc_start: 0.8254 (m) cc_final: 0.7974 (p) REVERT: H 137 GLU cc_start: 0.7889 (tt0) cc_final: 0.7591 (mt-10) REVERT: S 238 LYS cc_start: 0.8089 (mtpp) cc_final: 0.7806 (ttpp) REVERT: S 282 ILE cc_start: 0.8243 (pt) cc_final: 0.7973 (pt) REVERT: S 284 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7434 (mm-30) REVERT: S 330 THR cc_start: 0.8107 (p) cc_final: 0.7779 (m) REVERT: S 332 GLU cc_start: 0.7838 (tp30) cc_final: 0.7512 (tp30) REVERT: S 353 ARG cc_start: 0.8687 (ptt90) cc_final: 0.8469 (ptt90) REVERT: S 470 ILE cc_start: 0.7722 (OUTLIER) cc_final: 0.7479 (mm) REVERT: S 479 GLU cc_start: 0.7700 (tt0) cc_final: 0.7139 (tt0) REVERT: S 484 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.7661 (mmm160) REVERT: S 587 GLU cc_start: 0.7984 (pt0) cc_final: 0.7335 (pt0) REVERT: S 622 ILE cc_start: 0.8176 (mm) cc_final: 0.7848 (pt) REVERT: S 640 LYS cc_start: 0.8149 (mttm) cc_final: 0.7762 (mttm) REVERT: S 641 LYS cc_start: 0.8421 (pttt) cc_final: 0.8081 (ptmm) REVERT: c 24 ARG cc_start: 0.8169 (mmt180) cc_final: 0.7889 (mmt-90) REVERT: c 29 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8071 (mm) REVERT: c 37 ARG cc_start: 0.8541 (ttp80) cc_final: 0.7945 (ttp-170) REVERT: c 43 ARG cc_start: 0.8423 (ptt-90) cc_final: 0.8102 (ptt-90) REVERT: c 49 ARG cc_start: 0.8399 (ttp-170) cc_final: 0.8038 (ttp-170) REVERT: c 136 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.7145 (tp30) REVERT: c 139 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.7497 (ttt-90) REVERT: I 45 GLU cc_start: 0.7052 (tt0) cc_final: 0.6765 (mt-10) REVERT: I 75 LYS cc_start: 0.8379 (mtmm) cc_final: 0.8132 (mtmm) REVERT: I 76 LYS cc_start: 0.8863 (mttp) cc_final: 0.8521 (mttp) REVERT: I 167 ASN cc_start: 0.8100 (p0) cc_final: 0.7783 (p0) REVERT: I 191 THR cc_start: 0.8808 (m) cc_final: 0.8344 (p) REVERT: I 193 ARG cc_start: 0.8069 (ttt-90) cc_final: 0.7679 (mtt-85) outliers start: 111 outliers final: 83 residues processed: 581 average time/residue: 0.1495 time to fit residues: 123.8984 Evaluate side-chains 616 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 521 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 297 GLN Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain C residue 311 ARG Chi-restraints excluded: chain D residue 300 GLU Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 88 LYS Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 199 GLU Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 257 ASP Chi-restraints excluded: chain G residue 286 GLN Chi-restraints excluded: chain G residue 290 PHE Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 357 LYS Chi-restraints excluded: chain G residue 371 GLU Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 455 ARG Chi-restraints excluded: chain G residue 626 ARG Chi-restraints excluded: chain G residue 638 ASN Chi-restraints excluded: chain G residue 655 VAL Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain H residue 261 ILE Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 265 THR Chi-restraints excluded: chain H residue 271 ASP Chi-restraints excluded: chain H residue 275 MET Chi-restraints excluded: chain H residue 276 LEU Chi-restraints excluded: chain S residue 205 MET Chi-restraints excluded: chain S residue 216 TYR Chi-restraints excluded: chain S residue 248 VAL Chi-restraints excluded: chain S residue 251 ILE Chi-restraints excluded: chain S residue 275 GLU Chi-restraints excluded: chain S residue 315 MET Chi-restraints excluded: chain S residue 432 VAL Chi-restraints excluded: chain S residue 447 THR Chi-restraints excluded: chain S residue 470 ILE Chi-restraints excluded: chain S residue 484 ARG Chi-restraints excluded: chain S residue 614 SER Chi-restraints excluded: chain S residue 692 MET Chi-restraints excluded: chain c residue 23 ASP Chi-restraints excluded: chain c residue 29 LEU Chi-restraints excluded: chain c residue 54 VAL Chi-restraints excluded: chain c residue 68 LEU Chi-restraints excluded: chain c residue 94 MET Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain c residue 110 GLU Chi-restraints excluded: chain c residue 136 GLU Chi-restraints excluded: chain c residue 138 THR Chi-restraints excluded: chain c residue 139 ARG Chi-restraints excluded: chain c residue 142 SER Chi-restraints excluded: chain c residue 143 ILE Chi-restraints excluded: chain c residue 178 LEU Chi-restraints excluded: chain c residue 181 VAL Chi-restraints excluded: chain c residue 184 LEU Chi-restraints excluded: chain c residue 214 LEU Chi-restraints excluded: chain c residue 223 ARG Chi-restraints excluded: chain c residue 239 LEU Chi-restraints excluded: chain c residue 251 HIS Chi-restraints excluded: chain c residue 261 ILE Chi-restraints excluded: chain c residue 267 GLU Chi-restraints excluded: chain I residue 49 GLU Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 120 HIS Chi-restraints excluded: chain I residue 136 LYS Chi-restraints excluded: chain I residue 180 CYS Chi-restraints excluded: chain I residue 190 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 98 optimal weight: 0.9990 chunk 167 optimal weight: 0.6980 chunk 128 optimal weight: 0.4980 chunk 32 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 127 optimal weight: 0.6980 chunk 203 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 20 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 143 HIS ** G 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 342 GLN S 350 GLN S 503 GLN S 651 HIS c 109 HIS c 229 GLN I 183 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.129034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.110098 restraints weight = 31282.032| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.52 r_work: 0.3320 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 18051 Z= 0.232 Angle : 0.685 13.880 24469 Z= 0.349 Chirality : 0.046 0.225 2585 Planarity : 0.005 0.069 3186 Dihedral : 5.207 58.591 2404 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.51 % Favored : 95.44 % Rotamer: Outliers : 5.65 % Allowed : 26.50 % Favored : 67.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.54 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 aren not related in a simple way. whole: -0.85 (0.18), residues: 2129 helix: 0.42 (0.22), residues: 561 sheet: -1.34 (0.25), residues: 419 loop : -0.68 (0.18), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 66 TYR 0.023 0.002 TYR F 44 PHE 0.035 0.002 PHE B 298 TRP 0.017 0.001 TRP A 36 HIS 0.005 0.001 HIS F 154 Details of bonding type rmsd covalent geometry : bond 0.00534 (18051) covalent geometry : angle 0.68502 (24469) hydrogen bonds : bond 0.03699 ( 633) hydrogen bonds : angle 5.22353 ( 1761) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 539 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 ILE cc_start: 0.7633 (mm) cc_final: 0.7213 (tp) REVERT: B 231 PHE cc_start: 0.8738 (m-10) cc_final: 0.8522 (m-10) REVERT: B 234 TYR cc_start: 0.8408 (t80) cc_final: 0.7764 (t80) REVERT: B 265 VAL cc_start: 0.8683 (t) cc_final: 0.8442 (m) REVERT: C 311 ARG cc_start: 0.6780 (OUTLIER) cc_final: 0.5910 (mtt90) REVERT: D 300 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7302 (mp0) REVERT: E 88 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.8033 (mtmm) REVERT: E 95 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7337 (mt-10) REVERT: E 142 MET cc_start: 0.8643 (tpp) cc_final: 0.8416 (tpp) REVERT: E 161 ILE cc_start: 0.7960 (mt) cc_final: 0.7727 (mm) REVERT: E 188 LEU cc_start: 0.8008 (tp) cc_final: 0.7795 (tp) REVERT: F 20 TYR cc_start: 0.8286 (t80) cc_final: 0.7968 (t80) REVERT: F 60 LYS cc_start: 0.8678 (mttm) cc_final: 0.8465 (mttt) REVERT: F 89 ARG cc_start: 0.8415 (ttp80) cc_final: 0.8058 (ttp-110) REVERT: F 97 ASP cc_start: 0.7268 (OUTLIER) cc_final: 0.6903 (t70) REVERT: G 233 SER cc_start: 0.8065 (m) cc_final: 0.7739 (p) REVERT: G 281 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7502 (mt-10) REVERT: G 284 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7569 (mm-30) REVERT: G 314 VAL cc_start: 0.8180 (OUTLIER) cc_final: 0.7912 (t) REVERT: G 341 LYS cc_start: 0.8320 (tttp) cc_final: 0.8115 (tttp) REVERT: G 466 ASP cc_start: 0.7588 (t0) cc_final: 0.7235 (t0) REVERT: G 626 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.7817 (mtm-85) REVERT: G 688 GLN cc_start: 0.7841 (pp30) cc_final: 0.7615 (pp30) REVERT: H 98 VAL cc_start: 0.8283 (m) cc_final: 0.7997 (p) REVERT: S 238 LYS cc_start: 0.8092 (mtpp) cc_final: 0.7814 (ttpp) REVERT: S 282 ILE cc_start: 0.8308 (pt) cc_final: 0.8059 (pt) REVERT: S 284 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7490 (mm-30) REVERT: S 330 THR cc_start: 0.8160 (p) cc_final: 0.7870 (m) REVERT: S 332 GLU cc_start: 0.7879 (tp30) cc_final: 0.7574 (tp30) REVERT: S 345 ASP cc_start: 0.7933 (m-30) cc_final: 0.7612 (m-30) REVERT: S 466 ASP cc_start: 0.7507 (t0) cc_final: 0.7178 (t0) REVERT: S 470 ILE cc_start: 0.7891 (mt) cc_final: 0.7678 (mm) REVERT: S 484 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.7559 (mmm160) REVERT: S 587 GLU cc_start: 0.8060 (pt0) cc_final: 0.7430 (pt0) REVERT: S 622 ILE cc_start: 0.8197 (mm) cc_final: 0.7921 (pt) REVERT: S 640 LYS cc_start: 0.8217 (mttm) cc_final: 0.7821 (mttm) REVERT: S 641 LYS cc_start: 0.8474 (pttt) cc_final: 0.8129 (ptmm) REVERT: S 678 GLU cc_start: 0.7656 (mp0) cc_final: 0.7129 (mp0) REVERT: c 24 ARG cc_start: 0.8191 (mmt180) cc_final: 0.7950 (mmt-90) REVERT: c 29 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8174 (mm) REVERT: c 37 ARG cc_start: 0.8582 (ttp80) cc_final: 0.7910 (ttp-170) REVERT: c 43 ARG cc_start: 0.8435 (ptt-90) cc_final: 0.8112 (ptt-90) REVERT: c 49 ARG cc_start: 0.8434 (ttp-170) cc_final: 0.8049 (ttp-170) REVERT: c 136 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.7196 (tp30) REVERT: c 139 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.7586 (ttt-90) REVERT: I 45 GLU cc_start: 0.7090 (tt0) cc_final: 0.6785 (mt-10) REVERT: I 76 LYS cc_start: 0.8899 (mttp) cc_final: 0.8474 (mttp) REVERT: I 167 ASN cc_start: 0.8130 (p0) cc_final: 0.7784 (p0) REVERT: I 191 THR cc_start: 0.8814 (m) cc_final: 0.8327 (p) REVERT: I 193 ARG cc_start: 0.8062 (ttt-90) cc_final: 0.7673 (mtt-85) outliers start: 107 outliers final: 77 residues processed: 587 average time/residue: 0.1600 time to fit residues: 133.2322 Evaluate side-chains 618 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 531 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain C residue 311 ARG Chi-restraints excluded: chain D residue 300 GLU Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 88 LYS Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 199 GLU Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 286 GLN Chi-restraints excluded: chain G residue 290 PHE Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain G residue 357 LYS Chi-restraints excluded: chain G residue 371 GLU Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain G residue 433 CYS Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 455 ARG Chi-restraints excluded: chain G residue 626 ARG Chi-restraints excluded: chain G residue 638 ASN Chi-restraints excluded: chain G residue 655 VAL Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 265 THR Chi-restraints excluded: chain H residue 271 ASP Chi-restraints excluded: chain H residue 275 MET Chi-restraints excluded: chain H residue 276 LEU Chi-restraints excluded: chain S residue 216 TYR Chi-restraints excluded: chain S residue 275 GLU Chi-restraints excluded: chain S residue 432 VAL Chi-restraints excluded: chain S residue 447 THR Chi-restraints excluded: chain S residue 484 ARG Chi-restraints excluded: chain S residue 533 ILE Chi-restraints excluded: chain S residue 614 SER Chi-restraints excluded: chain S residue 692 MET Chi-restraints excluded: chain c residue 23 ASP Chi-restraints excluded: chain c residue 29 LEU Chi-restraints excluded: chain c residue 54 VAL Chi-restraints excluded: chain c residue 68 LEU Chi-restraints excluded: chain c residue 94 MET Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain c residue 110 GLU Chi-restraints excluded: chain c residue 136 GLU Chi-restraints excluded: chain c residue 138 THR Chi-restraints excluded: chain c residue 139 ARG Chi-restraints excluded: chain c residue 142 SER Chi-restraints excluded: chain c residue 178 LEU Chi-restraints excluded: chain c residue 181 VAL Chi-restraints excluded: chain c residue 184 LEU Chi-restraints excluded: chain c residue 214 LEU Chi-restraints excluded: chain c residue 223 ARG Chi-restraints excluded: chain c residue 239 LEU Chi-restraints excluded: chain c residue 251 HIS Chi-restraints excluded: chain c residue 261 ILE Chi-restraints excluded: chain c residue 267 GLU Chi-restraints excluded: chain I residue 49 GLU Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 120 HIS Chi-restraints excluded: chain I residue 136 LYS Chi-restraints excluded: chain I residue 180 CYS Chi-restraints excluded: chain I residue 190 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 120 optimal weight: 0.0670 chunk 80 optimal weight: 0.6980 chunk 25 optimal weight: 0.2980 chunk 139 optimal weight: 0.0050 chunk 142 optimal weight: 0.0970 chunk 151 optimal weight: 0.2980 chunk 166 optimal weight: 0.6980 chunk 117 optimal weight: 0.9980 chunk 183 optimal weight: 0.1980 chunk 201 optimal weight: 0.6980 chunk 161 optimal weight: 0.0030 overall best weight: 0.0740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 157 HIS G 256 GLN G 342 GLN ** H 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 541 ASN S 651 HIS I 183 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.132624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.114156 restraints weight = 31460.294| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.51 r_work: 0.3380 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18051 Z= 0.122 Angle : 0.645 13.597 24469 Z= 0.328 Chirality : 0.043 0.213 2585 Planarity : 0.005 0.068 3186 Dihedral : 5.044 58.797 2404 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.23 % Favored : 95.73 % Rotamer: Outliers : 4.54 % Allowed : 27.93 % Favored : 67.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.54 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -0.78 (0.18), residues: 2129 helix: 0.53 (0.22), residues: 570 sheet: -1.29 (0.26), residues: 406 loop : -0.68 (0.18), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 224 TYR 0.018 0.001 TYR F 44 PHE 0.024 0.001 PHE B 231 TRP 0.015 0.001 TRP I 94 HIS 0.005 0.001 HIS F 157 Details of bonding type rmsd covalent geometry : bond 0.00278 (18051) covalent geometry : angle 0.64508 (24469) hydrogen bonds : bond 0.03453 ( 633) hydrogen bonds : angle 5.10746 ( 1761) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 532 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 ILE cc_start: 0.7428 (mm) cc_final: 0.6997 (tp) REVERT: B 234 TYR cc_start: 0.8218 (t80) cc_final: 0.7673 (t80) REVERT: C 311 ARG cc_start: 0.6553 (OUTLIER) cc_final: 0.5877 (ttt90) REVERT: D 296 MET cc_start: 0.8450 (mmm) cc_final: 0.7734 (mmm) REVERT: D 300 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7286 (mp0) REVERT: E 88 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7932 (mtmm) REVERT: E 95 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7224 (mt-10) REVERT: E 142 MET cc_start: 0.8490 (tpp) cc_final: 0.8237 (tpp) REVERT: E 161 ILE cc_start: 0.7889 (mt) cc_final: 0.7651 (mm) REVERT: F 20 TYR cc_start: 0.8263 (t80) cc_final: 0.7946 (t80) REVERT: F 89 ARG cc_start: 0.8250 (ttp80) cc_final: 0.7981 (ttp-110) REVERT: F 97 ASP cc_start: 0.7162 (OUTLIER) cc_final: 0.6802 (t70) REVERT: G 252 GLU cc_start: 0.7492 (tp30) cc_final: 0.7133 (tp30) REVERT: G 281 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7473 (mt-10) REVERT: G 284 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7446 (mm-30) REVERT: G 438 ARG cc_start: 0.8102 (mmt90) cc_final: 0.7900 (mtt90) REVERT: G 466 ASP cc_start: 0.7528 (t0) cc_final: 0.7172 (t0) REVERT: G 626 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.7628 (mtm-85) REVERT: G 685 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7598 (pp20) REVERT: H 24 ARG cc_start: 0.8211 (mmt90) cc_final: 0.7948 (mmt90) REVERT: H 43 ARG cc_start: 0.8333 (mtm110) cc_final: 0.7877 (ttp80) REVERT: H 98 VAL cc_start: 0.8284 (m) cc_final: 0.7998 (p) REVERT: S 238 LYS cc_start: 0.7996 (mtpp) cc_final: 0.7745 (ttpp) REVERT: S 282 ILE cc_start: 0.8284 (pt) cc_final: 0.8010 (pt) REVERT: S 284 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7439 (mm-30) REVERT: S 330 THR cc_start: 0.8078 (p) cc_final: 0.7825 (m) REVERT: S 332 GLU cc_start: 0.7874 (tp30) cc_final: 0.7556 (tp30) REVERT: S 470 ILE cc_start: 0.7705 (OUTLIER) cc_final: 0.7460 (mm) REVERT: S 484 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.7603 (mmm160) REVERT: S 587 GLU cc_start: 0.8019 (pt0) cc_final: 0.7392 (pt0) REVERT: S 622 ILE cc_start: 0.8162 (mm) cc_final: 0.7867 (pt) REVERT: S 640 LYS cc_start: 0.8040 (mttm) cc_final: 0.7655 (mttm) REVERT: S 641 LYS cc_start: 0.8405 (pttt) cc_final: 0.8056 (ptmm) REVERT: c 24 ARG cc_start: 0.8253 (mmt180) cc_final: 0.7967 (mmt-90) REVERT: c 29 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8119 (mm) REVERT: c 37 ARG cc_start: 0.8456 (ttp80) cc_final: 0.7666 (ttp-170) REVERT: c 43 ARG cc_start: 0.8385 (ptt-90) cc_final: 0.8052 (ptt-90) REVERT: c 139 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.8175 (ttt90) REVERT: I 45 GLU cc_start: 0.7054 (tt0) cc_final: 0.6765 (mt-10) REVERT: I 63 ASN cc_start: 0.8406 (p0) cc_final: 0.7706 (m-40) REVERT: I 76 LYS cc_start: 0.8884 (mttp) cc_final: 0.8562 (mttp) REVERT: I 167 ASN cc_start: 0.8070 (p0) cc_final: 0.7707 (p0) REVERT: I 191 THR cc_start: 0.8706 (m) cc_final: 0.8248 (p) REVERT: I 193 ARG cc_start: 0.8004 (ttt-90) cc_final: 0.7619 (mtt-85) outliers start: 86 outliers final: 68 residues processed: 571 average time/residue: 0.1614 time to fit residues: 130.6785 Evaluate side-chains 591 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 514 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 297 GLN Chi-restraints excluded: chain B residue 306 LYS Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain C residue 311 ARG Chi-restraints excluded: chain D residue 300 GLU Chi-restraints excluded: chain D residue 303 MET Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 88 LYS Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 199 GLU Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 286 GLN Chi-restraints excluded: chain G residue 290 PHE Chi-restraints excluded: chain G residue 357 LYS Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 455 ARG Chi-restraints excluded: chain G residue 626 ARG Chi-restraints excluded: chain G residue 638 ASN Chi-restraints excluded: chain G residue 655 VAL Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain H residue 261 ILE Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 271 ASP Chi-restraints excluded: chain H residue 275 MET Chi-restraints excluded: chain H residue 276 LEU Chi-restraints excluded: chain S residue 216 TYR Chi-restraints excluded: chain S residue 275 GLU Chi-restraints excluded: chain S residue 432 VAL Chi-restraints excluded: chain S residue 447 THR Chi-restraints excluded: chain S residue 470 ILE Chi-restraints excluded: chain S residue 484 ARG Chi-restraints excluded: chain S residue 614 SER Chi-restraints excluded: chain c residue 23 ASP Chi-restraints excluded: chain c residue 29 LEU Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain c residue 110 GLU Chi-restraints excluded: chain c residue 138 THR Chi-restraints excluded: chain c residue 139 ARG Chi-restraints excluded: chain c residue 143 ILE Chi-restraints excluded: chain c residue 178 LEU Chi-restraints excluded: chain c residue 184 LEU Chi-restraints excluded: chain c residue 214 LEU Chi-restraints excluded: chain c residue 223 ARG Chi-restraints excluded: chain c residue 239 LEU Chi-restraints excluded: chain c residue 251 HIS Chi-restraints excluded: chain c residue 261 ILE Chi-restraints excluded: chain c residue 267 GLU Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 120 HIS Chi-restraints excluded: chain I residue 136 LYS Chi-restraints excluded: chain I residue 197 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 207 optimal weight: 0.3980 chunk 11 optimal weight: 0.7980 chunk 132 optimal weight: 0.7980 chunk 172 optimal weight: 0.1980 chunk 103 optimal weight: 0.2980 chunk 166 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 176 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 33 optimal weight: 0.0270 overall best weight: 0.3038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 HIS E 56 ASN G 342 GLN ** H 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 350 GLN S 651 HIS c 109 HIS I 183 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.131260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.112531 restraints weight = 31522.144| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.54 r_work: 0.3364 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18051 Z= 0.155 Angle : 0.666 13.522 24469 Z= 0.336 Chirality : 0.044 0.225 2585 Planarity : 0.005 0.067 3186 Dihedral : 5.009 56.048 2404 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.32 % Favored : 95.58 % Rotamer: Outliers : 4.22 % Allowed : 28.72 % Favored : 67.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.54 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 aren not related in a simple way. whole: -0.71 (0.18), residues: 2129 helix: 0.59 (0.22), residues: 565 sheet: -1.33 (0.25), residues: 423 loop : -0.58 (0.18), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 40 TYR 0.024 0.001 TYR F 44 PHE 0.028 0.001 PHE B 231 TRP 0.014 0.001 TRP A 36 HIS 0.007 0.001 HIS c 109 Details of bonding type rmsd covalent geometry : bond 0.00361 (18051) covalent geometry : angle 0.66615 (24469) hydrogen bonds : bond 0.03516 ( 633) hydrogen bonds : angle 5.08716 ( 1761) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 523 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 210 ASP cc_start: 0.8105 (t0) cc_final: 0.7828 (t0) REVERT: B 265 VAL cc_start: 0.8677 (t) cc_final: 0.8403 (m) REVERT: C 311 ARG cc_start: 0.6551 (OUTLIER) cc_final: 0.5917 (ttt180) REVERT: D 296 MET cc_start: 0.8459 (mmm) cc_final: 0.7739 (mmm) REVERT: D 300 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7309 (mp0) REVERT: E 95 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7265 (mt-10) REVERT: E 142 MET cc_start: 0.8562 (tpp) cc_final: 0.8307 (tpp) REVERT: F 20 TYR cc_start: 0.8277 (t80) cc_final: 0.7981 (t80) REVERT: F 35 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7953 (mttm) REVERT: F 89 ARG cc_start: 0.8339 (ttp80) cc_final: 0.8001 (ttp-110) REVERT: F 97 ASP cc_start: 0.7187 (OUTLIER) cc_final: 0.6831 (t70) REVERT: G 252 GLU cc_start: 0.7552 (tp30) cc_final: 0.7212 (tp30) REVERT: G 281 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7535 (mt-10) REVERT: G 284 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7475 (mm-30) REVERT: G 438 ARG cc_start: 0.8128 (mmt90) cc_final: 0.7922 (mtt90) REVERT: G 466 ASP cc_start: 0.7538 (t0) cc_final: 0.7192 (t0) REVERT: G 479 GLU cc_start: 0.7923 (tt0) cc_final: 0.7678 (tt0) REVERT: G 626 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7761 (mtm-85) REVERT: G 685 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7559 (pp20) REVERT: H 24 ARG cc_start: 0.8223 (mmt90) cc_final: 0.7985 (mmt90) REVERT: H 28 LEU cc_start: 0.8141 (mm) cc_final: 0.7865 (mp) REVERT: H 43 ARG cc_start: 0.8309 (mtm110) cc_final: 0.7863 (ttp80) REVERT: H 66 ASP cc_start: 0.8358 (t0) cc_final: 0.8085 (t0) REVERT: H 98 VAL cc_start: 0.8278 (m) cc_final: 0.7999 (p) REVERT: S 238 LYS cc_start: 0.7973 (mtpp) cc_final: 0.7723 (ttpp) REVERT: S 282 ILE cc_start: 0.8262 (pt) cc_final: 0.8025 (pt) REVERT: S 284 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7489 (mm-30) REVERT: S 287 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.8054 (mptt) REVERT: S 330 THR cc_start: 0.8085 (p) cc_final: 0.7855 (m) REVERT: S 332 GLU cc_start: 0.7890 (tp30) cc_final: 0.7552 (tp30) REVERT: S 470 ILE cc_start: 0.7780 (OUTLIER) cc_final: 0.7552 (mm) REVERT: S 484 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.7574 (mmm160) REVERT: S 587 GLU cc_start: 0.8034 (pt0) cc_final: 0.7443 (pt0) REVERT: S 622 ILE cc_start: 0.8208 (mm) cc_final: 0.7952 (pt) REVERT: S 640 LYS cc_start: 0.8089 (mttm) cc_final: 0.7715 (mttm) REVERT: S 641 LYS cc_start: 0.8400 (pttt) cc_final: 0.8045 (ptmm) REVERT: c 24 ARG cc_start: 0.8254 (mmt180) cc_final: 0.8006 (mmt-90) REVERT: c 29 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8139 (mm) REVERT: c 37 ARG cc_start: 0.8441 (ttp80) cc_final: 0.7643 (ttp-170) REVERT: c 43 ARG cc_start: 0.8384 (ptt-90) cc_final: 0.8045 (ptt-90) REVERT: c 102 ARG cc_start: 0.7893 (mtp85) cc_final: 0.7565 (mtp180) REVERT: c 110 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6943 (mp0) REVERT: c 139 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7534 (ttt-90) REVERT: I 45 GLU cc_start: 0.7091 (tt0) cc_final: 0.6785 (mt-10) REVERT: I 63 ASN cc_start: 0.8429 (p0) cc_final: 0.7795 (m-40) REVERT: I 76 LYS cc_start: 0.8884 (mttp) cc_final: 0.8545 (mttp) REVERT: I 167 ASN cc_start: 0.8084 (p0) cc_final: 0.7706 (p0) REVERT: I 191 THR cc_start: 0.8725 (m) cc_final: 0.8265 (p) REVERT: I 193 ARG cc_start: 0.8077 (ttt-90) cc_final: 0.7683 (mtt-85) outliers start: 80 outliers final: 63 residues processed: 557 average time/residue: 0.1415 time to fit residues: 113.0898 Evaluate side-chains 586 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 512 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 297 GLN Chi-restraints excluded: chain B residue 306 LYS Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain C residue 311 ARG Chi-restraints excluded: chain D residue 300 GLU Chi-restraints excluded: chain D residue 303 MET Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 199 GLU Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 257 ASP Chi-restraints excluded: chain G residue 286 GLN Chi-restraints excluded: chain G residue 290 PHE Chi-restraints excluded: chain G residue 357 LYS Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 455 ARG Chi-restraints excluded: chain G residue 626 ARG Chi-restraints excluded: chain G residue 638 ASN Chi-restraints excluded: chain G residue 655 VAL Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain H residue 261 ILE Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 271 ASP Chi-restraints excluded: chain H residue 275 MET Chi-restraints excluded: chain H residue 276 LEU Chi-restraints excluded: chain S residue 216 TYR Chi-restraints excluded: chain S residue 275 GLU Chi-restraints excluded: chain S residue 287 LYS Chi-restraints excluded: chain S residue 432 VAL Chi-restraints excluded: chain S residue 447 THR Chi-restraints excluded: chain S residue 470 ILE Chi-restraints excluded: chain S residue 484 ARG Chi-restraints excluded: chain S residue 523 GLU Chi-restraints excluded: chain c residue 23 ASP Chi-restraints excluded: chain c residue 29 LEU Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain c residue 110 GLU Chi-restraints excluded: chain c residue 138 THR Chi-restraints excluded: chain c residue 139 ARG Chi-restraints excluded: chain c residue 143 ILE Chi-restraints excluded: chain c residue 178 LEU Chi-restraints excluded: chain c residue 184 LEU Chi-restraints excluded: chain c residue 214 LEU Chi-restraints excluded: chain c residue 239 LEU Chi-restraints excluded: chain c residue 251 HIS Chi-restraints excluded: chain c residue 261 ILE Chi-restraints excluded: chain c residue 267 GLU Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 120 HIS Chi-restraints excluded: chain I residue 136 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 58 optimal weight: 0.5980 chunk 116 optimal weight: 0.9990 chunk 185 optimal weight: 0.0470 chunk 142 optimal weight: 0.0010 chunk 69 optimal weight: 0.4980 chunk 84 optimal weight: 0.0980 chunk 145 optimal weight: 0.0980 chunk 93 optimal weight: 0.4980 chunk 121 optimal weight: 0.6980 chunk 10 optimal weight: 0.0870 chunk 92 optimal weight: 0.2980 overall best weight: 0.0662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 HIS F 77 HIS G 256 GLN G 342 GLN ** H 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 503 GLN S 651 HIS c 109 HIS I 183 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.134409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.116035 restraints weight = 31367.748| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.51 r_work: 0.3413 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18051 Z= 0.118 Angle : 0.661 13.234 24469 Z= 0.333 Chirality : 0.043 0.232 2585 Planarity : 0.005 0.066 3186 Dihedral : 4.863 51.787 2404 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.96 % Allowed : 29.30 % Favored : 66.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.54 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -0.67 (0.18), residues: 2129 helix: 0.70 (0.22), residues: 555 sheet: -1.36 (0.25), residues: 411 loop : -0.58 (0.18), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 66 TYR 0.021 0.001 TYR F 44 PHE 0.016 0.001 PHE B 231 TRP 0.015 0.001 TRP I 94 HIS 0.008 0.001 HIS c 109 Details of bonding type rmsd covalent geometry : bond 0.00270 (18051) covalent geometry : angle 0.66121 (24469) hydrogen bonds : bond 0.03412 ( 633) hydrogen bonds : angle 5.03256 ( 1761) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4258 Ramachandran restraints generated. 2129 Oldfield, 0 Emsley, 2129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 520 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 210 ASP cc_start: 0.7994 (t0) cc_final: 0.7744 (t0) REVERT: C 311 ARG cc_start: 0.6383 (OUTLIER) cc_final: 0.5843 (ttt180) REVERT: D 296 MET cc_start: 0.8422 (mmm) cc_final: 0.7712 (mmm) REVERT: D 300 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7301 (mp0) REVERT: E 95 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7244 (mt-10) REVERT: E 142 MET cc_start: 0.8439 (tpp) cc_final: 0.8134 (tpp) REVERT: F 20 TYR cc_start: 0.8245 (t80) cc_final: 0.7971 (t80) REVERT: F 89 ARG cc_start: 0.8191 (ttp80) cc_final: 0.7974 (ttp-110) REVERT: F 97 ASP cc_start: 0.7122 (OUTLIER) cc_final: 0.6765 (t70) REVERT: F 136 LYS cc_start: 0.8551 (mtmm) cc_final: 0.8331 (mtmm) REVERT: G 252 GLU cc_start: 0.7503 (tp30) cc_final: 0.7124 (tp30) REVERT: G 281 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7498 (mt-10) REVERT: G 284 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7483 (mm-30) REVERT: G 286 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7955 (mm-40) REVERT: G 365 TYR cc_start: 0.8617 (m-80) cc_final: 0.8386 (m-80) REVERT: G 466 ASP cc_start: 0.7484 (t0) cc_final: 0.7091 (t0) REVERT: G 479 GLU cc_start: 0.7868 (tt0) cc_final: 0.7606 (tt0) REVERT: G 626 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7634 (mtm-85) REVERT: G 685 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7544 (pp20) REVERT: H 24 ARG cc_start: 0.8168 (mmt90) cc_final: 0.7885 (mmt90) REVERT: H 28 LEU cc_start: 0.8025 (mm) cc_final: 0.7786 (mp) REVERT: H 43 ARG cc_start: 0.8206 (mtm110) cc_final: 0.7850 (ttp80) REVERT: H 66 ASP cc_start: 0.8364 (t0) cc_final: 0.8087 (t0) REVERT: H 98 VAL cc_start: 0.8262 (m) cc_final: 0.7983 (p) REVERT: H 137 GLU cc_start: 0.7884 (tt0) cc_final: 0.7666 (mt-10) REVERT: S 238 LYS cc_start: 0.7840 (mtpp) cc_final: 0.7608 (ttpp) REVERT: S 282 ILE cc_start: 0.8203 (pt) cc_final: 0.7981 (pt) REVERT: S 284 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7420 (mm-30) REVERT: S 332 GLU cc_start: 0.7860 (tp30) cc_final: 0.7502 (tp30) REVERT: S 470 ILE cc_start: 0.7588 (OUTLIER) cc_final: 0.7350 (mm) REVERT: S 587 GLU cc_start: 0.8016 (pt0) cc_final: 0.7409 (pt0) REVERT: S 622 ILE cc_start: 0.8187 (mm) cc_final: 0.7931 (pt) REVERT: S 641 LYS cc_start: 0.8311 (pttt) cc_final: 0.8109 (pttp) REVERT: c 24 ARG cc_start: 0.8233 (mmt180) cc_final: 0.7988 (mmt-90) REVERT: c 29 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8110 (mm) REVERT: c 37 ARG cc_start: 0.8277 (ttp80) cc_final: 0.7645 (ttp-170) REVERT: c 43 ARG cc_start: 0.8369 (ptt-90) cc_final: 0.7998 (ptt-90) REVERT: c 49 ARG cc_start: 0.8385 (ttp-170) cc_final: 0.7957 (ttp-170) REVERT: c 139 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.8088 (ttt90) REVERT: I 45 GLU cc_start: 0.7033 (tt0) cc_final: 0.6740 (mt-10) REVERT: I 63 ASN cc_start: 0.8392 (p0) cc_final: 0.7863 (m-40) REVERT: I 191 THR cc_start: 0.8718 (m) cc_final: 0.8210 (p) REVERT: I 193 ARG cc_start: 0.8009 (ttt-90) cc_final: 0.7630 (mtt-85) outliers start: 75 outliers final: 59 residues processed: 552 average time/residue: 0.1326 time to fit residues: 105.6854 Evaluate side-chains 580 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 513 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 297 GLN Chi-restraints excluded: chain B residue 306 LYS Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain C residue 311 ARG Chi-restraints excluded: chain D residue 300 GLU Chi-restraints excluded: chain D residue 303 MET Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 199 GLU Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain G residue 257 ASP Chi-restraints excluded: chain G residue 286 GLN Chi-restraints excluded: chain G residue 290 PHE Chi-restraints excluded: chain G residue 357 LYS Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain G residue 455 ARG Chi-restraints excluded: chain G residue 526 ASP Chi-restraints excluded: chain G residue 626 ARG Chi-restraints excluded: chain G residue 655 VAL Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain H residue 261 ILE Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 271 ASP Chi-restraints excluded: chain H residue 275 MET Chi-restraints excluded: chain H residue 276 LEU Chi-restraints excluded: chain S residue 205 MET Chi-restraints excluded: chain S residue 275 GLU Chi-restraints excluded: chain S residue 315 MET Chi-restraints excluded: chain S residue 432 VAL Chi-restraints excluded: chain S residue 447 THR Chi-restraints excluded: chain S residue 470 ILE Chi-restraints excluded: chain S residue 484 ARG Chi-restraints excluded: chain c residue 23 ASP Chi-restraints excluded: chain c residue 29 LEU Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain c residue 139 ARG Chi-restraints excluded: chain c residue 143 ILE Chi-restraints excluded: chain c residue 178 LEU Chi-restraints excluded: chain c residue 184 LEU Chi-restraints excluded: chain c residue 214 LEU Chi-restraints excluded: chain c residue 251 HIS Chi-restraints excluded: chain c residue 261 ILE Chi-restraints excluded: chain c residue 263 VAL Chi-restraints excluded: chain c residue 267 GLU Chi-restraints excluded: chain I residue 62 LYS Chi-restraints excluded: chain I residue 120 HIS Chi-restraints excluded: chain I residue 136 LYS Chi-restraints excluded: chain I residue 197 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 171 optimal weight: 0.1980 chunk 142 optimal weight: 0.2980 chunk 32 optimal weight: 0.8980 chunk 122 optimal weight: 0.4980 chunk 138 optimal weight: 0.4980 chunk 139 optimal weight: 0.5980 chunk 131 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 182 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 147 optimal weight: 0.9980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 77 HIS F 165 ASN ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 342 GLN ** H 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 342 GLN S 503 GLN S 651 HIS c 109 HIS I 183 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.130888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.112141 restraints weight = 31439.139| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.53 r_work: 0.3357 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18051 Z= 0.186 Angle : 0.689 13.545 24469 Z= 0.348 Chirality : 0.045 0.256 2585 Planarity : 0.005 0.067 3186 Dihedral : 4.938 43.048 2404 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.51 % Favored : 95.40 % Rotamer: Outliers : 3.80 % Allowed : 29.04 % Favored : 67.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.54 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 aren not related in a simple way. whole: -0.65 (0.18), residues: 2129 helix: 0.68 (0.22), residues: 562 sheet: -1.29 (0.25), residues: 428 loop : -0.57 (0.18), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 66 TYR 0.021 0.002 TYR F 44 PHE 0.051 0.002 PHE B 213 TRP 0.016 0.001 TRP A 36 HIS 0.007 0.001 HIS c 109 Details of bonding type rmsd covalent geometry : bond 0.00436 (18051) covalent geometry : angle 0.68927 (24469) hydrogen bonds : bond 0.03640 ( 633) hydrogen bonds : angle 5.07898 ( 1761) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4641.62 seconds wall clock time: 80 minutes 12.25 seconds (4812.25 seconds total)